diff --git a/prepare/r-a4/PKGBUILD b/prepare/r-a4/PKGBUILD new file mode 100644 index 0000000000..37164526da --- /dev/null +++ b/prepare/r-a4/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=a4 +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automated Affymetrix Array Analysis Umbrella Package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-a4base + r-a4classif + r-a4core + r-a4preproc + r-a4reporting +) +optdepends=( + r-all + r-cairo + r-gostats + r-mlp + r-nlcv + r-rgraphviz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-a4/lilac.py b/prepare/r-a4/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-a4/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-a4/lilac.yaml b/prepare/r-a4/lilac.yaml new file mode 100644 index 0000000000..8096e2d8c3 --- /dev/null +++ b/prepare/r-a4/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-a4base +- r-a4classif +- r-a4core +- r-a4preproc +- r-a4reporting +update_on: +- regex: a4_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/a4 diff --git a/prepare/r-a4base/PKGBUILD b/prepare/r-a4base/PKGBUILD new file mode 100644 index 0000000000..16d4b937af --- /dev/null +++ b/prepare/r-a4base/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=a4Base +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automated Affymetrix Array Analysis Base Package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-a4core + r-a4preproc + r-annaffy + r-biobase + r-genefilter + r-glmnet + r-gplots + r-limma + r-mpm + r-multtest +) +optdepends=( + r-all + r-cairo + r-gridsvg + r-hgu95av2.db + r-javagd + r-nlcv +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-a4base/lilac.py b/prepare/r-a4base/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-a4base/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-a4base/lilac.yaml b/prepare/r-a4base/lilac.yaml new file mode 100644 index 0000000000..fcf9e5db23 --- /dev/null +++ b/prepare/r-a4base/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-a4core +- r-a4preproc +- r-annaffy +- r-biobase +- r-genefilter +- r-glmnet +- r-gplots +- r-limma +- r-mpm +- r-multtest +update_on: +- regex: a4Base_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/a4Base diff --git a/prepare/r-a4classif/PKGBUILD b/prepare/r-a4classif/PKGBUILD new file mode 100644 index 0000000000..ed2fc13839 --- /dev/null +++ b/prepare/r-a4classif/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=a4Classif +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automated Affymetrix Array Analysis Classification Package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-a4core + r-a4preproc + r-biobase + r-glmnet + r-pamr + r-rocr + r-varselrf +) +optdepends=( + r-all + r-hgu95av2.db + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-a4classif/lilac.py b/prepare/r-a4classif/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-a4classif/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-a4classif/lilac.yaml b/prepare/r-a4classif/lilac.yaml new file mode 100644 index 0000000000..eff3be7f97 --- /dev/null +++ b/prepare/r-a4classif/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-a4core +- r-a4preproc +- r-biobase +- r-glmnet +- r-pamr +- r-rocr +- r-varselrf +update_on: +- regex: a4Classif_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/a4Classif diff --git a/prepare/r-a4core/PKGBUILD b/prepare/r-a4core/PKGBUILD new file mode 100644 index 0000000000..a0758a7467 --- /dev/null +++ b/prepare/r-a4core/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=a4Core +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automated Affymetrix Array Analysis Core Package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-glmnet +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-a4core/lilac.py b/prepare/r-a4core/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-a4core/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-a4core/lilac.yaml b/prepare/r-a4core/lilac.yaml new file mode 100644 index 0000000000..2aa6102306 --- /dev/null +++ b/prepare/r-a4core/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-glmnet +update_on: +- regex: a4Core_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/a4Core diff --git a/prepare/r-a4preproc/PKGBUILD b/prepare/r-a4preproc/PKGBUILD new file mode 100644 index 0000000000..98f9bdaf01 --- /dev/null +++ b/prepare/r-a4preproc/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=a4Preproc +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automated Affymetrix Array Analysis Preprocessing Package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics +) +optdepends=( + r-all + r-hgu95av2.db + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-a4preproc/lilac.py b/prepare/r-a4preproc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-a4preproc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-a4preproc/lilac.yaml b/prepare/r-a4preproc/lilac.yaml new file mode 100644 index 0000000000..553516c6a3 --- /dev/null +++ b/prepare/r-a4preproc/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +update_on: +- regex: a4Preproc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/a4Preproc diff --git a/prepare/r-a4reporting/PKGBUILD b/prepare/r-a4reporting/PKGBUILD new file mode 100644 index 0000000000..58dba78d5a --- /dev/null +++ b/prepare/r-a4reporting/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=a4Reporting +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automated Affymetrix Array Analysis Reporting Package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-xtable +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-a4reporting/lilac.py b/prepare/r-a4reporting/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-a4reporting/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-a4reporting/lilac.yaml b/prepare/r-a4reporting/lilac.yaml new file mode 100644 index 0000000000..295f51f518 --- /dev/null +++ b/prepare/r-a4reporting/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-xtable +update_on: +- regex: a4Reporting_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/a4Reporting diff --git a/prepare/r-abadata/PKGBUILD b/prepare/r-abadata/PKGBUILD new file mode 100644 index 0000000000..5803bf48af --- /dev/null +++ b/prepare/r-abadata/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ABAData +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Averaged gene expression in human brain regions from Allen Brain Atlas' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-abaenrichment + r-biocstyle + r-knitr +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-abadata/lilac.py b/prepare/r-abadata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-abadata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-abadata/lilac.yaml b/prepare/r-abadata/lilac.yaml new file mode 100644 index 0000000000..525aaf4c72 --- /dev/null +++ b/prepare/r-abadata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ABAData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ABAData diff --git a/prepare/r-abaenrichment/PKGBUILD b/prepare/r-abaenrichment/PKGBUILD new file mode 100644 index 0000000000..7752c4ad95 --- /dev/null +++ b/prepare/r-abaenrichment/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ABAEnrichment +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene expression enrichment in human brain regions' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-abadata + r-data.table + r-gofuncr + r-gplots + r-gtools + r-rcpp +) +optdepends=( + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-abaenrichment/lilac.py b/prepare/r-abaenrichment/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-abaenrichment/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-abaenrichment/lilac.yaml b/prepare/r-abaenrichment/lilac.yaml new file mode 100644 index 0000000000..4c50de6a23 --- /dev/null +++ b/prepare/r-abaenrichment/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abadata +- r-data.table +- r-gofuncr +- r-gplots +- r-gtools +- r-rcpp +update_on: +- regex: ABAEnrichment_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ABAEnrichment diff --git a/prepare/r-abarray/PKGBUILD b/prepare/r-abarray/PKGBUILD new file mode 100644 index 0000000000..696a6744a6 --- /dev/null +++ b/prepare/r-abarray/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ABarray +_pkgver=1.62.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-multtest +) +optdepends=( + r-limma + r-lpe +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-abarray/lilac.py b/prepare/r-abarray/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-abarray/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-abarray/lilac.yaml b/prepare/r-abarray/lilac.yaml new file mode 100644 index 0000000000..21f9d53409 --- /dev/null +++ b/prepare/r-abarray/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-multtest +update_on: +- regex: ABarray_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ABarray diff --git a/prepare/r-abind/PKGBUILD b/prepare/r-abind/PKGBUILD new file mode 100644 index 0000000000..3e6051c41b --- /dev/null +++ b/prepare/r-abind/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=abind +_pkgver=1.4-5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Combine Multidimensional Arrays' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-abind/lilac.py b/prepare/r-abind/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-abind/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-abind/lilac.yaml b/prepare/r-abind/lilac.yaml new file mode 100644 index 0000000000..3feb1c96b8 --- /dev/null +++ b/prepare/r-abind/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: abind_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=abind diff --git a/prepare/r-abseqr/PKGBUILD b/prepare/r-abseqr/PKGBUILD new file mode 100644 index 0000000000..785d556c68 --- /dev/null +++ b/prepare/r-abseqr/PKGBUILD @@ -0,0 +1,48 @@ +# system requirements: pandoc (>= 1.19.2.1) +# Maintainer: Guoyi Zhang + +_pkgname=abseqR +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-biocstyle + r-circlize + r-flexdashboard + r-ggcorrplot + r-ggdendro + r-ggplot2 + r-gridextra + r-knitr + r-plotly + r-plyr + r-png + r-rcolorbrewer + r-reshape2 + r-rmarkdown + r-stringr + r-vegan + r-venndiagram +) +optdepends=( + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-abseqr/lilac.py b/prepare/r-abseqr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-abseqr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-abseqr/lilac.yaml b/prepare/r-abseqr/lilac.yaml new file mode 100644 index 0000000000..bf09cc2869 --- /dev/null +++ b/prepare/r-abseqr/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-biocstyle +- r-circlize +- r-flexdashboard +- r-ggcorrplot +- r-ggdendro +- r-ggplot2 +- r-gridextra +- r-knitr +- r-plotly +- r-plyr +- r-png +- r-rcolorbrewer +- r-reshape2 +- r-rmarkdown +- r-stringr +- r-vegan +- r-venndiagram +update_on: +- regex: abseqR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/abseqR diff --git a/prepare/r-absseq/PKGBUILD b/prepare/r-absseq/PKGBUILD new file mode 100644 index 0000000000..3db0d8702d --- /dev/null +++ b/prepare/r-absseq/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ABSSeq +_pkgver=1.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-limma + r-locfit +) +optdepends=( + r-edger +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-absseq/lilac.py b/prepare/r-absseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-absseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-absseq/lilac.yaml b/prepare/r-absseq/lilac.yaml new file mode 100644 index 0000000000..0da3bcce8d --- /dev/null +++ b/prepare/r-absseq/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-limma +- r-locfit +update_on: +- regex: ABSSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ABSSeq diff --git a/prepare/r-acde/PKGBUILD b/prepare/r-acde/PKGBUILD new file mode 100644 index 0000000000..3a55cc5060 --- /dev/null +++ b/prepare/r-acde/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=acde +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Artificial Components Detection of Differentially Expressed Genes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-acde/lilac.py b/prepare/r-acde/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-acde/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-acde/lilac.yaml b/prepare/r-acde/lilac.yaml new file mode 100644 index 0000000000..1e4bd80c69 --- /dev/null +++ b/prepare/r-acde/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: acde_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/acde diff --git a/prepare/r-ace/PKGBUILD b/prepare/r-ace/PKGBUILD new file mode 100644 index 0000000000..023fb2851c --- /dev/null +++ b/prepare/r-ace/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ACE +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-genomicranges + r-ggplot2 + r-qdnaseq +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ace/lilac.py b/prepare/r-ace/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ace/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ace/lilac.yaml b/prepare/r-ace/lilac.yaml new file mode 100644 index 0000000000..9b03d3dfd9 --- /dev/null +++ b/prepare/r-ace/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-genomicranges +- r-ggplot2 +- r-qdnaseq +update_on: +- regex: ACE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ACE diff --git a/prepare/r-acgh/PKGBUILD b/prepare/r-acgh/PKGBUILD new file mode 100644 index 0000000000..76fd5da41e --- /dev/null +++ b/prepare/r-acgh/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=aCGH +_pkgver=1.72.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Classes and functions for Array Comparative Genomic Hybridization data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-multtest +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-acgh/lilac.py b/prepare/r-acgh/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-acgh/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-acgh/lilac.yaml b/prepare/r-acgh/lilac.yaml new file mode 100644 index 0000000000..b6c958aa7c --- /dev/null +++ b/prepare/r-acgh/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-multtest +update_on: +- regex: aCGH_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/aCGH diff --git a/prepare/r-acme/PKGBUILD b/prepare/r-acme/PKGBUILD new file mode 100644 index 0000000000..09dd3a515e --- /dev/null +++ b/prepare/r-acme/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ACME +_pkgver=2.50.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Algorithms for Calculating Microarray Enrichment (ACME)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-acme/lilac.py b/prepare/r-acme/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-acme/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-acme/lilac.yaml b/prepare/r-acme/lilac.yaml new file mode 100644 index 0000000000..ea2bd43ae5 --- /dev/null +++ b/prepare/r-acme/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +update_on: +- regex: ACME_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ACME diff --git a/prepare/r-ada/PKGBUILD b/prepare/r-ada/PKGBUILD new file mode 100644 index 0000000000..620150cea0 --- /dev/null +++ b/prepare/r-ada/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ada +_pkgver=2.0-5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The R Package Ada for Stochastic Boosting' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ada/lilac.py b/prepare/r-ada/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ada/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ada/lilac.yaml b/prepare/r-ada/lilac.yaml new file mode 100644 index 0000000000..57e9013b30 --- /dev/null +++ b/prepare/r-ada/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ada_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ada diff --git a/prepare/r-adabag/PKGBUILD b/prepare/r-adabag/PKGBUILD new file mode 100644 index 0000000000..1f810987d0 --- /dev/null +++ b/prepare/r-adabag/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=adabag +_pkgver=4.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Applies Multiclass AdaBoost.M1, SAMME and Bagging' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-caret + r-doparallel + r-foreach +) +optdepends=( + r-mlbench +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-adabag/lilac.py b/prepare/r-adabag/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-adabag/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-adabag/lilac.yaml b/prepare/r-adabag/lilac.yaml new file mode 100644 index 0000000000..9020498840 --- /dev/null +++ b/prepare/r-adabag/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-caret +- r-doparallel +- r-foreach +update_on: +- regex: adabag_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=adabag diff --git a/prepare/r-adacgh2/PKGBUILD b/prepare/r-adacgh2/PKGBUILD new file mode 100644 index 0000000000..fc983085a2 --- /dev/null +++ b/prepare/r-adacgh2/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ADaCGH2 +_pkgver=2.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of big data from aCGH experiments using parallel computing and ff objects' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-acgh + r-bit + r-dnacopy + r-ff + r-ffbase + r-glad + r-snapcgh + r-tilingarray + r-waveslim +) +optdepends=( + r-cairo + r-cghregions + r-limma + r-rmpi +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-adacgh2/lilac.py b/prepare/r-adacgh2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-adacgh2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-adacgh2/lilac.yaml b/prepare/r-adacgh2/lilac.yaml new file mode 100644 index 0000000000..45fd2aed01 --- /dev/null +++ b/prepare/r-adacgh2/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-acgh +- r-bit +- r-dnacopy +- r-ff +- r-ffbase +- r-glad +- r-snapcgh +- r-tilingarray +- r-waveslim +update_on: +- regex: ADaCGH2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ADaCGH2 diff --git a/prepare/r-adam/PKGBUILD b/prepare/r-adam/PKGBUILD new file mode 100644 index 0000000000..add6a3c068 --- /dev/null +++ b/prepare/r-adam/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=ADAM +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ADAM: Activity and Diversity Analysis Module' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-dt + r-go.db + r-keggrest + r-knitr + r-pbapply + r-rcpp + r-stringr + r-summarizedexperiment +) +optdepends=( + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-adam/lilac.py b/prepare/r-adam/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-adam/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-adam/lilac.yaml b/prepare/r-adam/lilac.yaml new file mode 100644 index 0000000000..8ab678fbae --- /dev/null +++ b/prepare/r-adam/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-dt +- r-go.db +- r-keggrest +- r-knitr +- r-pbapply +- r-rcpp +- r-stringr +- r-summarizedexperiment +update_on: +- regex: ADAM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ADAM diff --git a/prepare/r-adamgui/PKGBUILD b/prepare/r-adamgui/PKGBUILD new file mode 100644 index 0000000000..8cd930b090 --- /dev/null +++ b/prepare/r-adamgui/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ADAMgui +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Activity and Diversity Analysis Module Graphical User Interface' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-adam + r-colorramps + r-data.table + r-dplyr + r-dt + r-ggplot2 + r-ggpubr + r-ggrepel + r-ggsignif + r-go.db + r-gridextra + r-knitr + r-rcolorbrewer + r-reshape2 + r-shiny + r-shinyjs + r-stringi + r-stringr + r-testthat + r-varhandle +) +optdepends=( + r-biocstyle + r-markdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-adamgui/lilac.py b/prepare/r-adamgui/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-adamgui/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-adamgui/lilac.yaml b/prepare/r-adamgui/lilac.yaml new file mode 100644 index 0000000000..17bcdc44f9 --- /dev/null +++ b/prepare/r-adamgui/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-adam +- r-colorramps +- r-data.table +- r-dplyr +- r-dt +- r-ggplot2 +- r-ggpubr +- r-ggrepel +- r-ggsignif +- r-go.db +- r-gridextra +- r-knitr +- r-rcolorbrewer +- r-reshape2 +- r-shiny +- r-shinyjs +- r-stringi +- r-stringr +- r-testthat +- r-varhandle +update_on: +- regex: ADAMgui_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ADAMgui diff --git a/prepare/r-adaptgauss/PKGBUILD b/prepare/r-adaptgauss/PKGBUILD new file mode 100644 index 0000000000..747e8656f7 --- /dev/null +++ b/prepare/r-adaptgauss/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AdaptGauss +_pkgver=1.5.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gaussian Mixture Models (GMM)' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-datavisualizations + r-pracma + r-rcpp + r-shiny +) +optdepends=( + r-dqrng + r-foreach + r-ggplot2 + r-grid + r-knitr + r-mclust + r-paralleldist + r-reshape2 + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-adaptgauss/lilac.py b/prepare/r-adaptgauss/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-adaptgauss/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-adaptgauss/lilac.yaml b/prepare/r-adaptgauss/lilac.yaml new file mode 100644 index 0000000000..3a5e58e32f --- /dev/null +++ b/prepare/r-adaptgauss/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-datavisualizations +- r-pracma +- r-rcpp +- r-shiny +update_on: +- regex: AdaptGauss_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=AdaptGauss diff --git a/prepare/r-additivitytests/PKGBUILD b/prepare/r-additivitytests/PKGBUILD new file mode 100644 index 0000000000..0c26a488b8 --- /dev/null +++ b/prepare/r-additivitytests/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=additivityTests +_pkgver=1.1-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Additivity Tests in the Two Way Anova with Single Sub-class Numbers' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-additivitytests/lilac.py b/prepare/r-additivitytests/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-additivitytests/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-additivitytests/lilac.yaml b/prepare/r-additivitytests/lilac.yaml new file mode 100644 index 0000000000..04d8478ce1 --- /dev/null +++ b/prepare/r-additivitytests/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: additivityTests_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=additivityTests diff --git a/prepare/r-adductdata/PKGBUILD b/prepare/r-adductdata/PKGBUILD new file mode 100644 index 0000000000..65b41befa4 --- /dev/null +++ b/prepare/r-adductdata/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=adductData +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data from untargeted MS of modifications to Cys34 of serum albumin' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationhub + r-experimenthub +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-adductdata/lilac.py b/prepare/r-adductdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-adductdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-adductdata/lilac.yaml b/prepare/r-adductdata/lilac.yaml new file mode 100644 index 0000000000..edeb797c13 --- /dev/null +++ b/prepare/r-adductdata/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-experimenthub +update_on: +- regex: adductData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/adductData diff --git a/prepare/r-adductomicsr/PKGBUILD b/prepare/r-adductomicsr/PKGBUILD new file mode 100644 index 0000000000..7072146a83 --- /dev/null +++ b/prepare/r-adductomicsr/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=adductomicsR +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Processing of adductomic mass spectral datasets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-adductdata + r-ade4 + r-annotationhub + r-bootstrap + r-data.table + r-dosnow + r-dplyr + r-dt + r-experimenthub + r-fastcluster + r-foreach + r-fpc + r-mzr + r-orgmassspecr + r-pastecs + r-pracma + r-rcppeigen + r-reshape2 + r-rvest + r-smoother + r-zoo +) +optdepends=( + r-knitr + r-rdisop + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-adductomicsr/lilac.py b/prepare/r-adductomicsr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-adductomicsr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-adductomicsr/lilac.yaml b/prepare/r-adductomicsr/lilac.yaml new file mode 100644 index 0000000000..8868ae5e11 --- /dev/null +++ b/prepare/r-adductomicsr/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-adductdata +- r-ade4 +- r-annotationhub +- r-bootstrap +- r-data.table +- r-dosnow +- r-dplyr +- r-dt +- r-experimenthub +- r-fastcluster +- r-foreach +- r-fpc +- r-mzr +- r-orgmassspecr +- r-pastecs +- r-pracma +- r-rcppeigen +- r-reshape2 +- r-rvest +- r-smoother +- r-zoo +update_on: +- regex: adductomicsR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/adductomicsR diff --git a/prepare/r-ade4/PKGBUILD b/prepare/r-ade4/PKGBUILD new file mode 100644 index 0000000000..0123daaa4e --- /dev/null +++ b/prepare/r-ade4/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ade4 +_pkgver=1.7-18 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-pixmap + r-sp +) +optdepends=( + r-ade4tkgui + r-adegraphics + r-adephylo + r-ape + r-circstats + r-deldir + r-doparallel + r-foreach + r-iterators + r-lattice + r-parallel + r-progress + r-spdep + r-splancs + r-waveslim +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ade4/lilac.py b/prepare/r-ade4/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ade4/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ade4/lilac.yaml b/prepare/r-ade4/lilac.yaml new file mode 100644 index 0000000000..98a39cce42 --- /dev/null +++ b/prepare/r-ade4/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-pixmap +- r-sp +update_on: +- regex: ade4_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ade4 diff --git a/prepare/r-adehabitatlt/PKGBUILD b/prepare/r-adehabitatlt/PKGBUILD new file mode 100644 index 0000000000..c4a2754a1b --- /dev/null +++ b/prepare/r-adehabitatlt/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=adehabitatLT +_pkgver=0.3.25 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Animal Movements' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ade4 + r-adehabitatma + r-circstats + r-sp +) +optdepends=( + r-maptools + r-mass + r-tkrplot +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-adehabitatlt/lilac.py b/prepare/r-adehabitatlt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-adehabitatlt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-adehabitatlt/lilac.yaml b/prepare/r-adehabitatlt/lilac.yaml new file mode 100644 index 0000000000..de8b23caee --- /dev/null +++ b/prepare/r-adehabitatlt/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ade4 +- r-adehabitatma +- r-circstats +- r-sp +update_on: +- regex: adehabitatLT_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=adehabitatLT diff --git a/prepare/r-adehabitatma/PKGBUILD b/prepare/r-adehabitatma/PKGBUILD new file mode 100644 index 0000000000..6ce1526e95 --- /dev/null +++ b/prepare/r-adehabitatma/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=adehabitatMA +_pkgver=0.3.14 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools to Deal with Raster Maps' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-filehash + r-sp +) +optdepends=( + r-maptools + r-mass + r-tkrplot +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-adehabitatma/lilac.py b/prepare/r-adehabitatma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-adehabitatma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-adehabitatma/lilac.yaml b/prepare/r-adehabitatma/lilac.yaml new file mode 100644 index 0000000000..7658ba31e9 --- /dev/null +++ b/prepare/r-adehabitatma/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-filehash +- r-sp +update_on: +- regex: adehabitatMA_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=adehabitatMA diff --git a/prepare/r-adgoftest/PKGBUILD b/prepare/r-adgoftest/PKGBUILD new file mode 100644 index 0000000000..ecc260abe0 --- /dev/null +++ b/prepare/r-adgoftest/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ADGofTest +_pkgver=0.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Anderson-Darling GoF test' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-adgoftest/lilac.py b/prepare/r-adgoftest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-adgoftest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-adgoftest/lilac.yaml b/prepare/r-adgoftest/lilac.yaml new file mode 100644 index 0000000000..82f4d92ec1 --- /dev/null +++ b/prepare/r-adgoftest/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ADGofTest_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ADGofTest diff --git a/prepare/r-adimpute/PKGBUILD b/prepare/r-adimpute/PKGBUILD new file mode 100644 index 0000000000..c2a4ad0ca9 --- /dev/null +++ b/prepare/r-adimpute/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ADImpute +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Adaptive Dropout Imputer (ADImpute)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-checkmate + r-data.table + r-drimpute + r-kernlab + r-rsvd + r-s4vectors + r-saver + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-adimpute/lilac.py b/prepare/r-adimpute/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-adimpute/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-adimpute/lilac.yaml b/prepare/r-adimpute/lilac.yaml new file mode 100644 index 0000000000..bfda9fb051 --- /dev/null +++ b/prepare/r-adimpute/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-checkmate +- r-data.table +- r-drimpute +- r-kernlab +- r-rsvd +- r-s4vectors +- r-saver +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: ADImpute_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ADImpute diff --git a/prepare/r-admisc/PKGBUILD b/prepare/r-admisc/PKGBUILD new file mode 100644 index 0000000000..7236720f2d --- /dev/null +++ b/prepare/r-admisc/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=admisc +_pkgver=0.22 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Adrian Dusa's Miscellaneous" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-qca +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-admisc/lilac.py b/prepare/r-admisc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-admisc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-admisc/lilac.yaml b/prepare/r-admisc/lilac.yaml new file mode 100644 index 0000000000..6528744a82 --- /dev/null +++ b/prepare/r-admisc/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: admisc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=admisc diff --git a/prepare/r-adsplit/PKGBUILD b/prepare/r-adsplit/PKGBUILD new file mode 100644 index 0000000000..0447bffc25 --- /dev/null +++ b/prepare/r-adsplit/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=adSplit +_pkgver=1.64.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation-Driven Clustering' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biobase + r-go.db + r-keggrest + r-multtest +) +optdepends=( + r-golubesets + r-hu6800.db + r-vsn +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-adsplit/lilac.py b/prepare/r-adsplit/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-adsplit/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-adsplit/lilac.yaml b/prepare/r-adsplit/lilac.yaml new file mode 100644 index 0000000000..a69b8357ad --- /dev/null +++ b/prepare/r-adsplit/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-go.db +- r-keggrest +- r-multtest +update_on: +- regex: adSplit_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/adSplit diff --git a/prepare/r-affixcan/PKGBUILD b/prepare/r-affixcan/PKGBUILD new file mode 100644 index 0000000000..1562ff340d --- /dev/null +++ b/prepare/r-affixcan/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AffiXcan +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Functional Approach To Impute Genetically Regulated Expression' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-crayon + r-multiassayexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-affixcan/lilac.py b/prepare/r-affixcan/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-affixcan/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-affixcan/lilac.yaml b/prepare/r-affixcan/lilac.yaml new file mode 100644 index 0000000000..5ffb176658 --- /dev/null +++ b/prepare/r-affixcan/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-crayon +- r-multiassayexperiment +- r-summarizedexperiment +update_on: +- regex: AffiXcan_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AffiXcan diff --git a/prepare/r-affxparser/PKGBUILD b/prepare/r-affxparser/PKGBUILD new file mode 100644 index 0000000000..8d43858611 --- /dev/null +++ b/prepare/r-affxparser/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=affxparser +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Affymetrix File Parsing SDK' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +optdepends=( + r-affymetrixdatatestfiles + r-r.oo + r-r.utils +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-affxparser/lilac.py b/prepare/r-affxparser/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-affxparser/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-affxparser/lilac.yaml b/prepare/r-affxparser/lilac.yaml new file mode 100644 index 0000000000..fa42cb92dc --- /dev/null +++ b/prepare/r-affxparser/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: affxparser_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/affxparser diff --git a/prepare/r-affy/PKGBUILD b/prepare/r-affy/PKGBUILD new file mode 100644 index 0000000000..2fd7e818ba --- /dev/null +++ b/prepare/r-affy/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=affy +_pkgver=1.72.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methods for Affymetrix Oligonucleotide Arrays' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-affyio + r-biobase + r-biocgenerics + r-biocmanager + r-preprocesscore + r-zlibbioc +) +optdepends=( + r-affydata + r-tkwidgets + r-widgettools +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-affy/lilac.py b/prepare/r-affy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-affy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-affy/lilac.yaml b/prepare/r-affy/lilac.yaml new file mode 100644 index 0000000000..e77b409ea6 --- /dev/null +++ b/prepare/r-affy/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affyio +- r-biobase +- r-biocgenerics +- r-biocmanager +- r-preprocesscore +- r-zlibbioc +update_on: +- regex: affy_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/affy diff --git a/prepare/r-affycomp/PKGBUILD b/prepare/r-affycomp/PKGBUILD new file mode 100644 index 0000000000..3041dca223 --- /dev/null +++ b/prepare/r-affycomp/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=affycomp +_pkgver=1.70.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Graphics Toolbox for Assessment of Affymetrix Expression Measures' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +optdepends=( + r-affycompdata + r-splines +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-affycomp/lilac.py b/prepare/r-affycomp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-affycomp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-affycomp/lilac.yaml b/prepare/r-affycomp/lilac.yaml new file mode 100644 index 0000000000..5d58a8aa08 --- /dev/null +++ b/prepare/r-affycomp/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: affycomp_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/affycomp diff --git a/prepare/r-affycompatible/PKGBUILD b/prepare/r-affycompatible/PKGBUILD new file mode 100644 index 0000000000..cfecaf0e16 --- /dev/null +++ b/prepare/r-affycompatible/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AffyCompatible +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Affymetrix GeneChip software compatibility' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-rcurl + r-xml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-affycompatible/lilac.py b/prepare/r-affycompatible/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-affycompatible/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-affycompatible/lilac.yaml b/prepare/r-affycompatible/lilac.yaml new file mode 100644 index 0000000000..d057aa5b73 --- /dev/null +++ b/prepare/r-affycompatible/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-rcurl +- r-xml +update_on: +- regex: AffyCompatible_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AffyCompatible diff --git a/prepare/r-affycontam/PKGBUILD b/prepare/r-affycontam/PKGBUILD new file mode 100644 index 0000000000..855b941bb5 --- /dev/null +++ b/prepare/r-affycontam/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=affyContam +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='structured corruption of affymetrix cel file data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-affy + r-affydata + r-biobase +) +optdepends=( + r-hgu95av2cdf +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-affycontam/lilac.py b/prepare/r-affycontam/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-affycontam/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-affycontam/lilac.yaml b/prepare/r-affycontam/lilac.yaml new file mode 100644 index 0000000000..797e29dab4 --- /dev/null +++ b/prepare/r-affycontam/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-affydata +- r-biobase +update_on: +- regex: affyContam_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/affyContam diff --git a/prepare/r-affycoretools/PKGBUILD b/prepare/r-affycoretools/PKGBUILD new file mode 100644 index 0000000000..90284caeed --- /dev/null +++ b/prepare/r-affycoretools/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=affycoretools +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions useful for those doing repetitive analyses with Affymetrix GeneChips' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-affy + r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-edger + r-gcrma + r-ggplot2 + r-glimma + r-gostats + r-gplots + r-hwriter + r-limma + r-oligoclasses + r-reportingtools + r-rsqlite + r-s4vectors + r-xtable +) +optdepends=( + r-affydata + r-biocstyle + r-hgfocuscdf + r-hgu95av2.db + r-knitr + r-rgl + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-affycoretools/lilac.py b/prepare/r-affycoretools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-affycoretools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-affycoretools/lilac.yaml b/prepare/r-affycoretools/lilac.yaml new file mode 100644 index 0000000000..5a5a1a1b59 --- /dev/null +++ b/prepare/r-affycoretools/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-dbi +- r-edger +- r-gcrma +- r-ggplot2 +- r-glimma +- r-gostats +- r-gplots +- r-hwriter +- r-limma +- r-oligoclasses +- r-reportingtools +- r-rsqlite +- r-s4vectors +- r-xtable +update_on: +- regex: affycoretools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/affycoretools diff --git a/prepare/r-affydata/PKGBUILD b/prepare/r-affydata/PKGBUILD new file mode 100644 index 0000000000..d59f8e2abd --- /dev/null +++ b/prepare/r-affydata/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=affydata +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Affymetrix Data for Demonstration Purpose' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy +) +optdepends=( + r-hgu133acdf + r-hgu95av2cdf +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-affydata/lilac.py b/prepare/r-affydata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-affydata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-affydata/lilac.yaml b/prepare/r-affydata/lilac.yaml new file mode 100644 index 0000000000..cce984876d --- /dev/null +++ b/prepare/r-affydata/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +update_on: +- regex: affydata_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/affydata diff --git a/prepare/r-affyilm/PKGBUILD b/prepare/r-affyilm/PKGBUILD new file mode 100644 index 0000000000..8c73d2dd19 --- /dev/null +++ b/prepare/r-affyilm/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=affyILM +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Linear Model of background subtraction and the Langmuir isotherm' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affxparser + r-affy + r-biobase + r-gcrma +) +optdepends=( + r-affymetrixdatatestfiles + r-hgfocusprobe +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-affyilm/lilac.py b/prepare/r-affyilm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-affyilm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-affyilm/lilac.yaml b/prepare/r-affyilm/lilac.yaml new file mode 100644 index 0000000000..099ce241ca --- /dev/null +++ b/prepare/r-affyilm/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affxparser +- r-affy +- r-biobase +- r-gcrma +update_on: +- regex: affyILM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/affyILM diff --git a/prepare/r-affyio/PKGBUILD b/prepare/r-affyio/PKGBUILD new file mode 100644 index 0000000000..671c7ffb66 --- /dev/null +++ b/prepare/r-affyio/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=affyio +_pkgver=1.64.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for parsing Affymetrix data files' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-zlibbioc +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-affyio/lilac.py b/prepare/r-affyio/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-affyio/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-affyio/lilac.yaml b/prepare/r-affyio/lilac.yaml new file mode 100644 index 0000000000..d21a41b6fe --- /dev/null +++ b/prepare/r-affyio/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-zlibbioc +update_on: +- regex: affyio_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/affyio diff --git a/prepare/r-affylmgui/PKGBUILD b/prepare/r-affylmgui/PKGBUILD new file mode 100644 index 0000000000..a424417df4 --- /dev/null +++ b/prepare/r-affylmgui/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=affylmGUI +_pkgver=1.68.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GUI for limma Package with Affymetrix Microarrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-affyio + r-affyplm + r-annotationdbi + r-biocgenerics + r-biocmanager + r-gcrma + r-limma + r-r2html + r-tkrplot + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-affylmgui/lilac.py b/prepare/r-affylmgui/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-affylmgui/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-affylmgui/lilac.yaml b/prepare/r-affylmgui/lilac.yaml new file mode 100644 index 0000000000..1cdfa3bf13 --- /dev/null +++ b/prepare/r-affylmgui/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-affyio +- r-affyplm +- r-annotationdbi +- r-biocgenerics +- r-biocmanager +- r-gcrma +- r-limma +- r-r2html +- r-tkrplot +- r-xtable +update_on: +- regex: affylmGUI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/affylmGUI diff --git a/prepare/r-affypara/PKGBUILD b/prepare/r-affypara/PKGBUILD new file mode 100644 index 0000000000..356ae5f991 --- /dev/null +++ b/prepare/r-affypara/PKGBUILD @@ -0,0 +1,38 @@ + +_pkgname=affyPara +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sample size for RNAseq studies' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-snow + r-vsn + r-aplpack + r-affyio +) +makedepends=( + git + tar +) +optdepends=( + r-affydata +) +source=("git+https://git.bioconductor.org/packages/${_pkgname}.git") +sha256sums=('SKIP') + +build() { + tar -zcvf ${_pkgname}.tar.gz ${_pkgname} + R CMD INSTALL ${_pkgname}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-affypara/lilac.py b/prepare/r-affypara/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-affypara/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-affypara/lilac.yaml b/prepare/r-affypara/lilac.yaml new file mode 100644 index 0000000000..586c458a0a --- /dev/null +++ b/prepare/r-affypara/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-snow +- r-vsn +- r-aplpack +- r-affyio +update_on: +- regex: Version(\d+.\d+.\d+) + source: regex + url: https://bioconductor.org/packages/affyPara diff --git a/prepare/r-affyplm/PKGBUILD b/prepare/r-affyplm/PKGBUILD new file mode 100644 index 0000000000..04b60e4132 --- /dev/null +++ b/prepare/r-affyplm/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=affyPLM +_pkgver=1.70.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methods for fitting probe-level models' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-biobase + r-biocgenerics + r-gcrma + r-preprocesscore + r-zlibbioc +) +optdepends=( + r-affydata + r-mass +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-affyplm/lilac.py b/prepare/r-affyplm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-affyplm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-affyplm/lilac.yaml b/prepare/r-affyplm/lilac.yaml new file mode 100644 index 0000000000..bc3cc9a08c --- /dev/null +++ b/prepare/r-affyplm/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +- r-biocgenerics +- r-gcrma +- r-preprocesscore +- r-zlibbioc +update_on: +- regex: affyPLM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/affyPLM diff --git a/prepare/r-affyrnadegradation/PKGBUILD b/prepare/r-affyrnadegradation/PKGBUILD new file mode 100644 index 0000000000..87a9c091aa --- /dev/null +++ b/prepare/r-affyrnadegradation/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AffyRNADegradation +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analyze and correct probe positional bias in microarray data due to RNA degradation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy +) +optdepends=( + r-ampaffyexample +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-affyrnadegradation/lilac.py b/prepare/r-affyrnadegradation/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-affyrnadegradation/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-affyrnadegradation/lilac.yaml b/prepare/r-affyrnadegradation/lilac.yaml new file mode 100644 index 0000000000..3b1c6d48bf --- /dev/null +++ b/prepare/r-affyrnadegradation/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +update_on: +- regex: AffyRNADegradation_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AffyRNADegradation diff --git a/prepare/r-agdex/PKGBUILD b/prepare/r-agdex/PKGBUILD new file mode 100644 index 0000000000..f6ad36062b --- /dev/null +++ b/prepare/r-agdex/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AGDEX +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Agreement of Differential Expression Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-gseabase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-agdex/lilac.py b/prepare/r-agdex/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-agdex/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-agdex/lilac.yaml b/prepare/r-agdex/lilac.yaml new file mode 100644 index 0000000000..88eacc57d7 --- /dev/null +++ b/prepare/r-agdex/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-gseabase +update_on: +- regex: AGDEX_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AGDEX diff --git a/prepare/r-aggregatebiovar/PKGBUILD b/prepare/r-aggregatebiovar/PKGBUILD new file mode 100644 index 0000000000..5acc355049 --- /dev/null +++ b/prepare/r-aggregatebiovar/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=aggregateBioVar +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential Gene Expression Analysis for Multi-subject scRNA-seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rlang + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-tibble +) +optdepends=( + r-biocgenerics + r-biocstyle + r-cowplot + r-deseq2 + r-dplyr + r-ggplot2 + r-ggtext + r-knitr + r-magick + r-magrittr + r-pheatmap + r-rcolorbrewer + r-rmarkdown + r-testthat + r-viridis +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aggregatebiovar/lilac.py b/prepare/r-aggregatebiovar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aggregatebiovar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aggregatebiovar/lilac.yaml b/prepare/r-aggregatebiovar/lilac.yaml new file mode 100644 index 0000000000..0413f90a67 --- /dev/null +++ b/prepare/r-aggregatebiovar/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rlang +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +- r-tibble +update_on: +- regex: aggregateBioVar_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/aggregateBioVar diff --git a/prepare/r-aggregation/PKGBUILD b/prepare/r-aggregation/PKGBUILD new file mode 100644 index 0000000000..8c105a45b1 --- /dev/null +++ b/prepare/r-aggregation/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=aggregation +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='p-Value Aggregation Methods' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aggregation/lilac.py b/prepare/r-aggregation/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aggregation/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aggregation/lilac.yaml b/prepare/r-aggregation/lilac.yaml new file mode 100644 index 0000000000..3e30ce32ff --- /dev/null +++ b/prepare/r-aggregation/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: aggregation_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=aggregation diff --git a/prepare/r-agilp/PKGBUILD b/prepare/r-agilp/PKGBUILD new file mode 100644 index 0000000000..078d6d7e2a --- /dev/null +++ b/prepare/r-agilp/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=agilp +_pkgver=3.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Agilent expression array processing package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-agilp/lilac.py b/prepare/r-agilp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-agilp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-agilp/lilac.yaml b/prepare/r-agilp/lilac.yaml new file mode 100644 index 0000000000..c93a19b53b --- /dev/null +++ b/prepare/r-agilp/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: agilp_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/agilp diff --git a/prepare/r-agimicrorna/PKGBUILD b/prepare/r-agimicrorna/PKGBUILD new file mode 100644 index 0000000000..68b680cf96 --- /dev/null +++ b/prepare/r-agimicrorna/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AgiMicroRna +_pkgver=2.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Processing and Differential Expression Analysis of Agilent microRNA chips' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-affycoretools + r-biobase + r-limma + r-preprocesscore +) +optdepends=( + r-codelink + r-gdata + r-geneplotter + r-gplots + r-gtools + r-marray +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-agimicrorna/lilac.py b/prepare/r-agimicrorna/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-agimicrorna/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-agimicrorna/lilac.yaml b/prepare/r-agimicrorna/lilac.yaml new file mode 100644 index 0000000000..16caebb284 --- /dev/null +++ b/prepare/r-agimicrorna/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-affycoretools +- r-biobase +- r-limma +- r-preprocesscore +update_on: +- regex: AgiMicroRna_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AgiMicroRna diff --git a/prepare/r-agricolae/PKGBUILD b/prepare/r-agricolae/PKGBUILD new file mode 100644 index 0000000000..99fdc5128a --- /dev/null +++ b/prepare/r-agricolae/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=agricolae +_pkgver=1.3-5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Procedures for Agricultural Research' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-algdesign + r-klar +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-agricolae/lilac.py b/prepare/r-agricolae/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-agricolae/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-agricolae/lilac.yaml b/prepare/r-agricolae/lilac.yaml new file mode 100644 index 0000000000..9a6012b6dc --- /dev/null +++ b/prepare/r-agricolae/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-algdesign +- r-klar +update_on: +- regex: agricolae_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=agricolae diff --git a/prepare/r-ahocorasicktrie/PKGBUILD b/prepare/r-ahocorasicktrie/PKGBUILD new file mode 100644 index 0000000000..887b6b8380 --- /dev/null +++ b/prepare/r-ahocorasicktrie/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=AhoCorasickTrie +_pkgver=0.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast Searching for Multiple Keywords in Multiple Texts' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-rcpp +) +optdepends=( + r-biostrings + r-microbenchmark + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ahocorasicktrie/lilac.py b/prepare/r-ahocorasicktrie/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ahocorasicktrie/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ahocorasicktrie/lilac.yaml b/prepare/r-ahocorasicktrie/lilac.yaml new file mode 100644 index 0000000000..f55dc7220e --- /dev/null +++ b/prepare/r-ahocorasicktrie/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: AhoCorasickTrie_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=AhoCorasickTrie diff --git a/prepare/r-aims/PKGBUILD b/prepare/r-aims/PKGBUILD new file mode 100644 index 0000000000..74443b8204 --- /dev/null +++ b/prepare/r-aims/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AIMS +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-e1071 +) +optdepends=( + r-biocgenerics + r-breastcancervdx + r-hgu133a.db + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aims/lilac.py b/prepare/r-aims/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aims/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aims/lilac.yaml b/prepare/r-aims/lilac.yaml new file mode 100644 index 0000000000..35c2fb6b78 --- /dev/null +++ b/prepare/r-aims/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-e1071 +update_on: +- regex: AIMS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AIMS diff --git a/prepare/r-airpart/PKGBUILD b/prepare/r-airpart/PKGBUILD new file mode 100644 index 0000000000..eafd8127f8 --- /dev/null +++ b/prepare/r-airpart/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=airpart +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential cell-type-specific allelic imbalance' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-apeglm + r-clue + r-complexheatmap + r-dplyr + r-dynamictreecut + r-emdbook + r-forestplot + r-ggplot2 + r-lpsolve + r-matrixstats + r-mclust + r-pbapply + r-plyr + r-rcolorbrewer + r-rlang + r-s4vectors + r-scater + r-singlecellexperiment + r-smurf + r-summarizedexperiment +) +optdepends=( + r-gplots + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-airpart/lilac.py b/prepare/r-airpart/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-airpart/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-airpart/lilac.yaml b/prepare/r-airpart/lilac.yaml new file mode 100644 index 0000000000..c5fbcf60dc --- /dev/null +++ b/prepare/r-airpart/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-apeglm +- r-clue +- r-complexheatmap +- r-dplyr +- r-dynamictreecut +- r-emdbook +- r-forestplot +- r-ggplot2 +- r-lpsolve +- r-matrixstats +- r-mclust +- r-pbapply +- r-plyr +- r-rcolorbrewer +- r-rlang +- r-s4vectors +- r-scater +- r-singlecellexperiment +- r-smurf +- r-summarizedexperiment +update_on: +- regex: airpart_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/airpart diff --git a/prepare/r-airway/PKGBUILD b/prepare/r-airway/PKGBUILD new file mode 100644 index 0000000000..d4ae127e48 --- /dev/null +++ b/prepare/r-airway/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=airway +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-summarizedexperiment +) +optdepends=( + r-geoquery + r-knitr + r-markdown +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-airway/lilac.py b/prepare/r-airway/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-airway/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-airway/lilac.yaml b/prepare/r-airway/lilac.yaml new file mode 100644 index 0000000000..4ca1a6a690 --- /dev/null +++ b/prepare/r-airway/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-summarizedexperiment +update_on: +- regex: airway_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/airway diff --git a/prepare/r-akmbiclust/PKGBUILD b/prepare/r-akmbiclust/PKGBUILD new file mode 100644 index 0000000000..a7aabbcd02 --- /dev/null +++ b/prepare/r-akmbiclust/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=akmbiclust +_pkgver=0.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Alternating K-Means Biclustering' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-akmbiclust/lilac.py b/prepare/r-akmbiclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-akmbiclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-akmbiclust/lilac.yaml b/prepare/r-akmbiclust/lilac.yaml new file mode 100644 index 0000000000..c01d98eb88 --- /dev/null +++ b/prepare/r-akmbiclust/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: akmbiclust_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=akmbiclust diff --git a/prepare/r-alabama/PKGBUILD b/prepare/r-alabama/PKGBUILD new file mode 100644 index 0000000000..e00be56a2b --- /dev/null +++ b/prepare/r-alabama/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=alabama +_pkgver=2015.3-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Constrained Nonlinear Optimization' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-numderiv +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-alabama/lilac.py b/prepare/r-alabama/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-alabama/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-alabama/lilac.yaml b/prepare/r-alabama/lilac.yaml new file mode 100644 index 0000000000..3a63bb6aff --- /dev/null +++ b/prepare/r-alabama/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-numderiv +update_on: +- regex: alabama_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=alabama diff --git a/prepare/r-aldex2/PKGBUILD b/prepare/r-aldex2/PKGBUILD new file mode 100644 index 0000000000..00fb164102 --- /dev/null +++ b/prepare/r-aldex2/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ALDEx2 +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis Of Differential Abundance Taking Sample Variation Into Account' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-biocparallel + r-genomicranges + r-iranges + r-multtest + r-rfast + r-s4vectors + r-summarizedexperiment + r-zcompositions +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aldex2/lilac.py b/prepare/r-aldex2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aldex2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aldex2/lilac.yaml b/prepare/r-aldex2/lilac.yaml new file mode 100644 index 0000000000..74b52c45f5 --- /dev/null +++ b/prepare/r-aldex2/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-genomicranges +- r-iranges +- r-multtest +- r-rfast +- r-s4vectors +- r-summarizedexperiment +- r-zcompositions +update_on: +- regex: ALDEx2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ALDEx2 diff --git a/prepare/r-alevinqc/PKGBUILD b/prepare/r-alevinqc/PKGBUILD new file mode 100644 index 0000000000..63a178bc24 --- /dev/null +++ b/prepare/r-alevinqc/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=alevinQC +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generate QC Reports For Alevin Output' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-cowplot + r-dplyr + r-dt + r-ggally + r-ggplot2 + r-rjson + r-rlang + r-rmarkdown + r-shiny + r-shinydashboard + r-tximport +) +optdepends=( + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-alevinqc/lilac.py b/prepare/r-alevinqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-alevinqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-alevinqc/lilac.yaml b/prepare/r-alevinqc/lilac.yaml new file mode 100644 index 0000000000..800ce04779 --- /dev/null +++ b/prepare/r-alevinqc/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cowplot +- r-dplyr +- r-dt +- r-ggally +- r-ggplot2 +- r-rjson +- r-rlang +- r-rmarkdown +- r-shiny +- r-shinydashboard +- r-tximport +update_on: +- regex: alevinQC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/alevinQC diff --git a/prepare/r-algdesign/PKGBUILD b/prepare/r-algdesign/PKGBUILD new file mode 100644 index 0000000000..2a87324b1f --- /dev/null +++ b/prepare/r-algdesign/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AlgDesign +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Algorithmic Experimental Design' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-algdesign/lilac.py b/prepare/r-algdesign/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-algdesign/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-algdesign/lilac.yaml b/prepare/r-algdesign/lilac.yaml new file mode 100644 index 0000000000..b4c7251176 --- /dev/null +++ b/prepare/r-algdesign/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: AlgDesign_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=AlgDesign diff --git a/prepare/r-all/PKGBUILD b/prepare/r-all/PKGBUILD new file mode 100644 index 0000000000..bb75c7b3cd --- /dev/null +++ b/prepare/r-all/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ALL +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A data package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase +) +optdepends=( + r-rpart +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-all/lilac.py b/prepare/r-all/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-all/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-all/lilac.yaml b/prepare/r-all/lilac.yaml new file mode 100644 index 0000000000..26b130e6b5 --- /dev/null +++ b/prepare/r-all/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: ALL_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ALL diff --git a/prepare/r-allelicimbalance/PKGBUILD b/prepare/r-allelicimbalance/PKGBUILD new file mode 100644 index 0000000000..2d6b3c6659 --- /dev/null +++ b/prepare/r-allelicimbalance/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AllelicImbalance +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Investigates Allele Specific Expression' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocgenerics + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-gridextra + r-gviz + r-iranges + r-latticeextra + r-rsamtools + r-s4vectors + r-seqinr + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-biocstyle + r-knitr + r-org.hs.eg.db + r-rmarkdown + r-snplocs.hsapiens.dbsnp144.grch37 + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-allelicimbalance/lilac.py b/prepare/r-allelicimbalance/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-allelicimbalance/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-allelicimbalance/lilac.yaml b/prepare/r-allelicimbalance/lilac.yaml new file mode 100644 index 0000000000..a595f4759c --- /dev/null +++ b/prepare/r-allelicimbalance/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-gridextra +- r-gviz +- r-iranges +- r-latticeextra +- r-rsamtools +- r-s4vectors +- r-seqinr +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: AllelicImbalance_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AllelicImbalance diff --git a/prepare/r-alluvial/PKGBUILD b/prepare/r-alluvial/PKGBUILD new file mode 100644 index 0000000000..09af4b3d10 --- /dev/null +++ b/prepare/r-alluvial/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=alluvial +_pkgver=0.1-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Alluvial Diagrams' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-devtools + r-dplyr + r-knitr + r-reshape2 + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-alluvial/lilac.py b/prepare/r-alluvial/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-alluvial/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-alluvial/lilac.yaml b/prepare/r-alluvial/lilac.yaml new file mode 100644 index 0000000000..fe7eb4cfa6 --- /dev/null +++ b/prepare/r-alluvial/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: alluvial_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=alluvial diff --git a/prepare/r-alphabeta/PKGBUILD b/prepare/r-alphabeta/PKGBUILD new file mode 100644 index 0000000000..541fd8295f --- /dev/null +++ b/prepare/r-alphabeta/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AlphaBeta +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-data.table + r-dplyr + r-expm + r-ggplot2 + r-gtools + r-igraph + r-optimx + r-plotly + r-stringr +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-alphabeta/lilac.py b/prepare/r-alphabeta/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-alphabeta/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-alphabeta/lilac.yaml b/prepare/r-alphabeta/lilac.yaml new file mode 100644 index 0000000000..37c51ce51c --- /dev/null +++ b/prepare/r-alphabeta/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-data.table +- r-dplyr +- r-expm +- r-ggplot2 +- r-gtools +- r-igraph +- r-optimx +- r-plotly +- r-stringr +update_on: +- regex: AlphaBeta_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AlphaBeta diff --git a/prepare/r-alpine/PKGBUILD b/prepare/r-alpine/PKGBUILD new file mode 100644 index 0000000000..93f1dc9b26 --- /dev/null +++ b/prepare/r-alpine/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=alpine +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='alpine' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-rbgl + r-rsamtools + r-s4vectors + r-speedglm + r-stringr + r-summarizedexperiment +) +optdepends=( + r-alpinedata + r-bsgenome.hsapiens.ncbi.grch38 + r-ensembldb + r-knitr + r-markdown + r-rcolorbrewer + r-rtracklayer + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-alpine/lilac.py b/prepare/r-alpine/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-alpine/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-alpine/lilac.yaml b/prepare/r-alpine/lilac.yaml new file mode 100644 index 0000000000..9a4f0737c1 --- /dev/null +++ b/prepare/r-alpine/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-graph +- r-iranges +- r-rbgl +- r-rsamtools +- r-s4vectors +- r-speedglm +- r-stringr +- r-summarizedexperiment +update_on: +- regex: alpine_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/alpine diff --git a/prepare/r-alps/PKGBUILD b/prepare/r-alps/PKGBUILD new file mode 100644 index 0000000000..f7f7d4bb3c --- /dev/null +++ b/prepare/r-alps/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ALPS +_pkgver=1.0.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='AnaLysis routines for ePigenomicS data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-asserthat + r-biocparallel + r-chipseeker + r-corrplot + r-data.table + r-dplyr + r-genomicranges + r-ggally + r-genefilter + r-gghalves + r-ggplot2 + r-ggseqlogo + r-gviz + r-magrittr + r-org.hs.eg.db + r-plyr + r-reshape2 + r-rtracklayer + r-stringr + r-tibble + r-txdb.hsapiens.ucsc.hg38.knowngene +) +optdepends=( + r-rmarkdown + r-knitr + r-complexheatmap + r-circlize + r-testthat +) +makedepends=( + git + tar +) +source=("git+https://git.bioconductor.org/packages/${_pkgname}.git") +sha256sums=('SKIP') + +build() { + tar -zcvf ${_pkgname}.tar.gz ${_pkgname} + R CMD INSTALL ${_pkgname}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: + diff --git a/prepare/r-alps/lilac.py b/prepare/r-alps/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-alps/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-alps/lilac.yaml b/prepare/r-alps/lilac.yaml new file mode 100644 index 0000000000..de59f30412 --- /dev/null +++ b/prepare/r-alps/lilac.yaml @@ -0,0 +1,35 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-asserthat +- r-biocparallel +- r-chipseeker +- r-corrplot +- r-data.table +- r-dplyr +- r-genomicranges +- r-ggally +- r-genefilter +- r-gghalves +- r-ggplot2 +- r-ggseqlogo +- r-gviz +- r-magrittr +- r-org.hs.eg.db +- r-plyr +- r-reshape2 +- r-rtracklayer +- r-stringr +- r-tibble +- r-txdb.hsapiens.ucsc.hg38.knowngene +- r-rmarkdown +- r-knitr +- r-complexheatmap +- r-circlize +- r-testthat +update_on: +- regex: Version(\d+.\d+.\d+) + source: regex + url: https://bioconductor.org/packages/ALPS diff --git a/prepare/r-alpsnmr/PKGBUILD b/prepare/r-alpsnmr/PKGBUILD new file mode 100644 index 0000000000..3a6402c801 --- /dev/null +++ b/prepare/r-alpsnmr/PKGBUILD @@ -0,0 +1,67 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AlpsNMR +_pkgver=3.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automated spectraL Processing System for NMR' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-assertthat + r-baseline + r-biocparallel + r-dplyr + r-fs + r-furrr + r-future + r-ggally + r-ggplot2 + r-ggrepel + r-glue + r-htmltools + r-magrittr + r-matrixstats + r-mixomics + r-pcapp + r-plyr + r-purrr + r-readxl + r-reshape2 + r-rlang + r-rmarkdown + r-s4vectors + r-signal + r-speaq + r-stringr + r-summarizedexperiment + r-tibble + r-tidyr + r-tidyselect + r-vctrs + r-writexl + r-zip +) +optdepends=( + r-chemospec + r-dt + r-knitr + r-plotly + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-alpsnmr/lilac.py b/prepare/r-alpsnmr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-alpsnmr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-alpsnmr/lilac.yaml b/prepare/r-alpsnmr/lilac.yaml new file mode 100644 index 0000000000..ed58b28276 --- /dev/null +++ b/prepare/r-alpsnmr/lilac.yaml @@ -0,0 +1,42 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-baseline +- r-biocparallel +- r-dplyr +- r-fs +- r-furrr +- r-future +- r-ggally +- r-ggplot2 +- r-ggrepel +- r-glue +- r-htmltools +- r-magrittr +- r-matrixstats +- r-mixomics +- r-pcapp +- r-plyr +- r-purrr +- r-readxl +- r-reshape2 +- r-rlang +- r-rmarkdown +- r-s4vectors +- r-signal +- r-speaq +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-tidyr +- r-tidyselect +- r-vctrs +- r-writexl +- r-zip +update_on: +- regex: AlpsNMR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AlpsNMR diff --git a/prepare/r-als/PKGBUILD b/prepare/r-als/PKGBUILD new file mode 100644 index 0000000000..f0c64b6fe7 --- /dev/null +++ b/prepare/r-als/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ALS +_pkgver=0.0.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multivariate Curve Resolution Alternating Least Squares (MCR-ALS)' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-iso + r-nnls +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-als/lilac.py b/prepare/r-als/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-als/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-als/lilac.yaml b/prepare/r-als/lilac.yaml new file mode 100644 index 0000000000..d854f41100 --- /dev/null +++ b/prepare/r-als/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-iso +- r-nnls +update_on: +- regex: ALS_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ALS diff --git a/prepare/r-alsace/PKGBUILD b/prepare/r-alsace/PKGBUILD new file mode 100644 index 0000000000..013044a978 --- /dev/null +++ b/prepare/r-alsace/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=alsace +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ALS for the Automatic Chemical Exploration of mixtures' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-als + r-ptw +) +optdepends=( + r-knitr + r-lattice +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-alsace/lilac.py b/prepare/r-alsace/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-alsace/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-alsace/lilac.yaml b/prepare/r-alsace/lilac.yaml new file mode 100644 index 0000000000..dd60ba7b38 --- /dev/null +++ b/prepare/r-alsace/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-als +- r-ptw +update_on: +- regex: alsace_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/alsace diff --git a/prepare/r-altcdfenvs/PKGBUILD b/prepare/r-altcdfenvs/PKGBUILD new file mode 100644 index 0000000000..bd6e8f5065 --- /dev/null +++ b/prepare/r-altcdfenvs/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=altcdfenvs +_pkgver=2.56.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='alternative CDF environments (aka probeset mappings)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-biobase + r-biocgenerics + r-biostrings + r-hypergraph + r-makecdfenv + r-s4vectors +) +optdepends=( + r-hgu133a.db + r-hgu133acdf + r-hgu133aprobe + r-hgu95acdf + r-plasmodiumanophelescdf + r-rcolorbrewer + r-rgraphviz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-altcdfenvs/lilac.py b/prepare/r-altcdfenvs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-altcdfenvs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-altcdfenvs/lilac.yaml b/prepare/r-altcdfenvs/lilac.yaml new file mode 100644 index 0000000000..e5d93cf22f --- /dev/null +++ b/prepare/r-altcdfenvs/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +- r-biocgenerics +- r-biostrings +- r-hypergraph +- r-makecdfenv +- r-s4vectors +update_on: +- regex: altcdfenvs_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/altcdfenvs diff --git a/prepare/r-amap/PKGBUILD b/prepare/r-amap/PKGBUILD new file mode 100644 index 0000000000..9d46a4250b --- /dev/null +++ b/prepare/r-amap/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=amap +_pkgver=0.8-18 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Another Multidimensional Analysis Package' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biobase +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-amap/lilac.py b/prepare/r-amap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-amap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-amap/lilac.yaml b/prepare/r-amap/lilac.yaml new file mode 100644 index 0000000000..709b6d3601 --- /dev/null +++ b/prepare/r-amap/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: amap_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=amap diff --git a/prepare/r-amaretto/PKGBUILD b/prepare/r-amaretto/PKGBUILD new file mode 100644 index 0000000000..852c67ad90 --- /dev/null +++ b/prepare/r-amaretto/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AMARETTO +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Apache') +depends=( + r + r-biocfilecache + r-callr + r-circlize + r-complexheatmap + r-curatedtcgadata + r-doparallel + r-dplyr + r-dt + r-foreach + r-ggplot2 + r-glmnet + r-gridextra + r-httr + r-impute + r-knitr + r-limma + r-matrixstats + r-multiassayexperiment + r-rcpp + r-readr + r-reshape2 + r-rmarkdown + r-tibble +) +optdepends=( + r-knitr + r-mass + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-amaretto/lilac.py b/prepare/r-amaretto/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-amaretto/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-amaretto/lilac.yaml b/prepare/r-amaretto/lilac.yaml new file mode 100644 index 0000000000..39b1b39ab9 --- /dev/null +++ b/prepare/r-amaretto/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-callr +- r-circlize +- r-complexheatmap +- r-curatedtcgadata +- r-doparallel +- r-dplyr +- r-dt +- r-foreach +- r-ggplot2 +- r-glmnet +- r-gridextra +- r-httr +- r-impute +- r-knitr +- r-limma +- r-matrixstats +- r-multiassayexperiment +- r-rcpp +- r-readr +- r-reshape2 +- r-rmarkdown +- r-tibble +update_on: +- regex: AMARETTO_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AMARETTO diff --git a/prepare/r-amountain/PKGBUILD b/prepare/r-amountain/PKGBUILD new file mode 100644 index 0000000000..47313f9eb7 --- /dev/null +++ b/prepare/r-amountain/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: gsl +# Maintainer: Guoyi Zhang + +_pkgname=AMOUNTAIN +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biocstyle + r-knitr + r-qgraph + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-amountain/lilac.py b/prepare/r-amountain/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-amountain/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-amountain/lilac.yaml b/prepare/r-amountain/lilac.yaml new file mode 100644 index 0000000000..6fd6a53583 --- /dev/null +++ b/prepare/r-amountain/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: AMOUNTAIN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AMOUNTAIN diff --git a/prepare/r-amplican/PKGBUILD b/prepare/r-amplican/PKGBUILD new file mode 100644 index 0000000000..0e3f3ddb57 --- /dev/null +++ b/prepare/r-amplican/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=amplican +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automated analysis of CRISPR experiments' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-clustercrit + r-data.table + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-ggthemes + r-gridextra + r-gtable + r-iranges + r-knitr + r-matrixstats + r-rcpp + r-rmarkdown + r-s4vectors + r-shortread + r-stringr + r-waffle +) +optdepends=( + r-biocstyle + r-genomicalignments + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-amplican/lilac.py b/prepare/r-amplican/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-amplican/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-amplican/lilac.yaml b/prepare/r-amplican/lilac.yaml new file mode 100644 index 0000000000..9419ae0bf6 --- /dev/null +++ b/prepare/r-amplican/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-clustercrit +- r-data.table +- r-dplyr +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-ggthemes +- r-gridextra +- r-gtable +- r-iranges +- r-knitr +- r-matrixstats +- r-rcpp +- r-rmarkdown +- r-s4vectors +- r-shortread +- r-stringr +- r-waffle +update_on: +- regex: amplican_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/amplican diff --git a/prepare/r-anaquin/PKGBUILD b/prepare/r-anaquin/PKGBUILD new file mode 100644 index 0000000000..1460cafa09 --- /dev/null +++ b/prepare/r-anaquin/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Anaquin +_pkgver=2.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical analysis of sequins' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-deseq2 + r-ggplot2 + r-knitr + r-locfit + r-plyr + r-qvalue + r-rocr +) +optdepends=( + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-anaquin/lilac.py b/prepare/r-anaquin/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-anaquin/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-anaquin/lilac.yaml b/prepare/r-anaquin/lilac.yaml new file mode 100644 index 0000000000..35cd27d597 --- /dev/null +++ b/prepare/r-anaquin/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-deseq2 +- r-ggplot2 +- r-knitr +- r-locfit +- r-plyr +- r-qvalue +- r-rocr +update_on: +- regex: Anaquin_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Anaquin diff --git a/prepare/r-ancombc/PKGBUILD b/prepare/r-ancombc/PKGBUILD new file mode 100644 index 0000000000..3a1c059d59 --- /dev/null +++ b/prepare/r-ancombc/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ANCOMBC +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of compositions of microbiomes with bias correction' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-microbiome + r-nloptr + r-phyloseq + r-rdpack +) +optdepends=( + r-dt + r-knitr + r-magrittr + r-qwraps2 + r-rmarkdown + r-testthat + r-tidyverse +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ancombc/lilac.py b/prepare/r-ancombc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ancombc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ancombc/lilac.yaml b/prepare/r-ancombc/lilac.yaml new file mode 100644 index 0000000000..768e888839 --- /dev/null +++ b/prepare/r-ancombc/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-microbiome +- r-nloptr +- r-phyloseq +- r-rdpack +update_on: +- regex: ANCOMBC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ANCOMBC diff --git a/prepare/r-aneufinder/PKGBUILD b/prepare/r-aneufinder/PKGBUILD new file mode 100644 index 0000000000..85f898d2ab --- /dev/null +++ b/prepare/r-aneufinder/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AneuFinder +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Copy Number Variation in Single-Cell-Sequencing Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-aneufinderdata + r-bamsignals + r-biocgenerics + r-biostrings + r-cowplot + r-dnacopy + r-doparallel + r-ecp + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggdendro + r-ggplot2 + r-ggrepel + r-iranges + r-mclust + r-reordercluster + r-reshape2 + r-rsamtools + r-s4vectors +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.mmusculus.ucsc.mm10 + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aneufinder/lilac.py b/prepare/r-aneufinder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aneufinder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aneufinder/lilac.yaml b/prepare/r-aneufinder/lilac.yaml new file mode 100644 index 0000000000..b5669b3954 --- /dev/null +++ b/prepare/r-aneufinder/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aneufinderdata +- r-bamsignals +- r-biocgenerics +- r-biostrings +- r-cowplot +- r-dnacopy +- r-doparallel +- r-ecp +- r-foreach +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-ggdendro +- r-ggplot2 +- r-ggrepel +- r-iranges +- r-mclust +- r-reordercluster +- r-reshape2 +- r-rsamtools +- r-s4vectors +update_on: +- regex: AneuFinder_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AneuFinder diff --git a/prepare/r-aneufinderdata/PKGBUILD b/prepare/r-aneufinderdata/PKGBUILD new file mode 100644 index 0000000000..999d00848e --- /dev/null +++ b/prepare/r-aneufinderdata/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AneuFinderData +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='WGSCS Data for Demonstration Purposes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aneufinderdata/lilac.py b/prepare/r-aneufinderdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aneufinderdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aneufinderdata/lilac.yaml b/prepare/r-aneufinderdata/lilac.yaml new file mode 100644 index 0000000000..221a9bcc8e --- /dev/null +++ b/prepare/r-aneufinderdata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: AneuFinderData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AneuFinderData diff --git a/prepare/r-anf/PKGBUILD b/prepare/r-anf/PKGBUILD new file mode 100644 index 0000000000..496a1e43d6 --- /dev/null +++ b/prepare/r-anf/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ANF +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Affinity Network Fusion for Complex Patient Clustering' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-igraph + r-rcolorbrewer +) +optdepends=( + r-experimenthub + r-knitr + r-rmarkdown + r-snftool + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-anf/lilac.py b/prepare/r-anf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-anf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-anf/lilac.yaml b/prepare/r-anf/lilac.yaml new file mode 100644 index 0000000000..3ba53df656 --- /dev/null +++ b/prepare/r-anf/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-igraph +- r-rcolorbrewer +update_on: +- regex: ANF_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ANF diff --git a/prepare/r-animalcules/PKGBUILD b/prepare/r-animalcules/PKGBUILD new file mode 100644 index 0000000000..901b2fa302 --- /dev/null +++ b/prepare/r-animalcules/PKGBUILD @@ -0,0 +1,62 @@ +# Maintainer: Guoyi Zhang + +_pkgname=animalcules +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive microbiome analysis toolkit' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ape + r-assertthat + r-biomformat + r-caret + r-covr + r-deseq2 + r-dplyr + r-dt + r-forcats + r-ggplot2 + r-glmnet + r-gunifrac + r-limma + r-magrittr + r-multiassayexperiment + r-plotly + r-plotroc + r-rentrez + r-reshape2 + r-s4vectors + r-scales + r-shiny + r-shinyjs + r-summarizedexperiment + r-tibble + r-tsne + r-umap + r-vegan + r-xml +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat + r-usethis +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-animalcules/lilac.py b/prepare/r-animalcules/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-animalcules/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-animalcules/lilac.yaml b/prepare/r-animalcules/lilac.yaml new file mode 100644 index 0000000000..6c28695fcc --- /dev/null +++ b/prepare/r-animalcules/lilac.yaml @@ -0,0 +1,38 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-assertthat +- r-biomformat +- r-caret +- r-covr +- r-deseq2 +- r-dplyr +- r-dt +- r-forcats +- r-ggplot2 +- r-glmnet +- r-gunifrac +- r-limma +- r-magrittr +- r-multiassayexperiment +- r-plotly +- r-plotroc +- r-rentrez +- r-reshape2 +- r-s4vectors +- r-scales +- r-shiny +- r-shinyjs +- r-summarizedexperiment +- r-tibble +- r-tsne +- r-umap +- r-vegan +- r-xml +update_on: +- regex: animalcules_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/animalcules diff --git a/prepare/r-annaffy/PKGBUILD b/prepare/r-annaffy/PKGBUILD new file mode 100644 index 0000000000..e85bc43f20 --- /dev/null +++ b/prepare/r-annaffy/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=annaffy +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation tools for Affymetrix biological metadata' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-annotationdbi + r-biobase + r-biocmanager + r-dbi + r-go.db +) +optdepends=( + r-hgu95av2.db + r-multtest + r-tcltk +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-annaffy/lilac.py b/prepare/r-annaffy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-annaffy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-annaffy/lilac.yaml b/prepare/r-annaffy/lilac.yaml new file mode 100644 index 0000000000..ccdc50c9da --- /dev/null +++ b/prepare/r-annaffy/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocmanager +- r-dbi +- r-go.db +update_on: +- regex: annaffy_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/annaffy diff --git a/prepare/r-annmap/PKGBUILD b/prepare/r-annmap/PKGBUILD new file mode 100644 index 0000000000..63a1de8b20 --- /dev/null +++ b/prepare/r-annmap/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=annmap +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-dbi + r-digest + r-genefilter + r-genomicranges + r-iranges + r-rmysql + r-rsamtools +) +optdepends=( + r-gviz + r-rjson + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-annmap/lilac.py b/prepare/r-annmap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-annmap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-annmap/lilac.yaml b/prepare/r-annmap/lilac.yaml new file mode 100644 index 0000000000..55089ef982 --- /dev/null +++ b/prepare/r-annmap/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-dbi +- r-digest +- r-genefilter +- r-genomicranges +- r-iranges +- r-rmysql +- r-rsamtools +update_on: +- regex: annmap_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/annmap diff --git a/prepare/r-annotate/PKGBUILD b/prepare/r-annotate/PKGBUILD new file mode 100644 index 0000000000..4ad50cd69d --- /dev/null +++ b/prepare/r-annotate/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=annotate +_pkgver=1.72.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation for microarrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-httr + r-xml + r-xtable +) +optdepends=( + r-biostrings + r-genefilter + r-go.db + r-hgu95av2.db + r-humanchrloc + r-iranges + r-org.hs.eg.db + r-org.mm.eg.db + r-rae230a.db + r-rae230aprobe + r-rgraphviz + r-runit + r-tkwidgets +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-annotate/lilac.py b/prepare/r-annotate/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-annotate/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-annotate/lilac.yaml b/prepare/r-annotate/lilac.yaml new file mode 100644 index 0000000000..9b16c532be --- /dev/null +++ b/prepare/r-annotate/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-dbi +- r-httr +- r-xml +- r-xtable +update_on: +- regex: annotate_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/annotate diff --git a/prepare/r-annotationdbi/PKGBUILD b/prepare/r-annotationdbi/PKGBUILD new file mode 100644 index 0000000000..6f88bb9444 --- /dev/null +++ b/prepare/r-annotationdbi/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AnnotationDbi +_pkgver=1.56.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Manipulation of SQLite-based annotations in Bioconductor' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-dbi + r-iranges + r-keggrest + r-rsqlite + r-s4vectors +) +optdepends=( + r-annotationforge + r-biocstyle + r-ensdb.hsapiens.v75 + r-go.db + r-graph + r-hgu95av2.db + r-knitr + r-org.at.tair.db + r-org.hs.eg.db + r-org.sc.sgd.db + r-reactome.db + r-runit + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-annotationdbi/lilac.py b/prepare/r-annotationdbi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-annotationdbi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-annotationdbi/lilac.yaml b/prepare/r-annotationdbi/lilac.yaml new file mode 100644 index 0000000000..1f98b31082 --- /dev/null +++ b/prepare/r-annotationdbi/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-dbi +- r-iranges +- r-keggrest +- r-rsqlite +- r-s4vectors +update_on: +- regex: AnnotationDbi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AnnotationDbi diff --git a/prepare/r-annotationfilter/PKGBUILD b/prepare/r-annotationfilter/PKGBUILD new file mode 100644 index 0000000000..7f8355964f --- /dev/null +++ b/prepare/r-annotationfilter/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AnnotationFilter +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Facilities for Filtering Bioconductor Annotation Resources' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-genomicranges + r-lazyeval +) +optdepends=( + r-biocstyle + r-knitr + r-org.hs.eg.db + r-rmarkdown + r-rsqlite + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-annotationfilter/lilac.py b/prepare/r-annotationfilter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-annotationfilter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-annotationfilter/lilac.yaml b/prepare/r-annotationfilter/lilac.yaml new file mode 100644 index 0000000000..2ae66a48a5 --- /dev/null +++ b/prepare/r-annotationfilter/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-lazyeval +update_on: +- regex: AnnotationFilter_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AnnotationFilter diff --git a/prepare/r-annotationforge/PKGBUILD b/prepare/r-annotationforge/PKGBUILD new file mode 100644 index 0000000000..9880d36156 --- /dev/null +++ b/prepare/r-annotationforge/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AnnotationForge +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for building SQLite-based annotation data packages' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-rcurl + r-rsqlite + r-s4vectors + r-xml +) +optdepends=( + r-affy + r-biocfilecache + r-biocmanager + r-biocstyle + r-biomart + r-biostrings + r-genomeinfodb + r-go.db + r-hgu95av2.db + r-homo.sapiens + r-httr + r-human.db0 + r-knitr + r-markdown + r-org.hs.eg.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-annotationforge/lilac.py b/prepare/r-annotationforge/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-annotationforge/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-annotationforge/lilac.yaml b/prepare/r-annotationforge/lilac.yaml new file mode 100644 index 0000000000..b3ad630692 --- /dev/null +++ b/prepare/r-annotationforge/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-dbi +- r-rcurl +- r-rsqlite +- r-s4vectors +- r-xml +update_on: +- regex: AnnotationForge_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AnnotationForge diff --git a/prepare/r-annotationhub/PKGBUILD b/prepare/r-annotationhub/PKGBUILD new file mode 100644 index 0000000000..123e166b23 --- /dev/null +++ b/prepare/r-annotationhub/PKGBUILD @@ -0,0 +1,62 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AnnotationHub +_pkgver=3.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Client to access AnnotationHub resources' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biocfilecache + r-biocgenerics + r-biocmanager + r-biocversion + r-curl + r-dplyr + r-httr + r-interactivedisplaybase + r-rappdirs + r-rsqlite + r-s4vectors + r-yaml +) +optdepends=( + r-annotationforge + r-annotationhubdata + r-biocstyle + r-biostrings + r-experimenthub + r-gdsfmt + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-hubpub + r-iranges + r-knitr + r-msnbase + r-mzr + r-rbiopaxparser + r-rmarkdown + r-rsamtools + r-rtracklayer + r-runit + r-summarizedexperiment + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-annotationhub/lilac.py b/prepare/r-annotationhub/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-annotationhub/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-annotationhub/lilac.yaml b/prepare/r-annotationhub/lilac.yaml new file mode 100644 index 0000000000..d3019585e5 --- /dev/null +++ b/prepare/r-annotationhub/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocfilecache +- r-biocgenerics +- r-biocmanager +- r-biocversion +- r-curl +- r-dplyr +- r-httr +- r-interactivedisplaybase +- r-rappdirs +- r-rsqlite +- r-s4vectors +- r-yaml +update_on: +- regex: AnnotationHub_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AnnotationHub diff --git a/prepare/r-annotationhubdata/PKGBUILD b/prepare/r-annotationhubdata/PKGBUILD new file mode 100644 index 0000000000..9c831ca6bf --- /dev/null +++ b/prepare/r-annotationhubdata/PKGBUILD @@ -0,0 +1,59 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AnnotationHubData +_pkgver=1.24.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Transform public data resources into Bioconductor Data Structures' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-annotationforge + r-annotationhub + r-biobase + r-bioccheck + r-biocgenerics + r-biocmanager + r-biocviews + r-biostrings + r-dbi + r-futile.logger + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-jsonlite + r-organismdbi + r-rcurl + r-rsamtools + r-rsqlite + r-rtracklayer + r-s4vectors + r-xml +) +optdepends=( + r-biocstyle + r-genomeinfodbdata + r-grasp2db + r-hubpub + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-annotationhubdata/lilac.py b/prepare/r-annotationhubdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-annotationhubdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-annotationhubdata/lilac.yaml b/prepare/r-annotationhubdata/lilac.yaml new file mode 100644 index 0000000000..acd5b372c5 --- /dev/null +++ b/prepare/r-annotationhubdata/lilac.yaml @@ -0,0 +1,33 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationforge +- r-annotationhub +- r-biobase +- r-bioccheck +- r-biocgenerics +- r-biocmanager +- r-biocviews +- r-biostrings +- r-dbi +- r-futile.logger +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-graph +- r-iranges +- r-jsonlite +- r-organismdbi +- r-rcurl +- r-rsamtools +- r-rsqlite +- r-rtracklayer +- r-s4vectors +- r-xml +update_on: +- regex: AnnotationHubData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AnnotationHubData diff --git a/prepare/r-annotationtools/PKGBUILD b/prepare/r-annotationtools/PKGBUILD new file mode 100644 index 0000000000..1b3f8a58dc --- /dev/null +++ b/prepare/r-annotationtools/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=annotationTools +_pkgver=1.68.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotate microarrays and perform cross-species gene expression analyses using flat file databases' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-annotationtools/lilac.py b/prepare/r-annotationtools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-annotationtools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-annotationtools/lilac.yaml b/prepare/r-annotationtools/lilac.yaml new file mode 100644 index 0000000000..f65c7ff9b2 --- /dev/null +++ b/prepare/r-annotationtools/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: annotationTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/annotationTools diff --git a/prepare/r-annotatr/PKGBUILD b/prepare/r-annotatr/PKGBUILD new file mode 100644 index 0000000000..3c7688ee0f --- /dev/null +++ b/prepare/r-annotatr/PKGBUILD @@ -0,0 +1,62 @@ +# Maintainer: Guoyi Zhang + +_pkgname=annotatr +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation of Genomic Regions to Genomic Annotations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-annotationhub + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-readr + r-regioner + r-reshape2 + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocstyle + r-devtools + r-knitr + r-org.dm.eg.db + r-org.gg.eg.db + r-org.hs.eg.db + r-org.mm.eg.db + r-org.rn.eg.db + r-rmarkdown + r-roxygen2 + r-testthat + r-txdb.dmelanogaster.ucsc.dm3.ensgene + r-txdb.dmelanogaster.ucsc.dm6.ensgene + r-txdb.ggallus.ucsc.galgal5.refgene + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.hsapiens.ucsc.hg38.knowngene + r-txdb.mmusculus.ucsc.mm10.knowngene + r-txdb.mmusculus.ucsc.mm9.knowngene + r-txdb.rnorvegicus.ucsc.rn4.ensgene + r-txdb.rnorvegicus.ucsc.rn5.refgene + r-txdb.rnorvegicus.ucsc.rn6.refgene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-annotatr/lilac.py b/prepare/r-annotatr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-annotatr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-annotatr/lilac.yaml b/prepare/r-annotatr/lilac.yaml new file mode 100644 index 0000000000..45354bffaf --- /dev/null +++ b/prepare/r-annotatr/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-dplyr +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-readr +- r-regioner +- r-reshape2 +- r-rtracklayer +- r-s4vectors +update_on: +- regex: annotatr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/annotatr diff --git a/prepare/r-anocva/PKGBUILD b/prepare/r-anocva/PKGBUILD new file mode 100644 index 0000000000..a5d2f16518 --- /dev/null +++ b/prepare/r-anocva/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=anocva +_pkgver=0.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Non-Parametric Statistical Test to Compare Clustering Structures' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-igraph + r-mass +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-anocva/lilac.py b/prepare/r-anocva/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-anocva/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-anocva/lilac.yaml b/prepare/r-anocva/lilac.yaml new file mode 100644 index 0000000000..234bf22149 --- /dev/null +++ b/prepare/r-anocva/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: anocva_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=anocva diff --git a/prepare/r-anota/PKGBUILD b/prepare/r-anota/PKGBUILD new file mode 100644 index 0000000000..2ccde5421f --- /dev/null +++ b/prepare/r-anota/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=anota +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ANalysis Of Translational Activity (ANOTA).' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-multtest + r-qvalue +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-anota/lilac.py b/prepare/r-anota/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-anota/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-anota/lilac.yaml b/prepare/r-anota/lilac.yaml new file mode 100644 index 0000000000..03443b6969 --- /dev/null +++ b/prepare/r-anota/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-multtest +- r-qvalue +update_on: +- regex: anota_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/anota diff --git a/prepare/r-anota2seq/PKGBUILD b/prepare/r-anota2seq/PKGBUILD new file mode 100644 index 0000000000..604a9cbf30 --- /dev/null +++ b/prepare/r-anota2seq/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=anota2seq +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-deseq2 + r-edger + r-limma + r-multtest + r-qvalue + r-rcolorbrewer + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-anota2seq/lilac.py b/prepare/r-anota2seq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-anota2seq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-anota2seq/lilac.yaml b/prepare/r-anota2seq/lilac.yaml new file mode 100644 index 0000000000..8677a37814 --- /dev/null +++ b/prepare/r-anota2seq/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-deseq2 +- r-edger +- r-limma +- r-multtest +- r-qvalue +- r-rcolorbrewer +- r-summarizedexperiment +update_on: +- regex: anota2seq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/anota2seq diff --git a/prepare/r-antiprofiles/PKGBUILD b/prepare/r-antiprofiles/PKGBUILD new file mode 100644 index 0000000000..b1b348175f --- /dev/null +++ b/prepare/r-antiprofiles/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=antiProfiles +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Implementation of gene expression anti-profiles' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-locfit + r-matrixstats +) +optdepends=( + r-antiprofilesdata + r-rcolorbrewer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-antiprofiles/lilac.py b/prepare/r-antiprofiles/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-antiprofiles/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-antiprofiles/lilac.yaml b/prepare/r-antiprofiles/lilac.yaml new file mode 100644 index 0000000000..cf65c87366 --- /dev/null +++ b/prepare/r-antiprofiles/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-locfit +- r-matrixstats +update_on: +- regex: antiProfiles_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/antiProfiles diff --git a/prepare/r-anvil/PKGBUILD b/prepare/r-anvil/PKGBUILD new file mode 100644 index 0000000000..751e9c2c07 --- /dev/null +++ b/prepare/r-anvil/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AnVIL +_pkgver=1.6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bioconductor on the AnVIL compute environment' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocmanager + r-dplyr + r-futile.logger + r-httr + r-jsonlite + r-rapiclient + r-rlang + r-tibble + r-tidyr + r-tidyselect +) +optdepends=( + r-biocstyle + r-knitr + r-parallel + r-readr + r-rmarkdown + r-testthat + r-withr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-anvil/lilac.py b/prepare/r-anvil/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-anvil/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-anvil/lilac.yaml b/prepare/r-anvil/lilac.yaml new file mode 100644 index 0000000000..750008aff8 --- /dev/null +++ b/prepare/r-anvil/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocmanager +- r-dplyr +- r-futile.logger +- r-httr +- r-jsonlite +- r-rapiclient +- r-rlang +- r-tibble +- r-tidyr +- r-tidyselect +update_on: +- regex: AnVIL_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AnVIL diff --git a/prepare/r-anvilbilling/PKGBUILD b/prepare/r-anvilbilling/PKGBUILD new file mode 100644 index 0000000000..b3635e96e4 --- /dev/null +++ b/prepare/r-anvilbilling/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AnVILBilling +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (anvilproject.org).' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bigrquery + r-dbi + r-dplyr + r-dt + r-ggplot2 + r-lubridate + r-magrittr + r-plotly + r-shiny + r-shinytoastr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-anvilbilling/lilac.py b/prepare/r-anvilbilling/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-anvilbilling/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-anvilbilling/lilac.yaml b/prepare/r-anvilbilling/lilac.yaml new file mode 100644 index 0000000000..b97e08be2f --- /dev/null +++ b/prepare/r-anvilbilling/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bigrquery +- r-dbi +- r-dplyr +- r-dt +- r-ggplot2 +- r-lubridate +- r-magrittr +- r-plotly +- r-shiny +- r-shinytoastr +update_on: +- regex: AnVILBilling_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AnVILBilling diff --git a/prepare/r-anvilpublish/PKGBUILD b/prepare/r-anvilpublish/PKGBUILD new file mode 100644 index 0000000000..ebe307ba2a --- /dev/null +++ b/prepare/r-anvilpublish/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AnVILPublish +_pkgver=1.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Publish Packages and Other Resources to AnVIL Workspaces' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-anvil + r-httr + r-jsonlite + r-readr + r-rmarkdown + r-whisker + r-yaml +) +optdepends=( + r-biocmanager + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-anvilpublish/lilac.py b/prepare/r-anvilpublish/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-anvilpublish/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-anvilpublish/lilac.yaml b/prepare/r-anvilpublish/lilac.yaml new file mode 100644 index 0000000000..751349dca5 --- /dev/null +++ b/prepare/r-anvilpublish/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-anvil +- r-httr +- r-jsonlite +- r-readr +- r-rmarkdown +- r-whisker +- r-yaml +update_on: +- regex: AnVILPublish_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AnVILPublish diff --git a/prepare/r-anylib/PKGBUILD b/prepare/r-anylib/PKGBUILD new file mode 100644 index 0000000000..884a81b8c3 --- /dev/null +++ b/prepare/r-anylib/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=anyLib +_pkgver=1.0.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Install and Load Any Package from CRAN, Bioconductor or Github' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('CCPL:by-nc-sa') +depends=( + r + r-biocmanager + r-curl + r-devtools + r-httr + r-withr +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-anylib/lilac.py b/prepare/r-anylib/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-anylib/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-anylib/lilac.yaml b/prepare/r-anylib/lilac.yaml new file mode 100644 index 0000000000..1b8197885a --- /dev/null +++ b/prepare/r-anylib/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocmanager +- r-curl +- r-devtools +- r-httr +- r-withr +update_on: +- regex: anyLib_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=anyLib diff --git a/prepare/r-aod/PKGBUILD b/prepare/r-aod/PKGBUILD new file mode 100644 index 0000000000..bb5e766c32 --- /dev/null +++ b/prepare/r-aod/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=aod +_pkgver=1.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Overdispersed Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-boot + r-lme4 + r-mass +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aod/lilac.py b/prepare/r-aod/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aod/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aod/lilac.yaml b/prepare/r-aod/lilac.yaml new file mode 100644 index 0000000000..460b94f5ce --- /dev/null +++ b/prepare/r-aod/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: aod_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=aod diff --git a/prepare/r-apalyzer/PKGBUILD b/prepare/r-apalyzer/PKGBUILD new file mode 100644 index 0000000000..05ab40772e --- /dev/null +++ b/prepare/r-apalyzer/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=APAlyzer +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A toolkit for APA analysis using RNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-deseq2 + r-dplyr + r-ensembldb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggrepel + r-repmis + r-rsamtools + r-rsubread + r-rtracklayer + r-summarizedexperiment + r-tidyr + r-variantannotation +) +optdepends=( + r-annotationdbi + r-biocstyle + r-knitr + r-org.mm.eg.db + r-pasillabamsubset + r-rmarkdown + r-tbx20bamsubset + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-apalyzer/lilac.py b/prepare/r-apalyzer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-apalyzer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-apalyzer/lilac.yaml b/prepare/r-apalyzer/lilac.yaml new file mode 100644 index 0000000000..e94cd27295 --- /dev/null +++ b/prepare/r-apalyzer/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-deseq2 +- r-dplyr +- r-ensembldb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-ggrepel +- r-repmis +- r-rsamtools +- r-rsubread +- r-rtracklayer +- r-summarizedexperiment +- r-tidyr +- r-variantannotation +update_on: +- regex: APAlyzer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/APAlyzer diff --git a/prepare/r-apcluster/PKGBUILD b/prepare/r-apcluster/PKGBUILD new file mode 100644 index 0000000000..c49b6e0d6b --- /dev/null +++ b/prepare/r-apcluster/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=apcluster +_pkgver=1.4.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Affinity Propagation Clustering' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-biostrings + r-kebabs + r-knitr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-apcluster/lilac.py b/prepare/r-apcluster/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-apcluster/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-apcluster/lilac.yaml b/prepare/r-apcluster/lilac.yaml new file mode 100644 index 0000000000..dee941b4dc --- /dev/null +++ b/prepare/r-apcluster/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: apcluster_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=apcluster diff --git a/prepare/r-apcomplex/PKGBUILD b/prepare/r-apcomplex/PKGBUILD new file mode 100644 index 0000000000..6dcb0504ab --- /dev/null +++ b/prepare/r-apcomplex/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=apComplex +_pkgver=2.60.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimate protein complex membership using AP-MS protein data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-graph + r-org.sc.sgd.db + r-rbgl + r-rgraphviz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-apcomplex/lilac.py b/prepare/r-apcomplex/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-apcomplex/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-apcomplex/lilac.yaml b/prepare/r-apcomplex/lilac.yaml new file mode 100644 index 0000000000..a1edca7eb1 --- /dev/null +++ b/prepare/r-apcomplex/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +- r-org.sc.sgd.db +- r-rbgl +- r-rgraphviz +update_on: +- regex: apComplex_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/apComplex diff --git a/prepare/r-ape/PKGBUILD b/prepare/r-ape/PKGBUILD new file mode 100644 index 0000000000..dfd03e0f9c --- /dev/null +++ b/prepare/r-ape/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ape +_pkgver=5.6-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analyses of Phylogenetics and Evolution' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-expm + r-gee + r-igraph + r-phangorn +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ape/lilac.py b/prepare/r-ape/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ape/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ape/lilac.yaml b/prepare/r-ape/lilac.yaml new file mode 100644 index 0000000000..dc8695bcea --- /dev/null +++ b/prepare/r-ape/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: ape_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ape diff --git a/prepare/r-apeglm/PKGBUILD b/prepare/r-apeglm/PKGBUILD new file mode 100644 index 0000000000..761d4cbb3b --- /dev/null +++ b/prepare/r-apeglm/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=apeglm +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Approximate posterior estimation for GLM coefficients' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-emdbook + r-genomicranges + r-rcpp + r-rcppeigen + r-rcppnumerical + r-summarizedexperiment +) +optdepends=( + r-airway + r-deseq2 + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-apeglm/lilac.py b/prepare/r-apeglm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-apeglm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-apeglm/lilac.yaml b/prepare/r-apeglm/lilac.yaml new file mode 100644 index 0000000000..b9ba70e9ae --- /dev/null +++ b/prepare/r-apeglm/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-emdbook +- r-genomicranges +- r-rcpp +- r-rcppeigen +- r-rcppnumerical +- r-summarizedexperiment +update_on: +- regex: apeglm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/apeglm diff --git a/prepare/r-aplot/PKGBUILD b/prepare/r-aplot/PKGBUILD new file mode 100644 index 0000000000..74facc635e --- /dev/null +++ b/prepare/r-aplot/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=aplot +_pkgver=0.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Decorate a 'ggplot' with Associated Information" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ggfun + r-ggplot2 + r-ggplotify + r-magrittr + r-patchwork + r-yulab.utils +) +optdepends=( + r-ggtree +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aplot/lilac.py b/prepare/r-aplot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aplot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aplot/lilac.yaml b/prepare/r-aplot/lilac.yaml new file mode 100644 index 0000000000..ebed2e7cb3 --- /dev/null +++ b/prepare/r-aplot/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggfun +- r-ggplot2 +- r-ggplotify +- r-magrittr +- r-patchwork +- r-yulab.utils +update_on: +- regex: aplot_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=aplot diff --git a/prepare/r-aplpack/PKGBUILD b/prepare/r-aplpack/PKGBUILD new file mode 100644 index 0000000000..3b92204ccb --- /dev/null +++ b/prepare/r-aplpack/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=aplpack +_pkgver=1.3.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Another Plot Package: 'Bagplots', 'Iconplots', 'Summaryplots', Slider Functions and Others" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-jpeg + r-png + r-splines + r-tcltk + r-tkrplot + r-utils +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aplpack/lilac.py b/prepare/r-aplpack/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aplpack/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aplpack/lilac.yaml b/prepare/r-aplpack/lilac.yaml new file mode 100644 index 0000000000..c43df2bdac --- /dev/null +++ b/prepare/r-aplpack/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: aplpack_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=aplpack diff --git a/prepare/r-appreci8r/PKGBUILD b/prepare/r-appreci8r/PKGBUILD new file mode 100644 index 0000000000..e1f4763b96 --- /dev/null +++ b/prepare/r-appreci8r/PKGBUILD @@ -0,0 +1,59 @@ +# Maintainer: Guoyi Zhang + +_pkgname=appreci8R +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biostrings + r-bsgenome + r-bsgenome.hsapiens.ucsc.hg19 + r-cosmic.67 + r-dt + r-genomicfeatures + r-genomicranges + r-genomicscores + r-homo.sapiens + r-iranges + r-mafdb.1kgenomes.phase3.hs37d5 + r-mafdb.exac.r1.0.hs37d5 + r-mafdb.gnomadex.r2.1.hs37d5 + r-openxlsx + r-polyphen.hsapiens.dbsnp131 + r-rentrez + r-rsamtools + r-rsnps + r-s4vectors + r-seqinr + r-shiny + r-shinyjs + r-sift.hsapiens.dbsnp137 + r-snplocs.hsapiens.dbsnp144.grch37 + r-stringr + r-summarizedexperiment + r-txdb.hsapiens.ucsc.hg19.knowngene + r-variantannotation + r-xtrasnplocs.hsapiens.dbsnp144.grch37 +) +optdepends=( + r-go.db + r-org.hs.eg.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-appreci8r/lilac.py b/prepare/r-appreci8r/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-appreci8r/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-appreci8r/lilac.yaml b/prepare/r-appreci8r/lilac.yaml new file mode 100644 index 0000000000..cfef00fc92 --- /dev/null +++ b/prepare/r-appreci8r/lilac.yaml @@ -0,0 +1,38 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome +- r-bsgenome.hsapiens.ucsc.hg19 +- r-cosmic.67 +- r-dt +- r-genomicfeatures +- r-genomicranges +- r-genomicscores +- r-homo.sapiens +- r-iranges +- r-mafdb.1kgenomes.phase3.hs37d5 +- r-mafdb.exac.r1.0.hs37d5 +- r-mafdb.gnomadex.r2.1.hs37d5 +- r-openxlsx +- r-polyphen.hsapiens.dbsnp131 +- r-rentrez +- r-rsamtools +- r-rsnps +- r-s4vectors +- r-seqinr +- r-shiny +- r-shinyjs +- r-sift.hsapiens.dbsnp137 +- r-snplocs.hsapiens.dbsnp144.grch37 +- r-stringr +- r-summarizedexperiment +- r-txdb.hsapiens.ucsc.hg19.knowngene +- r-variantannotation +- r-xtrasnplocs.hsapiens.dbsnp144.grch37 +update_on: +- regex: appreci8R_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/appreci8R diff --git a/prepare/r-argparse/PKGBUILD b/prepare/r-argparse/PKGBUILD new file mode 100644 index 0000000000..dc0a157e8a --- /dev/null +++ b/prepare/r-argparse/PKGBUILD @@ -0,0 +1,35 @@ +# system requirements: python (>= 3.2) +# Maintainer: Guoyi Zhang + +_pkgname=argparse +_pkgver=2.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Command Line Optional and Positional Argument Parser' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-findpython + r-jsonlite + r-r6 +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-argparse/lilac.py b/prepare/r-argparse/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-argparse/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-argparse/lilac.yaml b/prepare/r-argparse/lilac.yaml new file mode 100644 index 0000000000..c7d547e913 --- /dev/null +++ b/prepare/r-argparse/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-findpython +- r-jsonlite +- r-r6 +update_on: +- regex: argparse_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=argparse diff --git a/prepare/r-aricode/PKGBUILD b/prepare/r-aricode/PKGBUILD new file mode 100644 index 0000000000..0ef2ec0044 --- /dev/null +++ b/prepare/r-aricode/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=aricode +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Efficient Computations of Standard Clustering Comparison Measures' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-spelling + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aricode/lilac.py b/prepare/r-aricode/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aricode/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aricode/lilac.yaml b/prepare/r-aricode/lilac.yaml new file mode 100644 index 0000000000..f6a9e0923d --- /dev/null +++ b/prepare/r-aricode/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: aricode_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=aricode diff --git a/prepare/r-arm/PKGBUILD b/prepare/r-arm/PKGBUILD new file mode 100644 index 0000000000..29b16e3912 --- /dev/null +++ b/prepare/r-arm/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=arm +_pkgver=1.12-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data Analysis Using Regression and Multilevel/Hierarchical Models' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-coda + r-lme4 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-arm/lilac.py b/prepare/r-arm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-arm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-arm/lilac.yaml b/prepare/r-arm/lilac.yaml new file mode 100644 index 0000000000..a96848975b --- /dev/null +++ b/prepare/r-arm/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-coda +- r-lme4 +update_on: +- regex: arm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=arm diff --git a/prepare/r-aroma.affymetrix/PKGBUILD b/prepare/r-aroma.affymetrix/PKGBUILD new file mode 100644 index 0000000000..bad909ba8f --- /dev/null +++ b/prepare/r-aroma.affymetrix/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=aroma.affymetrix +_pkgver=3.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Large Affymetrix Microarray Data Sets' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-aroma.apd + r-aroma.core + r-future + r-listenv + r-matrixstats + r-r.cache + r-r.devices + r-r.filesets + r-r.methodss3 + r-r.oo + r-r.utils +) +optdepends=( + r-affxparser + r-affy + r-affymetrixdatatestfiles + r-affyplm + r-aroma.light + r-biobase + r-biocgenerics + r-dbi + r-dchipio + r-gcrma + r-gsmoothr + r-limma + r-oligo + r-oligoclasses + r-pdinfobuilder + r-preprocesscore + r-rcolorbrewer +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aroma.affymetrix/lilac.py b/prepare/r-aroma.affymetrix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aroma.affymetrix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aroma.affymetrix/lilac.yaml b/prepare/r-aroma.affymetrix/lilac.yaml new file mode 100644 index 0000000000..9d127c0cd4 --- /dev/null +++ b/prepare/r-aroma.affymetrix/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aroma.apd +- r-aroma.core +- r-future +- r-listenv +- r-matrixstats +- r-r.cache +- r-r.devices +- r-r.filesets +- r-r.methodss3 +- r-r.oo +- r-r.utils +update_on: +- regex: aroma.affymetrix_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=aroma.affymetrix diff --git a/prepare/r-aroma.apd/PKGBUILD b/prepare/r-aroma.apd/PKGBUILD new file mode 100644 index 0000000000..a8bb6cbb55 --- /dev/null +++ b/prepare/r-aroma.apd/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=aroma.apd +_pkgver=0.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-r.huge + r-r.methodss3 + r-r.oo + r-r.utils +) +optdepends=( + r-affxparser +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aroma.apd/lilac.py b/prepare/r-aroma.apd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aroma.apd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aroma.apd/lilac.yaml b/prepare/r-aroma.apd/lilac.yaml new file mode 100644 index 0000000000..eead1eb235 --- /dev/null +++ b/prepare/r-aroma.apd/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-r.huge +- r-r.methodss3 +- r-r.oo +- r-r.utils +update_on: +- regex: aroma.apd_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=aroma.apd diff --git a/prepare/r-aroma.core/PKGBUILD b/prepare/r-aroma.core/PKGBUILD new file mode 100644 index 0000000000..f1fb64a87b --- /dev/null +++ b/prepare/r-aroma.core/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=aroma.core +_pkgver=3.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-biocmanager + r-future + r-listenv + r-matrixstats + r-pscbs + r-r.cache + r-r.devices + r-r.filesets + r-r.methodss3 + r-r.oo + r-r.rsp + r-r.utils + r-rcolorbrewer +) +optdepends=( + r-aroma.light + r-cairo + r-dnacopy + r-ebimage + r-expectile + r-glad + r-haarseg + r-kernsmooth + r-mpcbs + r-png + r-preprocesscore + r-sfit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aroma.core/lilac.py b/prepare/r-aroma.core/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aroma.core/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aroma.core/lilac.yaml b/prepare/r-aroma.core/lilac.yaml new file mode 100644 index 0000000000..d7bdddb4dd --- /dev/null +++ b/prepare/r-aroma.core/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocmanager +- r-future +- r-listenv +- r-matrixstats +- r-pscbs +- r-r.cache +- r-r.devices +- r-r.filesets +- r-r.methodss3 +- r-r.oo +- r-r.rsp +- r-r.utils +- r-rcolorbrewer +update_on: +- regex: aroma.core_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=aroma.core diff --git a/prepare/r-aroma.light/PKGBUILD b/prepare/r-aroma.light/PKGBUILD new file mode 100644 index 0000000000..83077c49ea --- /dev/null +++ b/prepare/r-aroma.light/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=aroma.light +_pkgver=3.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-matrixstats + r-r.methodss3 + r-r.oo + r-r.utils +) +optdepends=( + r-princurve +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aroma.light/lilac.py b/prepare/r-aroma.light/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aroma.light/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aroma.light/lilac.yaml b/prepare/r-aroma.light/lilac.yaml new file mode 100644 index 0000000000..e03059f7a9 --- /dev/null +++ b/prepare/r-aroma.light/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-matrixstats +- r-r.methodss3 +- r-r.oo +- r-r.utils +update_on: +- regex: aroma.light_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/aroma.light diff --git a/prepare/r-arrayexpress/PKGBUILD b/prepare/r-arrayexpress/PKGBUILD new file mode 100644 index 0000000000..c11eb6c706 --- /dev/null +++ b/prepare/r-arrayexpress/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ArrayExpress +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-limma + r-oligo + r-xml +) +optdepends=( + r-affy +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-arrayexpress/lilac.py b/prepare/r-arrayexpress/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-arrayexpress/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-arrayexpress/lilac.yaml b/prepare/r-arrayexpress/lilac.yaml new file mode 100644 index 0000000000..2ecabec772 --- /dev/null +++ b/prepare/r-arrayexpress/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-limma +- r-oligo +- r-xml +update_on: +- regex: ArrayExpress_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ArrayExpress diff --git a/prepare/r-arrayexpresshts/PKGBUILD b/prepare/r-arrayexpresshts/PKGBUILD new file mode 100644 index 0000000000..7e9f2e9535 --- /dev/null +++ b/prepare/r-arrayexpresshts/PKGBUILD @@ -0,0 +1,47 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=ArrayExpressHTS +_pkgver=1.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ArrayExpress High Throughput Sequencing Processing Pipeline' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-biomart + r-biostrings + r-bitops + r-edger + r-genomicranges + r-hmisc + r-iranges + r-r2html + r-rcolorbrewer + r-rhtslib + r-rjava + r-rsamtools + r-sampling + r-sendmailr + r-shortread + r-snow + r-svmisc + r-xml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-arrayexpresshts/lilac.py b/prepare/r-arrayexpresshts/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-arrayexpresshts/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-arrayexpresshts/lilac.yaml b/prepare/r-arrayexpresshts/lilac.yaml new file mode 100644 index 0000000000..a000c06d29 --- /dev/null +++ b/prepare/r-arrayexpresshts/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biomart +- r-biostrings +- r-bitops +- r-edger +- r-genomicranges +- r-hmisc +- r-iranges +- r-r2html +- r-rcolorbrewer +- r-rhtslib +- r-rjava +- r-rsamtools +- r-sampling +- r-sendmailr +- r-shortread +- r-snow +- r-svmisc +- r-xml +update_on: +- regex: ArrayExpressHTS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ArrayExpressHTS diff --git a/prepare/r-arrayhelpers/PKGBUILD b/prepare/r-arrayhelpers/PKGBUILD new file mode 100644 index 0000000000..7cd37d31ee --- /dev/null +++ b/prepare/r-arrayhelpers/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=arrayhelpers +_pkgver=1.1-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Convenience Functions for Arrays' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-svunit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-arrayhelpers/lilac.py b/prepare/r-arrayhelpers/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-arrayhelpers/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-arrayhelpers/lilac.yaml b/prepare/r-arrayhelpers/lilac.yaml new file mode 100644 index 0000000000..bd5addc51d --- /dev/null +++ b/prepare/r-arrayhelpers/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-svunit +update_on: +- regex: arrayhelpers_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=arrayhelpers diff --git a/prepare/r-arraymvout/PKGBUILD b/prepare/r-arraymvout/PKGBUILD new file mode 100644 index 0000000000..edcafa857d --- /dev/null +++ b/prepare/r-arraymvout/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=arrayMvout +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='multivariate outlier detection for expression array QA' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-affy + r-affycontam + r-biobase + r-lumi + r-mdqc + r-parody +) +optdepends=( + r-affydata + r-affyplm + r-hgu133atagcdf + r-lumibarnes + r-maqcsubset + r-mvoutdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-arraymvout/lilac.py b/prepare/r-arraymvout/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-arraymvout/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-arraymvout/lilac.yaml b/prepare/r-arraymvout/lilac.yaml new file mode 100644 index 0000000000..3ba217fd0a --- /dev/null +++ b/prepare/r-arraymvout/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-affycontam +- r-biobase +- r-lumi +- r-mdqc +- r-parody +update_on: +- regex: arrayMvout_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/arrayMvout diff --git a/prepare/r-arrayquality/PKGBUILD b/prepare/r-arrayquality/PKGBUILD new file mode 100644 index 0000000000..186a02d06c --- /dev/null +++ b/prepare/r-arrayquality/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=arrayQuality +_pkgver=1.72.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assessing array quality on spotted arrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-gridbase + r-hexbin + r-limma + r-marray + r-rcolorbrewer +) +optdepends=( + r-heebodata + r-mclust + r-meebodata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-arrayquality/lilac.py b/prepare/r-arrayquality/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-arrayquality/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-arrayquality/lilac.yaml b/prepare/r-arrayquality/lilac.yaml new file mode 100644 index 0000000000..56ba70483c --- /dev/null +++ b/prepare/r-arrayquality/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gridbase +- r-hexbin +- r-limma +- r-marray +- r-rcolorbrewer +update_on: +- regex: arrayQuality_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/arrayQuality diff --git a/prepare/r-arrayqualitymetrics/PKGBUILD b/prepare/r-arrayqualitymetrics/PKGBUILD new file mode 100644 index 0000000000..3ebc5d09bf --- /dev/null +++ b/prepare/r-arrayqualitymetrics/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=arrayQualityMetrics +_pkgver=3.50.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quality metrics report for microarray data sets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-affy + r-affyplm + r-beadarray + r-biobase + r-genefilter + r-gridsvg + r-hmisc + r-hwriter + r-latticeextra + r-limma + r-rcolorbrewer + r-setrng + r-svglite + r-vsn + r-xml +) +optdepends=( + r-allmll + r-biocstyle + r-ccl4 + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-arrayqualitymetrics/lilac.py b/prepare/r-arrayqualitymetrics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-arrayqualitymetrics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-arrayqualitymetrics/lilac.yaml b/prepare/r-arrayqualitymetrics/lilac.yaml new file mode 100644 index 0000000000..74f912cd53 --- /dev/null +++ b/prepare/r-arrayqualitymetrics/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-affyplm +- r-beadarray +- r-biobase +- r-genefilter +- r-gridsvg +- r-hmisc +- r-hwriter +- r-latticeextra +- r-limma +- r-rcolorbrewer +- r-setrng +- r-svglite +- r-vsn +- r-xml +update_on: +- regex: arrayQualityMetrics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/arrayQualityMetrics diff --git a/prepare/r-arrmdata/PKGBUILD b/prepare/r-arrmdata/PKGBUILD new file mode 100644 index 0000000000..c2173cdc47 --- /dev/null +++ b/prepare/r-arrmdata/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ARRmData +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Example dataset for normalization of Illumina 450k Methylation data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-arrmdata/lilac.py b/prepare/r-arrmdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-arrmdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-arrmdata/lilac.yaml b/prepare/r-arrmdata/lilac.yaml new file mode 100644 index 0000000000..8154f51a12 --- /dev/null +++ b/prepare/r-arrmdata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ARRmData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ARRmData diff --git a/prepare/r-arrmnormalization/PKGBUILD b/prepare/r-arrmnormalization/PKGBUILD new file mode 100644 index 0000000000..503580e5ab --- /dev/null +++ b/prepare/r-arrmnormalization/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ARRmNormalization +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Adaptive Robust Regression normalization for Illumina methylation data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-arrmdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-arrmnormalization/lilac.py b/prepare/r-arrmnormalization/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-arrmnormalization/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-arrmnormalization/lilac.yaml b/prepare/r-arrmnormalization/lilac.yaml new file mode 100644 index 0000000000..45161b941b --- /dev/null +++ b/prepare/r-arrmnormalization/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-arrmdata +update_on: +- regex: ARRmNormalization_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ARRmNormalization diff --git a/prepare/r-arrow/PKGBUILD b/prepare/r-arrow/PKGBUILD new file mode 100644 index 0000000000..c116011bd8 --- /dev/null +++ b/prepare/r-arrow/PKGBUILD @@ -0,0 +1,53 @@ +# system requirements: C++11; for AWS S3 support on Linux, libcurl andopenssl (optional) +# Maintainer: Guoyi Zhang + +_pkgname=arrow +_pkgver=6.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Integration to 'Apache' 'Arrow'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-assertthat + r-bit64 + r-purrr + r-r6 + r-rlang + r-tidyselect + r-vctrs +) +optdepends=( + r-dbi + r-dbplyr + r-decor + r-distro + r-dplyr + r-duckdb + r-hms + r-knitr + r-lubridate + r-pkgload + r-reticulate + r-rmarkdown + r-stringi + r-stringr + r-testthat + r-tibble + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-arrow/lilac.py b/prepare/r-arrow/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-arrow/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-arrow/lilac.yaml b/prepare/r-arrow/lilac.yaml new file mode 100644 index 0000000000..00b6b4762f --- /dev/null +++ b/prepare/r-arrow/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-bit64 +- r-purrr +- r-r6 +- r-rlang +- r-tidyselect +- r-vctrs +update_on: +- regex: arrow_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=arrow diff --git a/prepare/r-arsenal/PKGBUILD b/prepare/r-arsenal/PKGBUILD new file mode 100644 index 0000000000..5b31b2a81c --- /dev/null +++ b/prepare/r-arsenal/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=arsenal +_pkgver=3.6.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="An Arsenal of 'R' Functions for Large-Scale Statistical Summaries" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-knitr +) +optdepends=( + r-broom + r-coin + r-geepack + r-magrittr + r-mass + r-pander + r-proc + r-rmarkdown + r-rpart + r-splines + r-survival + r-testthat + r-xtable + r-yaml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-arsenal/lilac.py b/prepare/r-arsenal/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-arsenal/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-arsenal/lilac.yaml b/prepare/r-arsenal/lilac.yaml new file mode 100644 index 0000000000..38a6e43a11 --- /dev/null +++ b/prepare/r-arsenal/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-knitr +update_on: +- regex: arsenal_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=arsenal diff --git a/prepare/r-artms/PKGBUILD b/prepare/r-artms/PKGBUILD new file mode 100644 index 0000000000..449a8b0ead --- /dev/null +++ b/prepare/r-artms/PKGBUILD @@ -0,0 +1,64 @@ +# Maintainer: Guoyi Zhang + +_pkgname=artMS +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analytical R tools for Mass Spectrometry' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-bit64 + r-circlize + r-corrplot + r-data.table + r-dplyr + r-getopt + r-ggdendro + r-ggplot2 + r-ggrepel + r-gplots + r-limma + r-msstats + r-openxlsx + r-org.hs.eg.db + r-pheatmap + r-plotly + r-plyr + r-rcolorbrewer + r-scales + r-seqinr + r-stringr + r-tidyr + r-upsetr + r-venndiagram + r-yaml +) +optdepends=( + r-biocstyle + r-complexheatmap + r-factoextra + r-factominer + r-gprofiler + r-knitr + r-org.mm.eg.db + r-performanceanalytics + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-artms/lilac.py b/prepare/r-artms/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-artms/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-artms/lilac.yaml b/prepare/r-artms/lilac.yaml new file mode 100644 index 0000000000..8280470f1b --- /dev/null +++ b/prepare/r-artms/lilac.yaml @@ -0,0 +1,35 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-bit64 +- r-circlize +- r-corrplot +- r-data.table +- r-dplyr +- r-getopt +- r-ggdendro +- r-ggplot2 +- r-ggrepel +- r-gplots +- r-limma +- r-msstats +- r-openxlsx +- r-org.hs.eg.db +- r-pheatmap +- r-plotly +- r-plyr +- r-rcolorbrewer +- r-scales +- r-seqinr +- r-stringr +- r-tidyr +- r-upsetr +- r-venndiagram +- r-yaml +update_on: +- regex: artMS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/artMS diff --git a/prepare/r-arules/PKGBUILD b/prepare/r-arules/PKGBUILD new file mode 100644 index 0000000000..19368dde8c --- /dev/null +++ b/prepare/r-arules/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=arules +_pkgver=1.7-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mining Association Rules and Frequent Itemsets' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-generics +) +optdepends=( + r-arulescba + r-arulesviz + r-pmml + r-testthat + r-xml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-arules/lilac.py b/prepare/r-arules/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-arules/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-arules/lilac.yaml b/prepare/r-arules/lilac.yaml new file mode 100644 index 0000000000..a80f0aa686 --- /dev/null +++ b/prepare/r-arules/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-generics +update_on: +- regex: arules_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=arules diff --git a/prepare/r-asafe/PKGBUILD b/prepare/r-asafe/PKGBUILD new file mode 100644 index 0000000000..39cd955618 --- /dev/null +++ b/prepare/r-asafe/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ASAFE +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Ancestry Specific Allele Frequency Estimation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-asafe/lilac.py b/prepare/r-asafe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-asafe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-asafe/lilac.yaml b/prepare/r-asafe/lilac.yaml new file mode 100644 index 0000000000..a96525502b --- /dev/null +++ b/prepare/r-asafe/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ASAFE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ASAFE diff --git a/prepare/r-aseb/PKGBUILD b/prepare/r-aseb/PKGBUILD new file mode 100644 index 0000000000..2a1658ca19 --- /dev/null +++ b/prepare/r-aseb/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ASEB +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Predict Acetylated Lysine Sites' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aseb/lilac.py b/prepare/r-aseb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aseb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aseb/lilac.yaml b/prepare/r-aseb/lilac.yaml new file mode 100644 index 0000000000..d96fbb6e40 --- /dev/null +++ b/prepare/r-aseb/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ASEB_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ASEB diff --git a/prepare/r-asgsca/PKGBUILD b/prepare/r-asgsca/PKGBUILD new file mode 100644 index 0000000000..fa9f82ae55 --- /dev/null +++ b/prepare/r-asgsca/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ASGSCA +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Association Studies for multiple SNPs and multiple traits using Generalized Structured Equation Models' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-asgsca/lilac.py b/prepare/r-asgsca/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-asgsca/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-asgsca/lilac.yaml b/prepare/r-asgsca/lilac.yaml new file mode 100644 index 0000000000..a51cbaa6be --- /dev/null +++ b/prepare/r-asgsca/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ASGSCA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ASGSCA diff --git a/prepare/r-ash/PKGBUILD b/prepare/r-ash/PKGBUILD new file mode 100644 index 0000000000..127f7bb73d --- /dev/null +++ b/prepare/r-ash/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ash +_pkgver=1.0-15 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="David Scott's ASH Routines" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ash/lilac.py b/prepare/r-ash/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ash/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ash/lilac.yaml b/prepare/r-ash/lilac.yaml new file mode 100644 index 0000000000..fd720bc953 --- /dev/null +++ b/prepare/r-ash/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ash_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ash diff --git a/prepare/r-ashr/PKGBUILD b/prepare/r-ashr/PKGBUILD new file mode 100644 index 0000000000..519e966406 --- /dev/null +++ b/prepare/r-ashr/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ashr +_pkgver=2.2-47 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methods for Adaptive Shrinkage, using Empirical Bayes' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-etrunct + r-invgamma + r-mixsqp + r-rcpp + r-squarem + r-truncnorm +) +optdepends=( + r-ggplot2 + r-knitr + r-rebayes + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ashr/lilac.py b/prepare/r-ashr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ashr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ashr/lilac.yaml b/prepare/r-ashr/lilac.yaml new file mode 100644 index 0000000000..792013745c --- /dev/null +++ b/prepare/r-ashr/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-etrunct +- r-invgamma +- r-mixsqp +- r-rcpp +- r-squarem +- r-truncnorm +update_on: +- regex: ashr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ashr diff --git a/prepare/r-asics/PKGBUILD b/prepare/r-asics/PKGBUILD new file mode 100644 index 0000000000..56c3459c25 --- /dev/null +++ b/prepare/r-asics/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ASICS +_pkgver=2.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automatic Statistical Identification in Complex Spectra' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-ggplot2 + r-glmnet + r-gridextra + r-mvtnorm + r-pepsnmr + r-plyr + r-quadprog + r-ropls + r-summarizedexperiment + r-zoo +) +optdepends=( + r-asicsdata + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-asics/lilac.py b/prepare/r-asics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-asics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-asics/lilac.yaml b/prepare/r-asics/lilac.yaml new file mode 100644 index 0000000000..6ed22c8b3a --- /dev/null +++ b/prepare/r-asics/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-ggplot2 +- r-glmnet +- r-gridextra +- r-mvtnorm +- r-pepsnmr +- r-plyr +- r-quadprog +- r-ropls +- r-summarizedexperiment +- r-zoo +update_on: +- regex: ASICS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ASICS diff --git a/prepare/r-askpass/PKGBUILD b/prepare/r-askpass/PKGBUILD new file mode 100644 index 0000000000..c8ac365705 --- /dev/null +++ b/prepare/r-askpass/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=askpass +_pkgver=1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Safe Password Entry for R, Git, and SSH' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-sys +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-askpass/lilac.py b/prepare/r-askpass/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-askpass/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-askpass/lilac.yaml b/prepare/r-askpass/lilac.yaml new file mode 100644 index 0000000000..382482abbc --- /dev/null +++ b/prepare/r-askpass/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-sys +update_on: +- regex: askpass_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=askpass diff --git a/prepare/r-aspediafi/PKGBUILD b/prepare/r-aspediafi/PKGBUILD new file mode 100644 index 0000000000..099fba328c --- /dev/null +++ b/prepare/r-aspediafi/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ASpediaFI +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-biomart + r-dplyr + r-drawr + r-e1071 + r-fgsea + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-gviz + r-igraph + r-iranges + r-ivas + r-limma + r-mgsz + r-reshape2 + r-rocr + r-rsamtools + r-rtracklayer + r-s4vectors + r-scales + r-summarizedexperiment +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aspediafi/lilac.py b/prepare/r-aspediafi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aspediafi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aspediafi/lilac.yaml b/prepare/r-aspediafi/lilac.yaml new file mode 100644 index 0000000000..a7142e2ad8 --- /dev/null +++ b/prepare/r-aspediafi/lilac.yaml @@ -0,0 +1,33 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-biomart +- r-dplyr +- r-drawr +- r-e1071 +- r-fgsea +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-gviz +- r-igraph +- r-iranges +- r-ivas +- r-limma +- r-mgsz +- r-reshape2 +- r-rocr +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-scales +- r-summarizedexperiment +update_on: +- regex: ASpediaFI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ASpediaFI diff --git a/prepare/r-aspli/PKGBUILD b/prepare/r-aspli/PKGBUILD new file mode 100644 index 0000000000..8e7cb3d134 --- /dev/null +++ b/prepare/r-aspli/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ASpli +_pkgver=2.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Alternative Splicing Using RNA-Seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocgenerics + r-biocstyle + r-data.table + r-dt + r-edger + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-gviz + r-htmltools + r-igraph + r-iranges + r-limma + r-pbmcapply + r-rsamtools + r-s4vectors + r-tidyr + r-upsetr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aspli/lilac.py b/prepare/r-aspli/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aspli/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aspli/lilac.yaml b/prepare/r-aspli/lilac.yaml new file mode 100644 index 0000000000..0ec79ef7ab --- /dev/null +++ b/prepare/r-aspli/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-biocstyle +- r-data.table +- r-dt +- r-edger +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-gviz +- r-htmltools +- r-igraph +- r-iranges +- r-limma +- r-pbmcapply +- r-rsamtools +- r-s4vectors +- r-tidyr +- r-upsetr +update_on: +- regex: ASpli_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ASpli diff --git a/prepare/r-assertive.base/PKGBUILD b/prepare/r-assertive.base/PKGBUILD new file mode 100644 index 0000000000..6c082036a7 --- /dev/null +++ b/prepare/r-assertive.base/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=assertive.base +_pkgver=0.0-9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="A Lightweight Core of the 'assertive' Package" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertive.base/lilac.py b/prepare/r-assertive.base/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assertive.base/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assertive.base/lilac.yaml b/prepare/r-assertive.base/lilac.yaml new file mode 100644 index 0000000000..4ae3c5e861 --- /dev/null +++ b/prepare/r-assertive.base/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: assertive.base_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=assertive.base diff --git a/prepare/r-assertive.code/PKGBUILD b/prepare/r-assertive.code/PKGBUILD new file mode 100644 index 0000000000..aecb80014d --- /dev/null +++ b/prepare/r-assertive.code/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=assertive.code +_pkgver=0.0-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assertions to Check Properties of Code' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertive.base + r-assertive.properties + r-assertive.types +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertive.code/lilac.py b/prepare/r-assertive.code/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assertive.code/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assertive.code/lilac.yaml b/prepare/r-assertive.code/lilac.yaml new file mode 100644 index 0000000000..557b4a8d4f --- /dev/null +++ b/prepare/r-assertive.code/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertive.base +- r-assertive.properties +- r-assertive.types +update_on: +- regex: assertive.code_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=assertive.code diff --git a/prepare/r-assertive.data.uk/PKGBUILD b/prepare/r-assertive.data.uk/PKGBUILD new file mode 100644 index 0000000000..e11f1b5aa4 --- /dev/null +++ b/prepare/r-assertive.data.uk/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=assertive.data.uk +_pkgver=0.0-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assertions to Check Properties of Strings' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertive.base + r-assertive.strings +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertive.data.uk/lilac.py b/prepare/r-assertive.data.uk/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assertive.data.uk/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assertive.data.uk/lilac.yaml b/prepare/r-assertive.data.uk/lilac.yaml new file mode 100644 index 0000000000..a16f6c060a --- /dev/null +++ b/prepare/r-assertive.data.uk/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertive.base +- r-assertive.strings +update_on: +- regex: assertive.data.uk_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=assertive.data.uk diff --git a/prepare/r-assertive.data.us/PKGBUILD b/prepare/r-assertive.data.us/PKGBUILD new file mode 100644 index 0000000000..70860fcaca --- /dev/null +++ b/prepare/r-assertive.data.us/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=assertive.data.us +_pkgver=0.0-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assertions to Check Properties of Strings' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertive.base + r-assertive.strings +) +optdepends=( + r-devtools + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertive.data.us/lilac.py b/prepare/r-assertive.data.us/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assertive.data.us/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assertive.data.us/lilac.yaml b/prepare/r-assertive.data.us/lilac.yaml new file mode 100644 index 0000000000..ab20fed652 --- /dev/null +++ b/prepare/r-assertive.data.us/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertive.base +- r-assertive.strings +update_on: +- regex: assertive.data.us_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=assertive.data.us diff --git a/prepare/r-assertive.data/PKGBUILD b/prepare/r-assertive.data/PKGBUILD new file mode 100644 index 0000000000..596c8ec7d4 --- /dev/null +++ b/prepare/r-assertive.data/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=assertive.data +_pkgver=0.0-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assertions to Check Properties of Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertive.base + r-assertive.strings +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertive.data/lilac.py b/prepare/r-assertive.data/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assertive.data/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assertive.data/lilac.yaml b/prepare/r-assertive.data/lilac.yaml new file mode 100644 index 0000000000..186d096c51 --- /dev/null +++ b/prepare/r-assertive.data/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertive.base +- r-assertive.strings +update_on: +- regex: assertive.data_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=assertive.data diff --git a/prepare/r-assertive.datetimes/PKGBUILD b/prepare/r-assertive.datetimes/PKGBUILD new file mode 100644 index 0000000000..5a9b66cf53 --- /dev/null +++ b/prepare/r-assertive.datetimes/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=assertive.datetimes +_pkgver=0.0-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assertions to Check Properties of Dates and Times' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertive.base + r-assertive.types +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertive.datetimes/lilac.py b/prepare/r-assertive.datetimes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assertive.datetimes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assertive.datetimes/lilac.yaml b/prepare/r-assertive.datetimes/lilac.yaml new file mode 100644 index 0000000000..1578a1cc79 --- /dev/null +++ b/prepare/r-assertive.datetimes/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertive.base +- r-assertive.types +update_on: +- regex: assertive.datetimes_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=assertive.datetimes diff --git a/prepare/r-assertive.files/PKGBUILD b/prepare/r-assertive.files/PKGBUILD new file mode 100644 index 0000000000..4a43887407 --- /dev/null +++ b/prepare/r-assertive.files/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=assertive.files +_pkgver=0.0-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assertions to Check Properties of Files' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertive.base + r-assertive.numbers +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertive.files/lilac.py b/prepare/r-assertive.files/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assertive.files/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assertive.files/lilac.yaml b/prepare/r-assertive.files/lilac.yaml new file mode 100644 index 0000000000..c1c65a57fc --- /dev/null +++ b/prepare/r-assertive.files/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertive.base +- r-assertive.numbers +update_on: +- regex: assertive.files_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=assertive.files diff --git a/prepare/r-assertive.matrices/PKGBUILD b/prepare/r-assertive.matrices/PKGBUILD new file mode 100644 index 0000000000..6bff157315 --- /dev/null +++ b/prepare/r-assertive.matrices/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=assertive.matrices +_pkgver=0.0-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assertions to Check Properties of Matrices' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertive.base +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertive.matrices/lilac.py b/prepare/r-assertive.matrices/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assertive.matrices/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assertive.matrices/lilac.yaml b/prepare/r-assertive.matrices/lilac.yaml new file mode 100644 index 0000000000..33ee1e0e72 --- /dev/null +++ b/prepare/r-assertive.matrices/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertive.base +update_on: +- regex: assertive.matrices_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=assertive.matrices diff --git a/prepare/r-assertive.models/PKGBUILD b/prepare/r-assertive.models/PKGBUILD new file mode 100644 index 0000000000..393127f642 --- /dev/null +++ b/prepare/r-assertive.models/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=assertive.models +_pkgver=0.0-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assertions to Check Properties of Models' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertive.base +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertive.models/lilac.py b/prepare/r-assertive.models/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assertive.models/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assertive.models/lilac.yaml b/prepare/r-assertive.models/lilac.yaml new file mode 100644 index 0000000000..d4a2a413d6 --- /dev/null +++ b/prepare/r-assertive.models/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertive.base +update_on: +- regex: assertive.models_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=assertive.models diff --git a/prepare/r-assertive.numbers/PKGBUILD b/prepare/r-assertive.numbers/PKGBUILD new file mode 100644 index 0000000000..cf8a130e39 --- /dev/null +++ b/prepare/r-assertive.numbers/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=assertive.numbers +_pkgver=0.0-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assertions to Check Properties of Numbers' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertive.base +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertive.numbers/lilac.py b/prepare/r-assertive.numbers/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assertive.numbers/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assertive.numbers/lilac.yaml b/prepare/r-assertive.numbers/lilac.yaml new file mode 100644 index 0000000000..3aa64bc82d --- /dev/null +++ b/prepare/r-assertive.numbers/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertive.base +update_on: +- regex: assertive.numbers_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=assertive.numbers diff --git a/prepare/r-assertive.properties/PKGBUILD b/prepare/r-assertive.properties/PKGBUILD new file mode 100644 index 0000000000..8c22f1548d --- /dev/null +++ b/prepare/r-assertive.properties/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=assertive.properties +_pkgver=0.0-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assertions to Check Properties of Variables' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertive.base +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertive.properties/lilac.py b/prepare/r-assertive.properties/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assertive.properties/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assertive.properties/lilac.yaml b/prepare/r-assertive.properties/lilac.yaml new file mode 100644 index 0000000000..df1714069a --- /dev/null +++ b/prepare/r-assertive.properties/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertive.base +update_on: +- regex: assertive.properties_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=assertive.properties diff --git a/prepare/r-assertive.reflection/PKGBUILD b/prepare/r-assertive.reflection/PKGBUILD new file mode 100644 index 0000000000..c5e3f9c45f --- /dev/null +++ b/prepare/r-assertive.reflection/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=assertive.reflection +_pkgver=0.0-5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assertions for Checking the State of R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertive.base +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertive.reflection/lilac.py b/prepare/r-assertive.reflection/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assertive.reflection/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assertive.reflection/lilac.yaml b/prepare/r-assertive.reflection/lilac.yaml new file mode 100644 index 0000000000..bff7a5d0ec --- /dev/null +++ b/prepare/r-assertive.reflection/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertive.base +update_on: +- regex: assertive.reflection_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=assertive.reflection diff --git a/prepare/r-assertive.sets/PKGBUILD b/prepare/r-assertive.sets/PKGBUILD new file mode 100644 index 0000000000..86d195e930 --- /dev/null +++ b/prepare/r-assertive.sets/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=assertive.sets +_pkgver=0.0-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assertions to Check Properties of Sets' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertive.base +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertive.sets/lilac.py b/prepare/r-assertive.sets/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assertive.sets/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assertive.sets/lilac.yaml b/prepare/r-assertive.sets/lilac.yaml new file mode 100644 index 0000000000..10b1370112 --- /dev/null +++ b/prepare/r-assertive.sets/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertive.base +update_on: +- regex: assertive.sets_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=assertive.sets diff --git a/prepare/r-assertive.strings/PKGBUILD b/prepare/r-assertive.strings/PKGBUILD new file mode 100644 index 0000000000..776b708f6e --- /dev/null +++ b/prepare/r-assertive.strings/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=assertive.strings +_pkgver=0.0-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assertions to Check Properties of Strings' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertive.base + r-assertive.types + r-stringi +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertive.strings/lilac.py b/prepare/r-assertive.strings/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assertive.strings/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assertive.strings/lilac.yaml b/prepare/r-assertive.strings/lilac.yaml new file mode 100644 index 0000000000..8da343dde2 --- /dev/null +++ b/prepare/r-assertive.strings/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertive.base +- r-assertive.types +- r-stringi +update_on: +- regex: assertive.strings_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=assertive.strings diff --git a/prepare/r-assertive.types/PKGBUILD b/prepare/r-assertive.types/PKGBUILD new file mode 100644 index 0000000000..bd3e7def97 --- /dev/null +++ b/prepare/r-assertive.types/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=assertive.types +_pkgver=0.0-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assertions to Check Types of Variables' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertive.base + r-assertive.properties +) +optdepends=( + r-data.table + r-dplyr + r-testthat + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertive.types/lilac.py b/prepare/r-assertive.types/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assertive.types/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assertive.types/lilac.yaml b/prepare/r-assertive.types/lilac.yaml new file mode 100644 index 0000000000..5948934930 --- /dev/null +++ b/prepare/r-assertive.types/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertive.base +- r-assertive.properties +update_on: +- regex: assertive.types_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=assertive.types diff --git a/prepare/r-assertive/PKGBUILD b/prepare/r-assertive/PKGBUILD new file mode 100644 index 0000000000..cde8b991b9 --- /dev/null +++ b/prepare/r-assertive/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=assertive +_pkgver=0.3-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Readable Check Functions to Ensure Code Integrity' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertive.base + r-assertive.code + r-assertive.data + r-assertive.data.uk + r-assertive.data.us + r-assertive.datetimes + r-assertive.files + r-assertive.matrices + r-assertive.models + r-assertive.numbers + r-assertive.properties + r-assertive.reflection + r-assertive.sets + r-assertive.strings + r-assertive.types + r-knitr +) +optdepends=( + r-markdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertive/lilac.py b/prepare/r-assertive/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assertive/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assertive/lilac.yaml b/prepare/r-assertive/lilac.yaml new file mode 100644 index 0000000000..2b4dc59291 --- /dev/null +++ b/prepare/r-assertive/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertive.base +- r-assertive.code +- r-assertive.data +- r-assertive.data.uk +- r-assertive.data.us +- r-assertive.datetimes +- r-assertive.files +- r-assertive.matrices +- r-assertive.models +- r-assertive.numbers +- r-assertive.properties +- r-assertive.reflection +- r-assertive.sets +- r-assertive.strings +- r-assertive.types +- r-knitr +update_on: +- regex: assertive_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=assertive diff --git a/prepare/r-assertthat/PKGBUILD b/prepare/r-assertthat/PKGBUILD new file mode 100644 index 0000000000..78e512dddc --- /dev/null +++ b/prepare/r-assertthat/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=assertthat +_pkgver=0.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Easy Pre and Post Assertions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assertthat/lilac.py b/prepare/r-assertthat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assertthat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assertthat/lilac.yaml b/prepare/r-assertthat/lilac.yaml new file mode 100644 index 0000000000..bbc7a4e6b1 --- /dev/null +++ b/prepare/r-assertthat/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: assertthat_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=assertthat diff --git a/prepare/r-assessorf/PKGBUILD b/prepare/r-assessorf/PKGBUILD new file mode 100644 index 0000000000..3f4862293d --- /dev/null +++ b/prepare/r-assessorf/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AssessORF +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assess Gene Predictions Using Proteomics and Evolutionary Conservation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-decipher + r-genomicranges + r-iranges +) +optdepends=( + r-assessorfdata + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assessorf/lilac.py b/prepare/r-assessorf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assessorf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assessorf/lilac.yaml b/prepare/r-assessorf/lilac.yaml new file mode 100644 index 0000000000..23cb29237e --- /dev/null +++ b/prepare/r-assessorf/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-decipher +- r-genomicranges +- r-iranges +update_on: +- regex: AssessORF_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AssessORF diff --git a/prepare/r-asset/PKGBUILD b/prepare/r-asset/PKGBUILD new file mode 100644 index 0000000000..c0042b7f07 --- /dev/null +++ b/prepare/r-asset/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ASSET +_pkgver=2.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package for subset-based association analysis of heterogeneous traits and subtypes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-msm + r-rmeta +) +optdepends=( + r-biocgenerics + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-asset/lilac.py b/prepare/r-asset/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-asset/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-asset/lilac.yaml b/prepare/r-asset/lilac.yaml new file mode 100644 index 0000000000..607acdf233 --- /dev/null +++ b/prepare/r-asset/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-msm +- r-rmeta +update_on: +- regex: ASSET_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ASSET diff --git a/prepare/r-assign/PKGBUILD b/prepare/r-assign/PKGBUILD new file mode 100644 index 0000000000..b1b1f34f3e --- /dev/null +++ b/prepare/r-assign/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ASSIGN +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Adaptive Signature Selection and InteGratioN (ASSIGN)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-ggplot2 + r-gplots + r-msm + r-rlab + r-sva + r-yaml +) +optdepends=( + r-biocstyle + r-knitr + r-lintr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-assign/lilac.py b/prepare/r-assign/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-assign/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-assign/lilac.yaml b/prepare/r-assign/lilac.yaml new file mode 100644 index 0000000000..73359fc730 --- /dev/null +++ b/prepare/r-assign/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gplots +- r-msm +- r-rlab +- r-sva +- r-yaml +update_on: +- regex: ASSIGN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ASSIGN diff --git a/prepare/r-atacseqqc/PKGBUILD b/prepare/r-atacseqqc/PKGBUILD new file mode 100644 index 0000000000..fa9cae70ef --- /dev/null +++ b/prepare/r-atacseqqc/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ATACseqQC +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ATAC-seq Quality Control' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-bsgenome + r-chippeakanno + r-edger + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-genomicscores + r-iranges + r-limma + r-motifstack + r-preseqr + r-randomforest + r-rsamtools + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-knitr + r-motifdb + r-phastcons100way.ucsc.hg19 + r-rmarkdown + r-testthat + r-trackviewer + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-atacseqqc/lilac.py b/prepare/r-atacseqqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-atacseqqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-atacseqqc/lilac.yaml b/prepare/r-atacseqqc/lilac.yaml new file mode 100644 index 0000000000..a39e775a56 --- /dev/null +++ b/prepare/r-atacseqqc/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-chippeakanno +- r-edger +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-genomicscores +- r-iranges +- r-limma +- r-motifstack +- r-preseqr +- r-randomforest +- r-rsamtools +- r-rtracklayer +- r-s4vectors +update_on: +- regex: ATACseqQC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ATACseqQC diff --git a/prepare/r-atena/PKGBUILD b/prepare/r-atena/PKGBUILD new file mode 100644 index 0000000000..0f3319011f --- /dev/null +++ b/prepare/r-atena/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=atena +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Transposable Elements' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-rsamtools + r-s4vectors + r-sparsematrixstats + r-squarem + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-atena/lilac.py b/prepare/r-atena/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-atena/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-atena/lilac.yaml b/prepare/r-atena/lilac.yaml new file mode 100644 index 0000000000..ba5500d7a4 --- /dev/null +++ b/prepare/r-atena/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-rsamtools +- r-s4vectors +- r-sparsematrixstats +- r-squarem +- r-summarizedexperiment +update_on: +- regex: atena_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/atena diff --git a/prepare/r-atsnp/PKGBUILD b/prepare/r-atsnp/PKGBUILD new file mode 100644 index 0000000000..d9f378f2ea --- /dev/null +++ b/prepare/r-atsnp/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=atSNP +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Affinity test for identifying regulatory SNPs' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocfilecache + r-biocparallel + r-bsgenome + r-data.table + r-ggplot2 + r-lifecycle + r-motifstack + r-rappdirs + r-rcpp + r-testthat +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-atsnp/lilac.py b/prepare/r-atsnp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-atsnp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-atsnp/lilac.yaml b/prepare/r-atsnp/lilac.yaml new file mode 100644 index 0000000000..51f951df13 --- /dev/null +++ b/prepare/r-atsnp/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-biocparallel +- r-bsgenome +- r-data.table +- r-ggplot2 +- r-lifecycle +- r-motifstack +- r-rappdirs +- r-rcpp +- r-testthat +update_on: +- regex: atSNP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/atSNP diff --git a/prepare/r-attempt/PKGBUILD b/prepare/r-attempt/PKGBUILD new file mode 100644 index 0000000000..cb191d4954 --- /dev/null +++ b/prepare/r-attempt/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=attempt +_pkgver=0.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Defensive Programming' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-rlang +) +optdepends=( + r-curl + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-attempt/lilac.py b/prepare/r-attempt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-attempt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-attempt/lilac.yaml b/prepare/r-attempt/lilac.yaml new file mode 100644 index 0000000000..b17449974a --- /dev/null +++ b/prepare/r-attempt/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rlang +update_on: +- regex: attempt_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=attempt diff --git a/prepare/r-attract/PKGBUILD b/prepare/r-attract/PKGBUILD new file mode 100644 index 0000000000..d1c03fd86d --- /dev/null +++ b/prepare/r-attract/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=attract +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-annotationdbi + r-biobase + r-gostats + r-keggrest + r-limma + r-org.hs.eg.db + r-reactome.db +) +optdepends=( + r-illuminahumanv1.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-attract/lilac.py b/prepare/r-attract/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-attract/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-attract/lilac.yaml b/prepare/r-attract/lilac.yaml new file mode 100644 index 0000000000..288fdc6b32 --- /dev/null +++ b/prepare/r-attract/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-gostats +- r-keggrest +- r-limma +- r-org.hs.eg.db +- r-reactome.db +update_on: +- regex: attract_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/attract diff --git a/prepare/r-aucell/PKGBUILD b/prepare/r-aucell/PKGBUILD new file mode 100644 index 0000000000..94598a879d --- /dev/null +++ b/prepare/r-aucell/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AUCell +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-data.table + r-gseabase + r-mixtools + r-r.utils + r-s4vectors + r-shiny + r-summarizedexperiment +) +optdepends=( + r-biobase + r-biocstyle + r-domc + r-doparallel + r-dorng + r-dosnow + r-dt + r-dynamictreecut + r-foreach + r-geoquery + r-knitr + r-nmf + r-plotly + r-plyr + r-r2html + r-rbokeh + r-reshape2 + r-rmarkdown + r-rtsne + r-testthat + r-zoo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aucell/lilac.py b/prepare/r-aucell/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aucell/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aucell/lilac.yaml b/prepare/r-aucell/lilac.yaml new file mode 100644 index 0000000000..e41f34990f --- /dev/null +++ b/prepare/r-aucell/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-data.table +- r-gseabase +- r-mixtools +- r-r.utils +- r-s4vectors +- r-shiny +- r-summarizedexperiment +update_on: +- regex: AUCell_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AUCell diff --git a/prepare/r-autonomics/PKGBUILD b/prepare/r-autonomics/PKGBUILD new file mode 100644 index 0000000000..96e31ec7ab --- /dev/null +++ b/prepare/r-autonomics/PKGBUILD @@ -0,0 +1,78 @@ +# Maintainer: Guoyi Zhang + +_pkgname=autonomics +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generifying and intuifying cross-platform omics analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-assertive + r-biocfilecache + r-biocgenerics + r-colorspace + r-data.table + r-edger + r-ggplot2 + r-ggrepel + r-gridextra + r-limma + r-magrittr + r-matrixstats + r-multiassayexperiment + r-pcamethods + r-r.utils + r-rappdirs + r-readxl + r-rlang + r-s4vectors + r-scales + r-stringi + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-affy + r-annotationdbi + r-biocmanager + r-diagram + r-genomicranges + r-geoquery + r-hgu95av2.db + r-icsnp + r-knitr + r-lme4 + r-lmertest + r-mass + r-mixomics + r-mpm + r-nlme + r-org.hs.eg.db + r-org.mm.eg.db + r-rcurl + r-remotes + r-rmarkdown + r-ropls + r-rsubread + r-rtracklayer + r-seqinr + r-statmod + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-autonomics/lilac.py b/prepare/r-autonomics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-autonomics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-autonomics/lilac.yaml b/prepare/r-autonomics/lilac.yaml new file mode 100644 index 0000000000..73e9537ba8 --- /dev/null +++ b/prepare/r-autonomics/lilac.yaml @@ -0,0 +1,33 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-assertive +- r-biocfilecache +- r-biocgenerics +- r-colorspace +- r-data.table +- r-edger +- r-ggplot2 +- r-ggrepel +- r-gridextra +- r-limma +- r-magrittr +- r-matrixstats +- r-multiassayexperiment +- r-pcamethods +- r-r.utils +- r-rappdirs +- r-readxl +- r-rlang +- r-s4vectors +- r-scales +- r-stringi +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: autonomics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/autonomics diff --git a/prepare/r-autotuner/PKGBUILD b/prepare/r-autotuner/PKGBUILD new file mode 100644 index 0000000000..c4b81ed732 --- /dev/null +++ b/prepare/r-autotuner/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Autotuner +_pkgver=1.7.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automated parameter selection for untargeted metabolomics data processing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-assertthat + r-biobase + r-entropy + r-msnbase + r-mzr + r-rcolorbrewer + r-scales +) +optdepends=( + r-covr + r-devtools + r-knitr + r-mtbls2 + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-autotuner/lilac.py b/prepare/r-autotuner/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-autotuner/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-autotuner/lilac.yaml b/prepare/r-autotuner/lilac.yaml new file mode 100644 index 0000000000..ec6a8e78fa --- /dev/null +++ b/prepare/r-autotuner/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biobase +- r-entropy +- r-msnbase +- r-mzr +- r-rcolorbrewer +- r-scales +update_on: +- regex: Autotuner_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Autotuner diff --git a/prepare/r-av/PKGBUILD b/prepare/r-av/PKGBUILD new file mode 100644 index 0000000000..fb412b5501 --- /dev/null +++ b/prepare/r-av/PKGBUILD @@ -0,0 +1,34 @@ +# system requirements: FFmpeg (>= 3.2); with at least libx264 and lame(mp3) drivers. Debian/Ubuntu: libavfilter-dev, Fedora/CentOS:ffmpeg-devel (via https://rpmfusion.org), MacOS Homebrew:ffmpeg. +# Maintainer: Guoyi Zhang + +_pkgname=av +_pkgver=0.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Working with Audio and Video in R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-gapminder + r-ggplot2 + r-ps + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-av/lilac.py b/prepare/r-av/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-av/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-av/lilac.yaml b/prepare/r-av/lilac.yaml new file mode 100644 index 0000000000..c00cebc988 --- /dev/null +++ b/prepare/r-av/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: av_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=av diff --git a/prepare/r-available/PKGBUILD b/prepare/r-available/PKGBUILD new file mode 100644 index 0000000000..81ac85c741 --- /dev/null +++ b/prepare/r-available/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=available +_pkgver=1.0.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Check if the Title of a Package is Available, Appropriate and Interesting' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-cli + r-clisymbols + r-crayon + r-desc + r-glue + r-jsonlite + r-memoise + r-snowballc + r-stringdist + r-tibble + r-tidytext + r-udapi + r-yesno +) +optdepends=( + r-biocmanager + r-covr + r-testthat + r-usethis +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-available/lilac.py b/prepare/r-available/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-available/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-available/lilac.yaml b/prepare/r-available/lilac.yaml new file mode 100644 index 0000000000..4ec6df7200 --- /dev/null +++ b/prepare/r-available/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cli +- r-clisymbols +- r-crayon +- r-desc +- r-glue +- r-jsonlite +- r-memoise +- r-snowballc +- r-stringdist +- r-tibble +- r-tidytext +- r-udapi +- r-yesno +update_on: +- regex: available_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=available diff --git a/prepare/r-awfisher/PKGBUILD b/prepare/r-awfisher/PKGBUILD new file mode 100644 index 0000000000..5507d6d2c1 --- /dev/null +++ b/prepare/r-awfisher/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=AWFisher +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="An R package for fast computing for adaptively weighted fisher's method" +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-edger + r-limma +) +optdepends=( + r-knitr + r-tightclust +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-awfisher/lilac.py b/prepare/r-awfisher/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-awfisher/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-awfisher/lilac.yaml b/prepare/r-awfisher/lilac.yaml new file mode 100644 index 0000000000..443630a81d --- /dev/null +++ b/prepare/r-awfisher/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-edger +- r-limma +update_on: +- regex: AWFisher_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/AWFisher diff --git a/prepare/r-aws.s3/PKGBUILD b/prepare/r-aws.s3/PKGBUILD new file mode 100644 index 0000000000..9a2d92b846 --- /dev/null +++ b/prepare/r-aws.s3/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=aws.s3 +_pkgver=0.3.21 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'AWS S3' Client Package" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-aws.signature + r-base64enc + r-curl + r-digest + r-httr + r-xml2 +) +optdepends=( + r-datasets + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aws.s3/lilac.py b/prepare/r-aws.s3/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aws.s3/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aws.s3/lilac.yaml b/prepare/r-aws.s3/lilac.yaml new file mode 100644 index 0000000000..9c69c65a48 --- /dev/null +++ b/prepare/r-aws.s3/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aws.signature +- r-base64enc +- r-curl +- r-digest +- r-httr +- r-xml2 +update_on: +- regex: aws.s3_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=aws.s3 diff --git a/prepare/r-aws.signature/PKGBUILD b/prepare/r-aws.signature/PKGBUILD new file mode 100644 index 0000000000..747ca5512e --- /dev/null +++ b/prepare/r-aws.signature/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=aws.signature +_pkgver=0.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Amazon Web Services Request Signatures' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-base64enc + r-digest +) +optdepends=( + r-aws.ec2metadata + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aws.signature/lilac.py b/prepare/r-aws.signature/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aws.signature/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aws.signature/lilac.yaml b/prepare/r-aws.signature/lilac.yaml new file mode 100644 index 0000000000..26d0bddaf3 --- /dev/null +++ b/prepare/r-aws.signature/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-digest +update_on: +- regex: aws.signature_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=aws.signature diff --git a/prepare/r-aws/PKGBUILD b/prepare/r-aws/PKGBUILD new file mode 100644 index 0000000000..a20b90f89a --- /dev/null +++ b/prepare/r-aws/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=aws +_pkgver=2.5-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Adaptive Weights Smoothing' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-awsmethods + r-gsl +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-aws/lilac.py b/prepare/r-aws/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-aws/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-aws/lilac.yaml b/prepare/r-aws/lilac.yaml new file mode 100644 index 0000000000..f55cf3c221 --- /dev/null +++ b/prepare/r-aws/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-awsmethods +- r-gsl +update_on: +- regex: aws_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=aws diff --git a/prepare/r-awsmethods/PKGBUILD b/prepare/r-awsmethods/PKGBUILD new file mode 100644 index 0000000000..144cda322b --- /dev/null +++ b/prepare/r-awsmethods/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=awsMethods +_pkgver=1.1-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Class and Methods Definitions for Packages 'aws', 'adimpro', 'fmri', 'dwi'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-awsmethods/lilac.py b/prepare/r-awsmethods/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-awsmethods/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-awsmethods/lilac.yaml b/prepare/r-awsmethods/lilac.yaml new file mode 100644 index 0000000000..531b8c9b65 --- /dev/null +++ b/prepare/r-awsmethods/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: awsMethods_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=awsMethods diff --git a/prepare/r-awst/PKGBUILD b/prepare/r-awst/PKGBUILD new file mode 100644 index 0000000000..1c239d60ea --- /dev/null +++ b/prepare/r-awst/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=awst +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Asymmetric Within-Sample Transformation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-summarizedexperiment +) +optdepends=( + r-airway + r-biocstyle + r-edaseq + r-ggplot2 + r-knitr + r-refmanager + r-rmarkdown + r-sessioninfo + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-awst/lilac.py b/prepare/r-awst/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-awst/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-awst/lilac.yaml b/prepare/r-awst/lilac.yaml new file mode 100644 index 0000000000..e129352f1b --- /dev/null +++ b/prepare/r-awst/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-summarizedexperiment +update_on: +- regex: awst_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/awst diff --git a/prepare/r-baalchip/PKGBUILD b/prepare/r-baalchip/PKGBUILD new file mode 100644 index 0000000000..4f4a36151a --- /dev/null +++ b/prepare/r-baalchip/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BaalChIP +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-coda + r-doby + r-doparallel + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-reshape2 + r-rsamtools + r-scales +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-baalchip/lilac.py b/prepare/r-baalchip/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-baalchip/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-baalchip/lilac.yaml b/prepare/r-baalchip/lilac.yaml new file mode 100644 index 0000000000..0236828a27 --- /dev/null +++ b/prepare/r-baalchip/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-coda +- r-doby +- r-doparallel +- r-foreach +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-reshape2 +- r-rsamtools +- r-scales +update_on: +- regex: BaalChIP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BaalChIP diff --git a/prepare/r-babelgene/PKGBUILD b/prepare/r-babelgene/PKGBUILD new file mode 100644 index 0000000000..40faf4571b --- /dev/null +++ b/prepare/r-babelgene/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=babelgene +_pkgver=21.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Orthologs for Model Organisms in a Tidy Data Format' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-rlang +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-babelgene/lilac.py b/prepare/r-babelgene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-babelgene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-babelgene/lilac.yaml b/prepare/r-babelgene/lilac.yaml new file mode 100644 index 0000000000..74b7c08245 --- /dev/null +++ b/prepare/r-babelgene/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-rlang +update_on: +- regex: babelgene_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=babelgene diff --git a/prepare/r-bac/PKGBUILD b/prepare/r-bac/PKGBUILD new file mode 100644 index 0000000000..5462881929 --- /dev/null +++ b/prepare/r-bac/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BAC +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian Analysis of Chip-chip experiment' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bac/lilac.py b/prepare/r-bac/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bac/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bac/lilac.yaml b/prepare/r-bac/lilac.yaml new file mode 100644 index 0000000000..27838020e2 --- /dev/null +++ b/prepare/r-bac/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: BAC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BAC diff --git a/prepare/r-backbone/PKGBUILD b/prepare/r-backbone/PKGBUILD new file mode 100644 index 0000000000..3481d30dd9 --- /dev/null +++ b/prepare/r-backbone/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=backbone +_pkgver=2.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Extracts the Backbone from Graphs' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-igraph + r-network + r-poissonbinomial + r-rcpp +) +optdepends=( + r-knitr + r-mass + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-backbone/lilac.py b/prepare/r-backbone/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-backbone/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-backbone/lilac.yaml b/prepare/r-backbone/lilac.yaml new file mode 100644 index 0000000000..c1810c2c26 --- /dev/null +++ b/prepare/r-backbone/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +- r-network +- r-poissonbinomial +- r-rcpp +update_on: +- regex: backbone_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=backbone diff --git a/prepare/r-backports/PKGBUILD b/prepare/r-backports/PKGBUILD new file mode 100644 index 0000000000..cce6f43860 --- /dev/null +++ b/prepare/r-backports/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=backports +_pkgver=1.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Reimplementations of Functions Introduced Since R-3.0.0' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-backports/lilac.py b/prepare/r-backports/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-backports/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-backports/lilac.yaml b/prepare/r-backports/lilac.yaml new file mode 100644 index 0000000000..d4599af7ed --- /dev/null +++ b/prepare/r-backports/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: backports_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=backports diff --git a/prepare/r-bacon/PKGBUILD b/prepare/r-bacon/PKGBUILD new file mode 100644 index 0000000000..48b0bc18eb --- /dev/null +++ b/prepare/r-bacon/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bacon +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Controlling bias and inflation in association studies using the empirical null distribution' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-ellipse + r-ggplot2 +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bacon/lilac.py b/prepare/r-bacon/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bacon/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bacon/lilac.yaml b/prepare/r-bacon/lilac.yaml new file mode 100644 index 0000000000..95de2629a5 --- /dev/null +++ b/prepare/r-bacon/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-ellipse +- r-ggplot2 +update_on: +- regex: bacon_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bacon diff --git a/prepare/r-bader/PKGBUILD b/prepare/r-bader/PKGBUILD new file mode 100644 index 0000000000..7500939713 --- /dev/null +++ b/prepare/r-bader/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BADER +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian Analysis of Differential Expression in RNA Sequencing Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-pasilla +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bader/lilac.py b/prepare/r-bader/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bader/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bader/lilac.yaml b/prepare/r-bader/lilac.yaml new file mode 100644 index 0000000000..793d7e953c --- /dev/null +++ b/prepare/r-bader/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: BADER_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BADER diff --git a/prepare/r-badregionfinder/PKGBUILD b/prepare/r-badregionfinder/PKGBUILD new file mode 100644 index 0000000000..120a57f1c9 --- /dev/null +++ b/prepare/r-badregionfinder/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BadRegionFinder +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biomart + r-genomicranges + r-rsamtools + r-s4vectors + r-variantannotation +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg19 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-badregionfinder/lilac.py b/prepare/r-badregionfinder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-badregionfinder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-badregionfinder/lilac.yaml b/prepare/r-badregionfinder/lilac.yaml new file mode 100644 index 0000000000..5caa34fe2b --- /dev/null +++ b/prepare/r-badregionfinder/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-genomicranges +- r-rsamtools +- r-s4vectors +- r-variantannotation +update_on: +- regex: BadRegionFinder_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BadRegionFinder diff --git a/prepare/r-bags/PKGBUILD b/prepare/r-bags/PKGBUILD new file mode 100644 index 0000000000..7a125c42e4 --- /dev/null +++ b/prepare/r-bags/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BAGS +_pkgver=2.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Bayesian Approach for Geneset Selection' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-breastcancervdx +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bags/lilac.py b/prepare/r-bags/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bags/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bags/lilac.yaml b/prepare/r-bags/lilac.yaml new file mode 100644 index 0000000000..a9512f66d5 --- /dev/null +++ b/prepare/r-bags/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-breastcancervdx +update_on: +- regex: BAGS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BAGS diff --git a/prepare/r-ballgown/PKGBUILD b/prepare/r-ballgown/PKGBUILD new file mode 100644 index 0000000000..38ad45d0fe --- /dev/null +++ b/prepare/r-ballgown/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ballgown +_pkgver=2.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Flexible, isoform-level differential expression analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-genomeinfodb + r-genomicranges + r-iranges + r-limma + r-rcolorbrewer + r-rtracklayer + r-s4vectors + r-sva +) +optdepends=( + r-knitr + r-markdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ballgown/lilac.py b/prepare/r-ballgown/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ballgown/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ballgown/lilac.yaml b/prepare/r-ballgown/lilac.yaml new file mode 100644 index 0000000000..d757012824 --- /dev/null +++ b/prepare/r-ballgown/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-limma +- r-rcolorbrewer +- r-rtracklayer +- r-s4vectors +- r-sva +update_on: +- regex: ballgown_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ballgown diff --git a/prepare/r-bambu/PKGBUILD b/prepare/r-bambu/PKGBUILD new file mode 100644 index 0000000000..75113fe8b3 --- /dev/null +++ b/prepare/r-bambu/PKGBUILD @@ -0,0 +1,65 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bambu +_pkgver=2.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Reference-guided isoform reconstruction and quantification for long read RNA-Seq data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-data.table + r-dplyr + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-rcpp + r-rcpparmadillo + r-rsamtools + r-s4vectors + r-summarizedexperiment + r-tidyr + r-xgboost +) +optdepends=( + r-annotationdbi + r-apeglm + r-biocfilecache + r-biostrings + r-bsgenome + r-bsgenome.hsapiens.ncbi.grch38 + r-circlize + r-complexheatmap + r-deseq2 + r-dexseq + r-experimenthub + r-ggbio + r-ggplot2 + r-gridextra + r-knitr + r-nanoporernaseq + r-parallel + r-rmarkdown + r-testthat + r-txdb.hsapiens.ucsc.hg38.knowngene + r-utils +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bambu/lilac.py b/prepare/r-bambu/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bambu/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bambu/lilac.yaml b/prepare/r-bambu/lilac.yaml new file mode 100644 index 0000000000..c8c2956540 --- /dev/null +++ b/prepare/r-bambu/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-data.table +- r-dplyr +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-rcpp +- r-rcpparmadillo +- r-rsamtools +- r-s4vectors +- r-summarizedexperiment +- r-tidyr +- r-xgboost +update_on: +- regex: bambu_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bambu diff --git a/prepare/r-bamlss/PKGBUILD b/prepare/r-bamlss/PKGBUILD new file mode 100644 index 0000000000..613dc4f561 --- /dev/null +++ b/prepare/r-bamlss/PKGBUILD @@ -0,0 +1,62 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bamlss +_pkgver=1.1-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian Additive Models for Location, Scale, and Shape (and Beyond)' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-coda + r-colorspace + r-formula + r-mba + r-mvtnorm + r-sp +) +optdepends=( + r-akima + r-bayesx + r-bit + r-ff + r-ffbase + r-fields + r-gamlss + r-gamlss.dist + r-geor + r-glmnet + r-glogis + r-keras + r-knitr + r-mapdata + r-maps + r-maptools + r-mass + r-nnet + r-rjags + r-rmarkdown + r-scoringrules + r-sdprior + r-spatstat + r-spdep + r-splines2 + r-statmod + r-tensorflow + r-zoo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bamlss/lilac.py b/prepare/r-bamlss/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bamlss/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bamlss/lilac.yaml b/prepare/r-bamlss/lilac.yaml new file mode 100644 index 0000000000..9663b48adf --- /dev/null +++ b/prepare/r-bamlss/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-coda +- r-colorspace +- r-formula +- r-mba +- r-mvtnorm +- r-sp +update_on: +- regex: bamlss_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bamlss diff --git a/prepare/r-bamsignals/PKGBUILD b/prepare/r-bamsignals/PKGBUILD new file mode 100644 index 0000000000..3abed8e556 --- /dev/null +++ b/prepare/r-bamsignals/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=bamsignals +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Extract read count signals from bam files' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-genomicranges + r-iranges + r-rcpp + r-rhtslib + r-zlibbioc +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-rsamtools + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bamsignals/lilac.py b/prepare/r-bamsignals/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bamsignals/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bamsignals/lilac.yaml b/prepare/r-bamsignals/lilac.yaml new file mode 100644 index 0000000000..331b4030c1 --- /dev/null +++ b/prepare/r-bamsignals/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomicranges +- r-iranges +- r-rcpp +- r-rhtslib +- r-zlibbioc +update_on: +- regex: bamsignals_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bamsignals diff --git a/prepare/r-bandits/PKGBUILD b/prepare/r-bandits/PKGBUILD new file mode 100644 index 0000000000..015fa398e0 --- /dev/null +++ b/prepare/r-bandits/PKGBUILD @@ -0,0 +1,46 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=BANDITS +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='BANDITS: Bayesian ANalysis of DIfferenTial Splicing' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-data.table + r-doparallel + r-dorng + r-drimseq + r-foreach + r-ggplot2 + r-r.utils + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-biocstyle + r-biostrings + r-genomicfeatures + r-knitr + r-rmarkdown + r-testthat + r-tximport +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bandits/lilac.py b/prepare/r-bandits/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bandits/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bandits/lilac.yaml b/prepare/r-bandits/lilac.yaml new file mode 100644 index 0000000000..080d461514 --- /dev/null +++ b/prepare/r-bandits/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-data.table +- r-doparallel +- r-dorng +- r-drimseq +- r-foreach +- r-ggplot2 +- r-r.utils +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: BANDITS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BANDITS diff --git a/prepare/r-banocc/PKGBUILD b/prepare/r-banocc/PKGBUILD new file mode 100644 index 0000000000..d655da13aa --- /dev/null +++ b/prepare/r-banocc/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=banocc +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian ANalysis Of Compositional Covariance' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-coda + r-mvtnorm + r-rstan + r-stringr +) +optdepends=( + r-knitr + r-methods + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-banocc/lilac.py b/prepare/r-banocc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-banocc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-banocc/lilac.yaml b/prepare/r-banocc/lilac.yaml new file mode 100644 index 0000000000..fb7dc61f58 --- /dev/null +++ b/prepare/r-banocc/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-coda +- r-mvtnorm +- r-rstan +- r-stringr +update_on: +- regex: banocc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/banocc diff --git a/prepare/r-barcodetrackr/PKGBUILD b/prepare/r-barcodetrackr/PKGBUILD new file mode 100644 index 0000000000..72581547da --- /dev/null +++ b/prepare/r-barcodetrackr/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=barcodetrackR +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for Analyzing Cellular Barcoding Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-circlize + r-cowplot + r-dplyr + r-ggdendro + r-ggplot2 + r-ggridges + r-magrittr + r-plyr + r-proxy + r-rcolorbrewer + r-rlang + r-s4vectors + r-scales + r-shiny + r-summarizedexperiment + r-tibble + r-tidyr + r-vegan + r-viridis +) +optdepends=( + r-biocstyle + r-knitr + r-magick + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-barcodetrackr/lilac.py b/prepare/r-barcodetrackr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-barcodetrackr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-barcodetrackr/lilac.yaml b/prepare/r-barcodetrackr/lilac.yaml new file mode 100644 index 0000000000..46886a323d --- /dev/null +++ b/prepare/r-barcodetrackr/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circlize +- r-cowplot +- r-dplyr +- r-ggdendro +- r-ggplot2 +- r-ggridges +- r-magrittr +- r-plyr +- r-proxy +- r-rcolorbrewer +- r-rlang +- r-s4vectors +- r-scales +- r-shiny +- r-summarizedexperiment +- r-tibble +- r-tidyr +- r-vegan +- r-viridis +update_on: +- regex: barcodetrackR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/barcodetrackR diff --git a/prepare/r-base64/PKGBUILD b/prepare/r-base64/PKGBUILD new file mode 100644 index 0000000000..9214588147 --- /dev/null +++ b/prepare/r-base64/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=base64 +_pkgver=2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Base64 Encoder and Decoder' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-openssl +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-base64/lilac.py b/prepare/r-base64/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-base64/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-base64/lilac.yaml b/prepare/r-base64/lilac.yaml new file mode 100644 index 0000000000..ad4400eb77 --- /dev/null +++ b/prepare/r-base64/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-openssl +update_on: +- regex: base64_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=base64 diff --git a/prepare/r-base64enc/PKGBUILD b/prepare/r-base64enc/PKGBUILD new file mode 100644 index 0000000000..8385e2b0ad --- /dev/null +++ b/prepare/r-base64enc/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=base64enc +_pkgver=0.1-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for base64 encoding' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-png +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-base64enc/lilac.py b/prepare/r-base64enc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-base64enc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-base64enc/lilac.yaml b/prepare/r-base64enc/lilac.yaml new file mode 100644 index 0000000000..371c1f5ce4 --- /dev/null +++ b/prepare/r-base64enc/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: base64enc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=base64enc diff --git a/prepare/r-base64url/PKGBUILD b/prepare/r-base64url/PKGBUILD new file mode 100644 index 0000000000..d4e0883e73 --- /dev/null +++ b/prepare/r-base64url/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=base64url +_pkgver=1.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast and URL-Safe Base64 Encoder and Decoder' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-backports +) +optdepends=( + r-base64enc + r-checkmate + r-knitr + r-microbenchmark + r-openssl + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-base64url/lilac.py b/prepare/r-base64url/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-base64url/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-base64url/lilac.yaml b/prepare/r-base64url/lilac.yaml new file mode 100644 index 0000000000..233d01d389 --- /dev/null +++ b/prepare/r-base64url/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-backports +update_on: +- regex: base64url_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=base64url diff --git a/prepare/r-basecallqc/PKGBUILD b/prepare/r-basecallqc/PKGBUILD new file mode 100644 index 0000000000..28ca59f4e1 --- /dev/null +++ b/prepare/r-basecallqc/PKGBUILD @@ -0,0 +1,46 @@ +# system requirements: bcl2Fastq (versions >= 2.1.7) +# Maintainer: Guoyi Zhang + +_pkgname=basecallQC +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Working with Illumina Basecalling and Demultiplexing input and output files' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-dplyr + r-dt + r-ggplot2 + r-knitr + r-lazyeval + r-magrittr + r-prettydoc + r-raster + r-rmarkdown + r-shortread + r-stringr + r-tidyr + r-xml + r-yaml +) +optdepends=( + r-biocstyle + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-basecallqc/lilac.py b/prepare/r-basecallqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-basecallqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-basecallqc/lilac.yaml b/prepare/r-basecallqc/lilac.yaml new file mode 100644 index 0000000000..708d059d87 --- /dev/null +++ b/prepare/r-basecallqc/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-dplyr +- r-dt +- r-ggplot2 +- r-knitr +- r-lazyeval +- r-magrittr +- r-prettydoc +- r-raster +- r-rmarkdown +- r-shortread +- r-stringr +- r-tidyr +- r-xml +- r-yaml +update_on: +- regex: basecallQC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/basecallQC diff --git a/prepare/r-baseline/PKGBUILD b/prepare/r-baseline/PKGBUILD new file mode 100644 index 0000000000..e803bda8e2 --- /dev/null +++ b/prepare/r-baseline/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=baseline +_pkgver=1.3-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Baseline Correction of Spectra' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-limsolve + r-sparsem +) +optdepends=( + r-gwidgets2 + r-gwidgets2tcltk + r-idpmisc + r-lattice + r-mass + r-pls +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-baseline/lilac.py b/prepare/r-baseline/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-baseline/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-baseline/lilac.yaml b/prepare/r-baseline/lilac.yaml new file mode 100644 index 0000000000..d8327cea57 --- /dev/null +++ b/prepare/r-baseline/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-limsolve +- r-sparsem +update_on: +- regex: baseline_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=baseline diff --git a/prepare/r-basespacer/PKGBUILD b/prepare/r-basespacer/PKGBUILD new file mode 100644 index 0000000000..8411c99fab --- /dev/null +++ b/prepare/r-basespacer/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BaseSpaceR +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R SDK for BaseSpace RESTful API' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Apache') +depends=( + r + r-rcurl + r-rjsonio +) +optdepends=( + r-iranges + r-rsamtools + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-basespacer/lilac.py b/prepare/r-basespacer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-basespacer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-basespacer/lilac.yaml b/prepare/r-basespacer/lilac.yaml new file mode 100644 index 0000000000..7eb97eb5c6 --- /dev/null +++ b/prepare/r-basespacer/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcurl +- r-rjsonio +update_on: +- regex: BaseSpaceR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BaseSpaceR diff --git a/prepare/r-basic4cseq/PKGBUILD b/prepare/r-basic4cseq/PKGBUILD new file mode 100644 index 0000000000..372906452d --- /dev/null +++ b/prepare/r-basic4cseq/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Basic4Cseq +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biostrings + r-bsgenome.ecoli.ncbi.20080805 + r-catools + r-genomicalignments + r-genomicranges + r-rcircos +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg19 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-basic4cseq/lilac.py b/prepare/r-basic4cseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-basic4cseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-basic4cseq/lilac.yaml b/prepare/r-basic4cseq/lilac.yaml new file mode 100644 index 0000000000..43d8707c3f --- /dev/null +++ b/prepare/r-basic4cseq/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome.ecoli.ncbi.20080805 +- r-catools +- r-genomicalignments +- r-genomicranges +- r-rcircos +update_on: +- regex: Basic4Cseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Basic4Cseq diff --git a/prepare/r-basics/PKGBUILD b/prepare/r-basics/PKGBUILD new file mode 100644 index 0000000000..653d0a6754 --- /dev/null +++ b/prepare/r-basics/PKGBUILD @@ -0,0 +1,53 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=BASiCS +_pkgver=2.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian Analysis of Single-Cell Sequencing data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-biobase + r-biocgenerics + r-biocparallel + r-coda + r-cowplot + r-ggextra + r-ggplot2 + r-hexbin + r-matrixstats + r-rcpp + r-rcpparmadillo + r-reshape2 + r-s4vectors + r-scran + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-viridis +) +optdepends=( + r-biocstyle + r-knitr + r-magick + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-basics/lilac.py b/prepare/r-basics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-basics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-basics/lilac.yaml b/prepare/r-basics/lilac.yaml new file mode 100644 index 0000000000..86d087bcb6 --- /dev/null +++ b/prepare/r-basics/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-coda +- r-cowplot +- r-ggextra +- r-ggplot2 +- r-hexbin +- r-matrixstats +- r-rcpp +- r-rcpparmadillo +- r-reshape2 +- r-s4vectors +- r-scran +- r-scuttle +- r-singlecellexperiment +- r-summarizedexperiment +- r-viridis +update_on: +- regex: BASiCS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BASiCS diff --git a/prepare/r-basicstarrseq/PKGBUILD b/prepare/r-basicstarrseq/PKGBUILD new file mode 100644 index 0000000000..0c14ab2414 --- /dev/null +++ b/prepare/r-basicstarrseq/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BasicSTARRseq +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Basic peak calling on STARR-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-s4vectors +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-basicstarrseq/lilac.py b/prepare/r-basicstarrseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-basicstarrseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-basicstarrseq/lilac.yaml b/prepare/r-basicstarrseq/lilac.yaml new file mode 100644 index 0000000000..0fa4c423e5 --- /dev/null +++ b/prepare/r-basicstarrseq/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-s4vectors +update_on: +- regex: BasicSTARRseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BasicSTARRseq diff --git a/prepare/r-basictrendline/PKGBUILD b/prepare/r-basictrendline/PKGBUILD new file mode 100644 index 0000000000..5b479162b9 --- /dev/null +++ b/prepare/r-basictrendline/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=basicTrendline +_pkgver=2.0.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Add Trendline and Confidence Interval of Basic Regression Models to Plot' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-investr + r-scales +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-basictrendline/lilac.py b/prepare/r-basictrendline/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-basictrendline/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-basictrendline/lilac.yaml b/prepare/r-basictrendline/lilac.yaml new file mode 100644 index 0000000000..81350a6a41 --- /dev/null +++ b/prepare/r-basictrendline/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-investr +- r-scales +update_on: +- regex: basicTrendline_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=basicTrendline diff --git a/prepare/r-basilisk.utils/PKGBUILD b/prepare/r-basilisk.utils/PKGBUILD new file mode 100644 index 0000000000..910d319610 --- /dev/null +++ b/prepare/r-basilisk.utils/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=basilisk.utils +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Basilisk Installation Utilities' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dir.expiry +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-basilisk.utils/lilac.py b/prepare/r-basilisk.utils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-basilisk.utils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-basilisk.utils/lilac.yaml b/prepare/r-basilisk.utils/lilac.yaml new file mode 100644 index 0000000000..bf63d06dd3 --- /dev/null +++ b/prepare/r-basilisk.utils/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dir.expiry +update_on: +- regex: basilisk.utils_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/basilisk.utils diff --git a/prepare/r-basilisk/PKGBUILD b/prepare/r-basilisk/PKGBUILD new file mode 100644 index 0000000000..77046c8631 --- /dev/null +++ b/prepare/r-basilisk/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=basilisk +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Freezing Python Dependencies Inside Bioconductor Packages' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-basilisk.utils + r-dir.expiry + r-reticulate +) +optdepends=( + r-biocstyle + r-callr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-basilisk/lilac.py b/prepare/r-basilisk/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-basilisk/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-basilisk/lilac.yaml b/prepare/r-basilisk/lilac.yaml new file mode 100644 index 0000000000..918d917653 --- /dev/null +++ b/prepare/r-basilisk/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-basilisk.utils +- r-dir.expiry +- r-reticulate +update_on: +- regex: basilisk_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/basilisk diff --git a/prepare/r-batchelor/PKGBUILD b/prepare/r-batchelor/PKGBUILD new file mode 100644 index 0000000000..644587dc14 --- /dev/null +++ b/prepare/r-batchelor/PKGBUILD @@ -0,0 +1,52 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=batchelor +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Single-Cell Batch Correction Methods' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-beachmat + r-biocgenerics + r-biocneighbors + r-biocparallel + r-biocsingular + r-delayedarray + r-delayedmatrixstats + r-igraph + r-rcpp + r-residualmatrix + r-s4vectors + r-scaledmatrix + r-scuttle + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-bluster + r-knitr + r-rmarkdown + r-scater + r-scran + r-scrnaseq + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-batchelor/lilac.py b/prepare/r-batchelor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-batchelor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-batchelor/lilac.yaml b/prepare/r-batchelor/lilac.yaml new file mode 100644 index 0000000000..d40e6a2d45 --- /dev/null +++ b/prepare/r-batchelor/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beachmat +- r-biocgenerics +- r-biocneighbors +- r-biocparallel +- r-biocsingular +- r-delayedarray +- r-delayedmatrixstats +- r-igraph +- r-rcpp +- r-residualmatrix +- r-s4vectors +- r-scaledmatrix +- r-scuttle +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: batchelor_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/batchelor diff --git a/prepare/r-batchjobs/PKGBUILD b/prepare/r-batchjobs/PKGBUILD new file mode 100644 index 0000000000..58fdb6acd6 --- /dev/null +++ b/prepare/r-batchjobs/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BatchJobs +_pkgver=1.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Batch Computing with R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-backports + r-bbmisc + r-brew + r-checkmate + r-data.table + r-dbi + r-digest + r-rsqlite + r-sendmailr + r-stringi +) +optdepends=( + r-mass + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-batchjobs/lilac.py b/prepare/r-batchjobs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-batchjobs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-batchjobs/lilac.yaml b/prepare/r-batchjobs/lilac.yaml new file mode 100644 index 0000000000..7fb979295b --- /dev/null +++ b/prepare/r-batchjobs/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-backports +- r-bbmisc +- r-brew +- r-checkmate +- r-data.table +- r-dbi +- r-digest +- r-rsqlite +- r-sendmailr +- r-stringi +update_on: +- regex: BatchJobs_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=BatchJobs diff --git a/prepare/r-batchqc/PKGBUILD b/prepare/r-batchqc/PKGBUILD new file mode 100644 index 0000000000..66dcd829dd --- /dev/null +++ b/prepare/r-batchqc/PKGBUILD @@ -0,0 +1,44 @@ +# system requirements: pandoc (http://pandoc.org/installing.html) forgenerating reports from markdown files. +# Maintainer: Guoyi Zhang + +_pkgname=BatchQC +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Batch Effects Quality Control Software' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-corpcor + r-ggvis + r-gplots + r-heatmaply + r-knitr + r-limma + r-matrixstats + r-mcmcpack + r-moments + r-pander + r-reshape2 + r-rmarkdown + r-shiny + r-sva +) +optdepends=( + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-batchqc/lilac.py b/prepare/r-batchqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-batchqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-batchqc/lilac.yaml b/prepare/r-batchqc/lilac.yaml new file mode 100644 index 0000000000..2914fbd31e --- /dev/null +++ b/prepare/r-batchqc/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-corpcor +- r-ggvis +- r-gplots +- r-heatmaply +- r-knitr +- r-limma +- r-matrixstats +- r-mcmcpack +- r-moments +- r-pander +- r-reshape2 +- r-rmarkdown +- r-shiny +- r-sva +update_on: +- regex: BatchQC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BatchQC diff --git a/prepare/r-batchtools/PKGBUILD b/prepare/r-batchtools/PKGBUILD new file mode 100644 index 0000000000..cb24140474 --- /dev/null +++ b/prepare/r-batchtools/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=batchtools +_pkgver=0.9.15 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Computation on Batch Systems' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-backports + r-base64url + r-brew + r-checkmate + r-data.table + r-digest + r-fs + r-progress + r-r6 + r-rappdirs + r-stringi + r-withr +) +optdepends=( + r-debugme + r-dompi + r-doparallel + r-e1071 + r-foreach + r-future + r-future.batchtools + r-knitr + r-parallelmap + r-ranger + r-rmarkdown + r-rpart + r-snow + r-testthat + r-tibble +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-batchtools/lilac.py b/prepare/r-batchtools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-batchtools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-batchtools/lilac.yaml b/prepare/r-batchtools/lilac.yaml new file mode 100644 index 0000000000..97e2ff1fc2 --- /dev/null +++ b/prepare/r-batchtools/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-backports +- r-base64url +- r-brew +- r-checkmate +- r-data.table +- r-digest +- r-fs +- r-progress +- r-r6 +- r-rappdirs +- r-stringi +- r-withr +update_on: +- regex: batchtools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=batchtools diff --git a/prepare/r-bayesknockdown/PKGBUILD b/prepare/r-bayesknockdown/PKGBUILD new file mode 100644 index 0000000000..9432fc865b --- /dev/null +++ b/prepare/r-bayesknockdown/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BayesKnockdown +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bayesknockdown/lilac.py b/prepare/r-bayesknockdown/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bayesknockdown/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bayesknockdown/lilac.yaml b/prepare/r-bayesknockdown/lilac.yaml new file mode 100644 index 0000000000..c3d284658b --- /dev/null +++ b/prepare/r-bayesknockdown/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: BayesKnockdown_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BayesKnockdown diff --git a/prepare/r-bayesm/PKGBUILD b/prepare/r-bayesm/PKGBUILD new file mode 100644 index 0000000000..d1cc2ee236 --- /dev/null +++ b/prepare/r-bayesm/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bayesm +_pkgver=3.1-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian Inference for Marketing/Micro-Econometrics' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bayesm/lilac.py b/prepare/r-bayesm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bayesm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bayesm/lilac.yaml b/prepare/r-bayesm/lilac.yaml new file mode 100644 index 0000000000..9974b88b26 --- /dev/null +++ b/prepare/r-bayesm/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: bayesm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bayesm diff --git a/prepare/r-bayesspace/PKGBUILD b/prepare/r-bayesspace/PKGBUILD new file mode 100644 index 0000000000..3e5f3df5c3 --- /dev/null +++ b/prepare/r-bayesspace/PKGBUILD @@ -0,0 +1,61 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=BayesSpace +_pkgver=1.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clustering and Resolution Enhancement of Spatial Transcriptomes' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-assertthat + r-biocfilecache + r-biocsingular + r-coda + r-dirichletreg + r-ggplot2 + r-mclust + r-purrr + r-rcpp + r-rcpparmadillo + r-rcppdist + r-rcppprogress + r-rcurl + r-rhdf5 + r-s4vectors + r-scales + r-scater + r-scran + r-singlecellexperiment + r-summarizedexperiment + r-xgboost +) +optdepends=( + r-dplyr + r-igraph + r-knitr + r-patchwork + r-rcolorbrewer + r-rmarkdown + r-seurat + r-spatiallibd + r-testthat + r-viridis +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bayesspace/lilac.py b/prepare/r-bayesspace/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bayesspace/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bayesspace/lilac.yaml b/prepare/r-bayesspace/lilac.yaml new file mode 100644 index 0000000000..5845a25880 --- /dev/null +++ b/prepare/r-bayesspace/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biocfilecache +- r-biocsingular +- r-coda +- r-dirichletreg +- r-ggplot2 +- r-mclust +- r-purrr +- r-rcpp +- r-rcpparmadillo +- r-rcppdist +- r-rcppprogress +- r-rcurl +- r-rhdf5 +- r-s4vectors +- r-scales +- r-scater +- r-scran +- r-singlecellexperiment +- r-summarizedexperiment +- r-xgboost +update_on: +- regex: BayesSpace_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BayesSpace diff --git a/prepare/r-baynorm/PKGBUILD b/prepare/r-baynorm/PKGBUILD new file mode 100644 index 0000000000..d751c3e429 --- /dev/null +++ b/prepare/r-baynorm/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bayNorm +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Single-cell RNA sequencing data normalization' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bb + r-biocparallel + r-dosnow + r-fitdistrplus + r-foreach + r-iterators + r-locfit + r-rcpp + r-rcpparmadillo + r-rcppprogress + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-devtools + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-baynorm/lilac.py b/prepare/r-baynorm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-baynorm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-baynorm/lilac.yaml b/prepare/r-baynorm/lilac.yaml new file mode 100644 index 0000000000..018064c6c9 --- /dev/null +++ b/prepare/r-baynorm/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bb +- r-biocparallel +- r-dosnow +- r-fitdistrplus +- r-foreach +- r-iterators +- r-locfit +- r-rcpp +- r-rcpparmadillo +- r-rcppprogress +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: bayNorm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bayNorm diff --git a/prepare/r-bayseq/PKGBUILD b/prepare/r-bayseq/PKGBUILD new file mode 100644 index 0000000000..a62173b165 --- /dev/null +++ b/prepare/r-bayseq/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=baySeq +_pkgver=2.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Empirical Bayesian analysis of patterns of differential expression in count data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-edger + r-genomicranges +) +optdepends=( + r-biocgenerics + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bayseq/lilac.py b/prepare/r-bayseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bayseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bayseq/lilac.yaml b/prepare/r-bayseq/lilac.yaml new file mode 100644 index 0000000000..d34a065e13 --- /dev/null +++ b/prepare/r-bayseq/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-edger +- r-genomicranges +update_on: +- regex: baySeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/baySeq diff --git a/prepare/r-bb/PKGBUILD b/prepare/r-bb/PKGBUILD new file mode 100644 index 0000000000..d8b8ece060 --- /dev/null +++ b/prepare/r-bb/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BB +_pkgver=2019.10-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Solving and Optimizing Large-Scale Nonlinear Systems' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-quadprog +) +optdepends=( + r-hmisc + r-numderiv + r-setrng + r-survival +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bb/lilac.py b/prepare/r-bb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bb/lilac.yaml b/prepare/r-bb/lilac.yaml new file mode 100644 index 0000000000..ab16c716cf --- /dev/null +++ b/prepare/r-bb/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-quadprog +update_on: +- regex: BB_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=BB diff --git a/prepare/r-bbcanalyzer/PKGBUILD b/prepare/r-bbcanalyzer/PKGBUILD new file mode 100644 index 0000000000..64885cdbfc --- /dev/null +++ b/prepare/r-bbcanalyzer/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BBCAnalyzer +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='BBCAnalyzer: an R/Bioconductor package for visualizing base counts' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biostrings + r-genomicranges + r-iranges + r-rsamtools + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg19 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bbcanalyzer/lilac.py b/prepare/r-bbcanalyzer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bbcanalyzer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bbcanalyzer/lilac.yaml b/prepare/r-bbcanalyzer/lilac.yaml new file mode 100644 index 0000000000..fee3f61650 --- /dev/null +++ b/prepare/r-bbcanalyzer/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-genomicranges +- r-iranges +- r-rsamtools +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: BBCAnalyzer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BBCAnalyzer diff --git a/prepare/r-bbmisc/PKGBUILD b/prepare/r-bbmisc/PKGBUILD new file mode 100644 index 0000000000..e609901020 --- /dev/null +++ b/prepare/r-bbmisc/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BBmisc +_pkgver=1.11 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Miscellaneous Helper Functions for B. Bischl' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-checkmate +) +optdepends=( + r-codetools + r-microbenchmark + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bbmisc/lilac.py b/prepare/r-bbmisc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bbmisc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bbmisc/lilac.yaml b/prepare/r-bbmisc/lilac.yaml new file mode 100644 index 0000000000..c79a9a156e --- /dev/null +++ b/prepare/r-bbmisc/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-checkmate +update_on: +- regex: BBmisc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=BBmisc diff --git a/prepare/r-bbmle/PKGBUILD b/prepare/r-bbmle/PKGBUILD new file mode 100644 index 0000000000..c8f20b6c08 --- /dev/null +++ b/prepare/r-bbmle/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bbmle +_pkgver=1.0.24 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for General Maximum Likelihood Estimation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bdsmatrix + r-mvtnorm + r-numderiv +) +optdepends=( + r-aiccmodavg + r-emdbook + r-ggplot2 + r-hmisc + r-knitr + r-mumin + r-optimx + r-rms + r-runit + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bbmle/lilac.py b/prepare/r-bbmle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bbmle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bbmle/lilac.yaml b/prepare/r-bbmle/lilac.yaml new file mode 100644 index 0000000000..bf4a202820 --- /dev/null +++ b/prepare/r-bbmle/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bdsmatrix +- r-mvtnorm +- r-numderiv +update_on: +- regex: bbmle_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bbmle diff --git a/prepare/r-bc3net/PKGBUILD b/prepare/r-bc3net/PKGBUILD new file mode 100644 index 0000000000..6aae33be22 --- /dev/null +++ b/prepare/r-bc3net/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bc3net +_pkgver=1.0.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Regulatory Network Inference with Bc3net' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-c3net + r-igraph + r-infotheo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bc3net/lilac.py b/prepare/r-bc3net/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bc3net/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bc3net/lilac.yaml b/prepare/r-bc3net/lilac.yaml new file mode 100644 index 0000000000..c5547401b1 --- /dev/null +++ b/prepare/r-bc3net/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-c3net +- r-igraph +- r-infotheo +update_on: +- regex: bc3net_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bc3net diff --git a/prepare/r-bcellviper/PKGBUILD b/prepare/r-bcellviper/PKGBUILD new file mode 100644 index 0000000000..e5a7dec5e4 --- /dev/null +++ b/prepare/r-bcellviper/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bcellViper +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Human B-cell transcriptional interactome and normal human B-cell expression data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bcellviper/lilac.py b/prepare/r-bcellviper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bcellviper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bcellviper/lilac.yaml b/prepare/r-bcellviper/lilac.yaml new file mode 100644 index 0000000000..94f43f494f --- /dev/null +++ b/prepare/r-bcellviper/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: bcellViper_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bcellViper diff --git a/prepare/r-bcrank/PKGBUILD b/prepare/r-bcrank/PKGBUILD new file mode 100644 index 0000000000..c22ca31fac --- /dev/null +++ b/prepare/r-bcrank/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BCRANK +_pkgver=1.56.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Predicting binding site consensus from ranked DNA sequences' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings +) +optdepends=( + r-seqlogo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bcrank/lilac.py b/prepare/r-bcrank/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bcrank/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bcrank/lilac.yaml b/prepare/r-bcrank/lilac.yaml new file mode 100644 index 0000000000..b6073fae56 --- /dev/null +++ b/prepare/r-bcrank/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +update_on: +- regex: BCRANK_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BCRANK diff --git a/prepare/r-bcseq/PKGBUILD b/prepare/r-bcseq/PKGBUILD new file mode 100644 index 0000000000..0e695e5bff --- /dev/null +++ b/prepare/r-bcseq/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bcSeq +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-rcpp +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bcseq/lilac.py b/prepare/r-bcseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bcseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bcseq/lilac.yaml b/prepare/r-bcseq/lilac.yaml new file mode 100644 index 0000000000..84cf740183 --- /dev/null +++ b/prepare/r-bcseq/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-rcpp +update_on: +- regex: bcSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bcSeq diff --git a/prepare/r-bdmmacorrect/PKGBUILD b/prepare/r-bdmmacorrect/PKGBUILD new file mode 100644 index 0000000000..df38e23745 --- /dev/null +++ b/prepare/r-bdmmacorrect/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BDMMAcorrect +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Meta-analysis for the metagenomic read counts data from different cohorts' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-ellipse + r-ggplot2 + r-rcpp + r-rcpparmadillo + r-rcppeigen + r-summarizedexperiment + r-vegan +) +optdepends=( + r-biocgenerics + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bdmmacorrect/lilac.py b/prepare/r-bdmmacorrect/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bdmmacorrect/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bdmmacorrect/lilac.yaml b/prepare/r-bdmmacorrect/lilac.yaml new file mode 100644 index 0000000000..d372ae3636 --- /dev/null +++ b/prepare/r-bdmmacorrect/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-ellipse +- r-ggplot2 +- r-rcpp +- r-rcpparmadillo +- r-rcppeigen +- r-summarizedexperiment +- r-vegan +update_on: +- regex: BDMMAcorrect_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BDMMAcorrect diff --git a/prepare/r-bdsmatrix/PKGBUILD b/prepare/r-bdsmatrix/PKGBUILD new file mode 100644 index 0000000000..1e36656d7b --- /dev/null +++ b/prepare/r-bdsmatrix/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bdsmatrix +_pkgver=1.3-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Routines for Block Diagonal Symmetric Matrices' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bdsmatrix/lilac.py b/prepare/r-bdsmatrix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bdsmatrix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bdsmatrix/lilac.yaml b/prepare/r-bdsmatrix/lilac.yaml new file mode 100644 index 0000000000..6405fa38a0 --- /dev/null +++ b/prepare/r-bdsmatrix/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: bdsmatrix_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bdsmatrix diff --git a/prepare/r-beachmat/PKGBUILD b/prepare/r-beachmat/PKGBUILD new file mode 100644 index 0000000000..57e5874e30 --- /dev/null +++ b/prepare/r-beachmat/PKGBUILD @@ -0,0 +1,39 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=beachmat +_pkgver=2.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Compiling Bioconductor to Handle Each Matrix Type' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-delayedarray + r-rcpp +) +optdepends=( + r-biocparallel + r-biocstyle + r-hdf5array + r-knitr + r-rcmdcheck + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-beachmat/lilac.py b/prepare/r-beachmat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-beachmat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-beachmat/lilac.yaml b/prepare/r-beachmat/lilac.yaml new file mode 100644 index 0000000000..420b5f9173 --- /dev/null +++ b/prepare/r-beachmat/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-delayedarray +- r-rcpp +update_on: +- regex: beachmat_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/beachmat diff --git a/prepare/r-beadarray/PKGBUILD b/prepare/r-beadarray/PKGBUILD new file mode 100644 index 0000000000..3eca26581e --- /dev/null +++ b/prepare/r-beadarray/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=beadarray +_pkgver=2.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quality assessment and low-level analysis for Illumina BeadArray data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-beaddatapackr + r-biobase + r-biocgenerics + r-genomicranges + r-ggplot2 + r-hexbin + r-illuminaio + r-iranges + r-limma + r-reshape2 +) +optdepends=( + r-affy + r-beadarrayexampledata + r-biocstyle + r-ggbio + r-gridextra + r-hwriter + r-illuminahumanv3.db + r-knitr + r-lumi + r-nozzle.r1 + r-txdb.hsapiens.ucsc.hg19.knowngene + r-vsn +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-beadarray/lilac.py b/prepare/r-beadarray/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-beadarray/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-beadarray/lilac.yaml b/prepare/r-beadarray/lilac.yaml new file mode 100644 index 0000000000..67a42d3579 --- /dev/null +++ b/prepare/r-beadarray/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-beaddatapackr +- r-biobase +- r-biocgenerics +- r-genomicranges +- r-ggplot2 +- r-hexbin +- r-illuminaio +- r-iranges +- r-limma +- r-reshape2 +update_on: +- regex: beadarray_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/beadarray diff --git a/prepare/r-beadarraysnp/PKGBUILD b/prepare/r-beadarraysnp/PKGBUILD new file mode 100644 index 0000000000..f6e9d47a7c --- /dev/null +++ b/prepare/r-beadarraysnp/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=beadarraySNP +_pkgver=1.60.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Normalization and reporting of Illumina SNP bead arrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-quantsmooth +) +optdepends=( + r-acgh + r-affy + r-beadarray + r-dnacopy + r-limma + r-snapcgh +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-beadarraysnp/lilac.py b/prepare/r-beadarraysnp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-beadarraysnp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-beadarraysnp/lilac.yaml b/prepare/r-beadarraysnp/lilac.yaml new file mode 100644 index 0000000000..6cee8b76c8 --- /dev/null +++ b/prepare/r-beadarraysnp/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-quantsmooth +update_on: +- regex: beadarraySNP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/beadarraySNP diff --git a/prepare/r-beaddatapackr/PKGBUILD b/prepare/r-beaddatapackr/PKGBUILD new file mode 100644 index 0000000000..aa4773368a --- /dev/null +++ b/prepare/r-beaddatapackr/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BeadDataPackR +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Compression of Illumina BeadArray data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biocstyle + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-beaddatapackr/lilac.py b/prepare/r-beaddatapackr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-beaddatapackr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-beaddatapackr/lilac.yaml b/prepare/r-beaddatapackr/lilac.yaml new file mode 100644 index 0000000000..735957b62f --- /dev/null +++ b/prepare/r-beaddatapackr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: BeadDataPackR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BeadDataPackR diff --git a/prepare/r-beanplot/PKGBUILD b/prepare/r-beanplot/PKGBUILD new file mode 100644 index 0000000000..3925eb74ce --- /dev/null +++ b/prepare/r-beanplot/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=beanplot +_pkgver=1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization via Beanplots (like Boxplot/Stripchart/Violin Plot)' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-lattice + r-vioplot +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-beanplot/lilac.py b/prepare/r-beanplot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-beanplot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-beanplot/lilac.yaml b/prepare/r-beanplot/lilac.yaml new file mode 100644 index 0000000000..3237d05b61 --- /dev/null +++ b/prepare/r-beanplot/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: beanplot_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=beanplot diff --git a/prepare/r-bearscc/PKGBUILD b/prepare/r-bearscc/PKGBUILD new file mode 100644 index 0000000000..cc42963ac1 --- /dev/null +++ b/prepare/r-bearscc/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BEARscc +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-ggplot2 + r-singlecellexperiment +) +optdepends=( + r-biocstyle + r-cowplot + r-knitr + r-nmf + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bearscc/lilac.py b/prepare/r-bearscc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bearscc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bearscc/lilac.yaml b/prepare/r-bearscc/lilac.yaml new file mode 100644 index 0000000000..ca5de5bb13 --- /dev/null +++ b/prepare/r-bearscc/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-ggplot2 +- r-singlecellexperiment +update_on: +- regex: BEARscc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BEARscc diff --git a/prepare/r-beat/PKGBUILD b/prepare/r-beat/PKGBUILD new file mode 100644 index 0000000000..c5259c0279 --- /dev/null +++ b/prepare/r-beat/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BEAT +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='BEAT - BS-Seq Epimutation Analysis Toolkit' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biostrings + r-bsgenome + r-genomicranges + r-shortread +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-beat/lilac.py b/prepare/r-beat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-beat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-beat/lilac.yaml b/prepare/r-beat/lilac.yaml new file mode 100644 index 0000000000..9596ec40ee --- /dev/null +++ b/prepare/r-beat/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome +- r-genomicranges +- r-shortread +update_on: +- regex: BEAT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BEAT diff --git a/prepare/r-beclear/PKGBUILD b/prepare/r-beclear/PKGBUILD new file mode 100644 index 0000000000..db7a2e20c8 --- /dev/null +++ b/prepare/r-beclear/PKGBUILD @@ -0,0 +1,41 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=BEclear +_pkgver=2.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Correction of batch effects in DNA methylation data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-biocparallel + r-data.table + r-futile.logger + r-outliers + r-rcpp + r-rdpack +) +optdepends=( + r-biocstyle + r-knitr + r-pander + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-beclear/lilac.py b/prepare/r-beclear/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-beclear/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-beclear/lilac.yaml b/prepare/r-beclear/lilac.yaml new file mode 100644 index 0000000000..ff7c88dea6 --- /dev/null +++ b/prepare/r-beclear/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-biocparallel +- r-data.table +- r-futile.logger +- r-outliers +- r-rcpp +- r-rdpack +update_on: +- regex: BEclear_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BEclear diff --git a/prepare/r-beeswarm/PKGBUILD b/prepare/r-beeswarm/PKGBUILD new file mode 100644 index 0000000000..a007db6912 --- /dev/null +++ b/prepare/r-beeswarm/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=beeswarm +_pkgver=0.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The Bee Swarm Plot, an Alternative to Stripchart' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-beeswarm/lilac.py b/prepare/r-beeswarm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-beeswarm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-beeswarm/lilac.yaml b/prepare/r-beeswarm/lilac.yaml new file mode 100644 index 0000000000..d967d7bda5 --- /dev/null +++ b/prepare/r-beeswarm/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: beeswarm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=beeswarm diff --git a/prepare/r-benchdamic/PKGBUILD b/prepare/r-benchdamic/PKGBUILD new file mode 100644 index 0000000000..d20919409b --- /dev/null +++ b/prepare/r-benchdamic/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=benchdamic +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Benchmark of differential abundance methods on microbiome data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-aldex2 + r-biocparallel + r-corncob + r-cowplot + r-deseq2 + r-edger + r-ffpe + r-ggdendro + r-ggplot2 + r-limma + r-mast + r-metagenomeseq + r-mglm + r-phyloseq + r-plyr + r-rcolorbrewer + r-reshape2 + r-seurat + r-summarizedexperiment + r-zinbwave +) +optdepends=( + r-biocstyle + r-curatedmetagenomicdata + r-hmp16sdata + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-benchdamic/lilac.py b/prepare/r-benchdamic/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-benchdamic/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-benchdamic/lilac.yaml b/prepare/r-benchdamic/lilac.yaml new file mode 100644 index 0000000000..d5ac4d3b39 --- /dev/null +++ b/prepare/r-benchdamic/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aldex2 +- r-biocparallel +- r-corncob +- r-cowplot +- r-deseq2 +- r-edger +- r-ffpe +- r-ggdendro +- r-ggplot2 +- r-limma +- r-mast +- r-metagenomeseq +- r-mglm +- r-phyloseq +- r-plyr +- r-rcolorbrewer +- r-reshape2 +- r-seurat +- r-summarizedexperiment +- r-zinbwave +update_on: +- regex: benchdamic_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/benchdamic diff --git a/prepare/r-benchmarkme/PKGBUILD b/prepare/r-benchmarkme/PKGBUILD new file mode 100644 index 0000000000..f034b51078 --- /dev/null +++ b/prepare/r-benchmarkme/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=benchmarkme +_pkgver=1.0.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Crowd Sourced System Benchmarks' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-benchmarkmedata + r-doparallel + r-dplyr + r-foreach + r-httr + r-tibble +) +optdepends=( + r-covr + r-dt + r-ggplot2 + r-knitr + r-rcppziggurat + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-benchmarkme/lilac.py b/prepare/r-benchmarkme/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-benchmarkme/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-benchmarkme/lilac.yaml b/prepare/r-benchmarkme/lilac.yaml new file mode 100644 index 0000000000..b0e0ae37a6 --- /dev/null +++ b/prepare/r-benchmarkme/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-benchmarkmedata +- r-doparallel +- r-dplyr +- r-foreach +- r-httr +- r-tibble +update_on: +- regex: benchmarkme_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=benchmarkme diff --git a/prepare/r-benchmarkmedata/PKGBUILD b/prepare/r-benchmarkmedata/PKGBUILD new file mode 100644 index 0000000000..f3eb265c87 --- /dev/null +++ b/prepare/r-benchmarkmedata/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=benchmarkmeData +_pkgver=1.0.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Data Set for the 'benchmarkme' Package" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-tibble +) +optdepends=( + r-benchmarkme + r-covr + r-dt + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-benchmarkmedata/lilac.py b/prepare/r-benchmarkmedata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-benchmarkmedata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-benchmarkmedata/lilac.yaml b/prepare/r-benchmarkmedata/lilac.yaml new file mode 100644 index 0000000000..f9109b5f6d --- /dev/null +++ b/prepare/r-benchmarkmedata/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-tibble +update_on: +- regex: benchmarkmeData_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=benchmarkmeData diff --git a/prepare/r-betareg/PKGBUILD b/prepare/r-betareg/PKGBUILD new file mode 100644 index 0000000000..66da1f4d45 --- /dev/null +++ b/prepare/r-betareg/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=betareg +_pkgver=3.1-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Beta Regression' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-flexmix + r-formula + r-lmtest + r-modeltools + r-sandwich +) +optdepends=( + r-car + r-lattice + r-partykit + r-strucchange +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-betareg/lilac.py b/prepare/r-betareg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-betareg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-betareg/lilac.yaml b/prepare/r-betareg/lilac.yaml new file mode 100644 index 0000000000..db0f0acea8 --- /dev/null +++ b/prepare/r-betareg/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-flexmix +- r-formula +- r-lmtest +- r-modeltools +- r-sandwich +update_on: +- regex: betareg_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=betareg diff --git a/prepare/r-bezier/PKGBUILD b/prepare/r-bezier/PKGBUILD new file mode 100644 index 0000000000..0f84d00b13 --- /dev/null +++ b/prepare/r-bezier/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bezier +_pkgver=1.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Toolkit for Bezier Curves and Splines' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bezier/lilac.py b/prepare/r-bezier/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bezier/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bezier/lilac.yaml b/prepare/r-bezier/lilac.yaml new file mode 100644 index 0000000000..de5f0d8559 --- /dev/null +++ b/prepare/r-bezier/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: bezier_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bezier diff --git a/prepare/r-bgeecall/PKGBUILD b/prepare/r-bgeecall/PKGBUILD new file mode 100644 index 0000000000..49c106972d --- /dev/null +++ b/prepare/r-bgeecall/PKGBUILD @@ -0,0 +1,45 @@ +# system requirements: kallisto +# Maintainer: Guoyi Zhang + +_pkgname=BgeeCall +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automatic RNA-Seq present/absent gene expression calls generation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-biostrings + r-data.table + r-dplyr + r-genomicfeatures + r-jsonlite + r-rhdf5 + r-rslurm + r-rtracklayer + r-sjmisc + r-tximport +) +optdepends=( + r-annotationhub + r-httr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bgeecall/lilac.py b/prepare/r-bgeecall/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bgeecall/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bgeecall/lilac.yaml b/prepare/r-bgeecall/lilac.yaml new file mode 100644 index 0000000000..433809fd9e --- /dev/null +++ b/prepare/r-bgeecall/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-biostrings +- r-data.table +- r-dplyr +- r-genomicfeatures +- r-jsonlite +- r-rhdf5 +- r-rslurm +- r-rtracklayer +- r-sjmisc +- r-tximport +update_on: +- regex: BgeeCall_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BgeeCall diff --git a/prepare/r-bgeedb/PKGBUILD b/prepare/r-bgeedb/PKGBUILD new file mode 100644 index 0000000000..8534f1e966 --- /dev/null +++ b/prepare/r-bgeedb/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BgeeDB +_pkgver=2.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-curl + r-data.table + r-digest + r-dplyr + r-graph + r-r.utils + r-rcurl + r-rsqlite + r-tidyr + r-topgo +) +optdepends=( + r-biocstyle + r-knitr + r-markdown + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bgeedb/lilac.py b/prepare/r-bgeedb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bgeedb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bgeedb/lilac.yaml b/prepare/r-bgeedb/lilac.yaml new file mode 100644 index 0000000000..f8d79170e0 --- /dev/null +++ b/prepare/r-bgeedb/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-curl +- r-data.table +- r-digest +- r-dplyr +- r-graph +- r-r.utils +- r-rcurl +- r-rsqlite +- r-tidyr +- r-topgo +update_on: +- regex: BgeeDB_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BgeeDB diff --git a/prepare/r-bgmix/PKGBUILD b/prepare/r-bgmix/PKGBUILD new file mode 100644 index 0000000000..936c8bfc9a --- /dev/null +++ b/prepare/r-bgmix/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BGmix +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian models for differential gene expression' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bgmix/lilac.py b/prepare/r-bgmix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bgmix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bgmix/lilac.yaml b/prepare/r-bgmix/lilac.yaml new file mode 100644 index 0000000000..650ca8bb2a --- /dev/null +++ b/prepare/r-bgmix/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: BGmix_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BGmix diff --git a/prepare/r-bgx/PKGBUILD b/prepare/r-bgx/PKGBUILD new file mode 100644 index 0000000000..1ed47c7370 --- /dev/null +++ b/prepare/r-bgx/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bgx +_pkgver=1.60.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian Gene eXpression' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-biobase + r-gcrma + r-rcpp +) +optdepends=( + r-affydata + r-hgu95av2cdf +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bgx/lilac.py b/prepare/r-bgx/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bgx/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bgx/lilac.yaml b/prepare/r-bgx/lilac.yaml new file mode 100644 index 0000000000..013a7a178c --- /dev/null +++ b/prepare/r-bgx/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +- r-gcrma +- r-rcpp +update_on: +- regex: bgx_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bgx diff --git a/prepare/r-bhc/PKGBUILD b/prepare/r-bhc/PKGBUILD new file mode 100644 index 0000000000..ea1a2d5eff --- /dev/null +++ b/prepare/r-bhc/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BHC +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian Hierarchical Clustering' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bhc/lilac.py b/prepare/r-bhc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bhc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bhc/lilac.yaml b/prepare/r-bhc/lilac.yaml new file mode 100644 index 0000000000..045d520067 --- /dev/null +++ b/prepare/r-bhc/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: BHC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BHC diff --git a/prepare/r-biasedurn/PKGBUILD b/prepare/r-biasedurn/PKGBUILD new file mode 100644 index 0000000000..6bf01ab5bf --- /dev/null +++ b/prepare/r-biasedurn/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BiasedUrn +_pkgver=1.07 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Biased Urn Model Distributions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biasedurn/lilac.py b/prepare/r-biasedurn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biasedurn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biasedurn/lilac.yaml b/prepare/r-biasedurn/lilac.yaml new file mode 100644 index 0000000000..7a19856753 --- /dev/null +++ b/prepare/r-biasedurn/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: BiasedUrn_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=BiasedUrn diff --git a/prepare/r-bibitr/PKGBUILD b/prepare/r-bibitr/PKGBUILD new file mode 100644 index 0000000000..ee9807a7be --- /dev/null +++ b/prepare/r-bibitr/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: Java +# Maintainer: Guoyi Zhang + +_pkgname=BiBitR +_pkgver=0.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Wrapper for Java Implementation of BiBit' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-biclust + r-dendextend + r-randomcolor + r-viridis +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bibitr/lilac.py b/prepare/r-bibitr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bibitr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bibitr/lilac.yaml b/prepare/r-bibitr/lilac.yaml new file mode 100644 index 0000000000..2fe336a68a --- /dev/null +++ b/prepare/r-bibitr/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biclust +- r-dendextend +- r-randomcolor +- r-viridis +update_on: +- regex: BiBitR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=BiBitR diff --git a/prepare/r-bicare/PKGBUILD b/prepare/r-bicare/PKGBUILD new file mode 100644 index 0000000000..c241c459bd --- /dev/null +++ b/prepare/r-bicare/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BicARE +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Biclustering Analysis and Results Exploration' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-gseabase + r-multtest +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bicare/lilac.py b/prepare/r-bicare/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bicare/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bicare/lilac.yaml b/prepare/r-bicare/lilac.yaml new file mode 100644 index 0000000000..04617fc091 --- /dev/null +++ b/prepare/r-bicare/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-gseabase +- r-multtest +update_on: +- regex: BicARE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BicARE diff --git a/prepare/r-biclust/PKGBUILD b/prepare/r-biclust/PKGBUILD new file mode 100644 index 0000000000..f985949339 --- /dev/null +++ b/prepare/r-biclust/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biclust +_pkgver=2.0.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='BiCluster Algorithms' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-additivitytests + r-colorspace + r-flexclust + r-ggplot2 + r-tidyr +) +optdepends=( + r-isa2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biclust/lilac.py b/prepare/r-biclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biclust/lilac.yaml b/prepare/r-biclust/lilac.yaml new file mode 100644 index 0000000000..92bc6683d5 --- /dev/null +++ b/prepare/r-biclust/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-additivitytests +- r-colorspace +- r-flexclust +- r-ggplot2 +- r-tidyr +update_on: +- regex: biclust_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=biclust diff --git a/prepare/r-bifet/PKGBUILD b/prepare/r-bifet/PKGBUILD new file mode 100644 index 0000000000..9dbb096414 --- /dev/null +++ b/prepare/r-bifet/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BiFET +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bias-free Footprint Enrichment Test' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicranges + r-poibin +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bifet/lilac.py b/prepare/r-bifet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bifet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bifet/lilac.yaml b/prepare/r-bifet/lilac.yaml new file mode 100644 index 0000000000..75ccec09ac --- /dev/null +++ b/prepare/r-bifet/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-poibin +update_on: +- regex: BiFET_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiFET diff --git a/prepare/r-biganalytics/PKGBUILD b/prepare/r-biganalytics/PKGBUILD new file mode 100644 index 0000000000..fd13d1e59d --- /dev/null +++ b/prepare/r-biganalytics/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biganalytics +_pkgver=1.1.21 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Utilities for 'big.matrix' Objects from Package 'bigmemory'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-bh + r-biglm + r-bigmemory + r-foreach + r-rcpp +) +optdepends=( + r-methods +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biganalytics/lilac.py b/prepare/r-biganalytics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biganalytics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biganalytics/lilac.yaml b/prepare/r-biganalytics/lilac.yaml new file mode 100644 index 0000000000..9668c85c59 --- /dev/null +++ b/prepare/r-biganalytics/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-biglm +- r-bigmemory +- r-foreach +- r-rcpp +update_on: +- regex: biganalytics_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=biganalytics diff --git a/prepare/r-bigassertr/PKGBUILD b/prepare/r-bigassertr/PKGBUILD new file mode 100644 index 0000000000..b3d4f40abd --- /dev/null +++ b/prepare/r-bigassertr/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bigassertr +_pkgver=0.1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assertion and Message Functions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bigassertr/lilac.py b/prepare/r-bigassertr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bigassertr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bigassertr/lilac.yaml b/prepare/r-bigassertr/lilac.yaml new file mode 100644 index 0000000000..9daa407787 --- /dev/null +++ b/prepare/r-bigassertr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: bigassertr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bigassertr diff --git a/prepare/r-biggr/PKGBUILD b/prepare/r-biggr/PKGBUILD new file mode 100644 index 0000000000..bd81d074d1 --- /dev/null +++ b/prepare/r-biggr/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BiGGR +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Constraint based modeling in R using metabolic reconstruction databases' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-hyperdraw + r-hypergraph + r-lim + r-limsolve + r-rsbml + r-stringr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biggr/lilac.py b/prepare/r-biggr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biggr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biggr/lilac.yaml b/prepare/r-biggr/lilac.yaml new file mode 100644 index 0000000000..1bbffc35da --- /dev/null +++ b/prepare/r-biggr/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-hyperdraw +- r-hypergraph +- r-lim +- r-limsolve +- r-rsbml +- r-stringr +update_on: +- regex: BiGGR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiGGR diff --git a/prepare/r-biglm/PKGBUILD b/prepare/r-biglm/PKGBUILD new file mode 100644 index 0000000000..b3897d97e2 --- /dev/null +++ b/prepare/r-biglm/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biglm +_pkgver=0.9-2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bounded Memory Linear and Generalized Linear Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dbi +) +optdepends=( + r-leaps + r-rodbc + r-rsqlite +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biglm/lilac.py b/prepare/r-biglm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biglm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biglm/lilac.yaml b/prepare/r-biglm/lilac.yaml new file mode 100644 index 0000000000..fbb43e149c --- /dev/null +++ b/prepare/r-biglm/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dbi +update_on: +- regex: biglm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=biglm diff --git a/prepare/r-bigmelon/PKGBUILD b/prepare/r-bigmelon/PKGBUILD new file mode 100644 index 0000000000..1501b9a782 --- /dev/null +++ b/prepare/r-bigmelon/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bigmelon +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Illumina methylation array analysis for large experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-gdsfmt + r-geoquery + r-illuminaio + r-methylumi + r-minfi + r-watermelon +) +optdepends=( + r-biocgenerics + r-biocstyle + r-bumphunter + r-illuminahumanmethylation450kanno.ilmn12.hg19 + r-illuminahumanmethylationepicanno.ilm10b2.hg19 + r-minfidata + r-parallel + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bigmelon/lilac.py b/prepare/r-bigmelon/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bigmelon/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bigmelon/lilac.yaml b/prepare/r-bigmelon/lilac.yaml new file mode 100644 index 0000000000..a898978fde --- /dev/null +++ b/prepare/r-bigmelon/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-gdsfmt +- r-geoquery +- r-illuminaio +- r-methylumi +- r-minfi +- r-watermelon +update_on: +- regex: bigmelon_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bigmelon diff --git a/prepare/r-bigmemory.sri/PKGBUILD b/prepare/r-bigmemory.sri/PKGBUILD new file mode 100644 index 0000000000..683dcb6cd9 --- /dev/null +++ b/prepare/r-bigmemory.sri/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bigmemory.sri +_pkgver=0.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A shared resource interface for Bigmemory Project packages' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +optdepends=( + r-bigmemory + r-synchronicity +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bigmemory.sri/lilac.py b/prepare/r-bigmemory.sri/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bigmemory.sri/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bigmemory.sri/lilac.yaml b/prepare/r-bigmemory.sri/lilac.yaml new file mode 100644 index 0000000000..124ba8b60c --- /dev/null +++ b/prepare/r-bigmemory.sri/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: bigmemory.sri_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bigmemory.sri diff --git a/prepare/r-bigmemory/PKGBUILD b/prepare/r-bigmemory/PKGBUILD new file mode 100644 index 0000000000..e6ea8b3067 --- /dev/null +++ b/prepare/r-bigmemory/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bigmemory +_pkgver=4.5.36 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Manage Massive Matrices with Shared Memory and Memory-Mapped Files' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-bh + r-bigmemory.sri + r-rcpp +) +optdepends=( + r-biganalytics + r-bigtabulate + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bigmemory/lilac.py b/prepare/r-bigmemory/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bigmemory/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bigmemory/lilac.yaml b/prepare/r-bigmemory/lilac.yaml new file mode 100644 index 0000000000..8752438c8c --- /dev/null +++ b/prepare/r-bigmemory/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-bigmemory.sri +- r-rcpp +update_on: +- regex: bigmemory_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bigmemory diff --git a/prepare/r-bigparallelr/PKGBUILD b/prepare/r-bigparallelr/PKGBUILD new file mode 100644 index 0000000000..de6fa2d49a --- /dev/null +++ b/prepare/r-bigparallelr/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bigparallelr +_pkgver=0.3.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Easy Parallel Tools' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bigassertr + r-doparallel + r-flock + r-foreach + r-parallelly + r-rhpcblasctl +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bigparallelr/lilac.py b/prepare/r-bigparallelr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bigparallelr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bigparallelr/lilac.yaml b/prepare/r-bigparallelr/lilac.yaml new file mode 100644 index 0000000000..d7244a9b12 --- /dev/null +++ b/prepare/r-bigparallelr/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bigassertr +- r-doparallel +- r-flock +- r-foreach +- r-parallelly +- r-rhpcblasctl +update_on: +- regex: bigparallelr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bigparallelr diff --git a/prepare/r-bigpint/PKGBUILD b/prepare/r-bigpint/PKGBUILD new file mode 100644 index 0000000000..432d1800e3 --- /dev/null +++ b/prepare/r-bigpint/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bigPint +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Big multivariate data plotted interactively' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-delayedarray + r-dplyr + r-ggally + r-ggplot2 + r-gridextra + r-hexbin + r-hmisc + r-htmlwidgets + r-plotly + r-plyr + r-rcolorbrewer + r-reshape + r-shiny + r-shinycssloaders + r-shinydashboard + r-stringr + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-biocgenerics + r-data.table + r-edaseq + r-edger + r-gtools + r-knitr + r-matrixstats + r-rmarkdown + r-roxygen2 + r-runit + r-tibble +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bigpint/lilac.py b/prepare/r-bigpint/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bigpint/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bigpint/lilac.yaml b/prepare/r-bigpint/lilac.yaml new file mode 100644 index 0000000000..7afafc9f32 --- /dev/null +++ b/prepare/r-bigpint/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-delayedarray +- r-dplyr +- r-ggally +- r-ggplot2 +- r-gridextra +- r-hexbin +- r-hmisc +- r-htmlwidgets +- r-plotly +- r-plyr +- r-rcolorbrewer +- r-reshape +- r-shiny +- r-shinycssloaders +- r-shinydashboard +- r-stringr +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: bigPint_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bigPint diff --git a/prepare/r-bigrquery/PKGBUILD b/prepare/r-bigrquery/PKGBUILD new file mode 100644 index 0000000000..2c09aa25d5 --- /dev/null +++ b/prepare/r-bigrquery/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bigrquery +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="An Interface to Google's 'BigQuery' 'API'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-bit64 + r-curl + r-dbi + r-gargle + r-glue + r-httr + r-jsonlite + r-lifecycle + r-prettyunits + r-progress + r-rapidjsonr + r-rcpp + r-rlang + r-tibble +) +optdepends=( + r-blob + r-covr + r-dbitest + r-dbplyr + r-dplyr + r-hms + r-readr + r-sodium + r-testthat + r-withr + r-wk +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bigrquery/lilac.py b/prepare/r-bigrquery/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bigrquery/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bigrquery/lilac.yaml b/prepare/r-bigrquery/lilac.yaml new file mode 100644 index 0000000000..9561026231 --- /dev/null +++ b/prepare/r-bigrquery/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-bit64 +- r-curl +- r-dbi +- r-gargle +- r-glue +- r-httr +- r-jsonlite +- r-lifecycle +- r-prettyunits +- r-progress +- r-rapidjsonr +- r-rcpp +- r-rlang +- r-tibble +update_on: +- regex: bigrquery_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bigrquery diff --git a/prepare/r-bigstatsr/PKGBUILD b/prepare/r-bigstatsr/PKGBUILD new file mode 100644 index 0000000000..e439ce0b8f --- /dev/null +++ b/prepare/r-bigstatsr/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bigstatsr +_pkgver=1.5.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Tools for Filebacked Big Matrices' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bigassertr + r-bigparallelr + r-cowplot + r-foreach + r-ggplot2 + r-ps + r-rcpp + r-rcpparmadillo + r-rmio + r-rspectra + r-tibble +) +optdepends=( + r-biglasso + r-bigmemory + r-bigreadr + r-covr + r-data.table + r-dplyr + r-glmnet + r-hexbin + r-memuse + r-modelmetrics + r-ppcor + r-rhpcblasctl + r-spelling + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bigstatsr/lilac.py b/prepare/r-bigstatsr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bigstatsr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bigstatsr/lilac.yaml b/prepare/r-bigstatsr/lilac.yaml new file mode 100644 index 0000000000..b598ec2b2f --- /dev/null +++ b/prepare/r-bigstatsr/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bigassertr +- r-bigparallelr +- r-cowplot +- r-foreach +- r-ggplot2 +- r-ps +- r-rcpp +- r-rcpparmadillo +- r-rmio +- r-rspectra +- r-tibble +update_on: +- regex: bigstatsr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bigstatsr diff --git a/prepare/r-bindingsitefinder/PKGBUILD b/prepare/r-bindingsitefinder/PKGBUILD new file mode 100644 index 0000000000..5ac1d4bfc7 --- /dev/null +++ b/prepare/r-bindingsitefinder/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BindingSiteFinder +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Binding site defintion based on iCLIP data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-genomicranges + r-ggforce + r-ggplot2 + r-matrixstats + r-rtracklayer + r-s4vectors + r-tidyr +) +optdepends=( + r-biocstyle + r-complexheatmap + r-dplyr + r-forcats + r-genomeinfodb + r-genomicalignments + r-knitr + r-rmarkdown + r-scales + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bindingsitefinder/lilac.py b/prepare/r-bindingsitefinder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bindingsitefinder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bindingsitefinder/lilac.yaml b/prepare/r-bindingsitefinder/lilac.yaml new file mode 100644 index 0000000000..c14ba6ed50 --- /dev/null +++ b/prepare/r-bindingsitefinder/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-ggforce +- r-ggplot2 +- r-matrixstats +- r-rtracklayer +- r-s4vectors +- r-tidyr +update_on: +- regex: BindingSiteFinder_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BindingSiteFinder diff --git a/prepare/r-binom/PKGBUILD b/prepare/r-binom/PKGBUILD new file mode 100644 index 0000000000..8c19887390 --- /dev/null +++ b/prepare/r-binom/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=binom +_pkgver=1.1-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Binomial Confidence Intervals For Several Parameterizations' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-ggplot2 + r-lattice + r-polynom + r-tcltk +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-binom/lilac.py b/prepare/r-binom/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-binom/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-binom/lilac.yaml b/prepare/r-binom/lilac.yaml new file mode 100644 index 0000000000..62317a4107 --- /dev/null +++ b/prepare/r-binom/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: binom_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=binom diff --git a/prepare/r-binr/PKGBUILD b/prepare/r-binr/PKGBUILD new file mode 100644 index 0000000000..6f2bfe0d3c --- /dev/null +++ b/prepare/r-binr/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=binr +_pkgver=1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cut Numeric Values into Evenly Distributed Groups' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-binr/lilac.py b/prepare/r-binr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-binr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-binr/lilac.yaml b/prepare/r-binr/lilac.yaml new file mode 100644 index 0000000000..417de927c1 --- /dev/null +++ b/prepare/r-binr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: binr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=binr diff --git a/prepare/r-bioassayr/PKGBUILD b/prepare/r-bioassayr/PKGBUILD new file mode 100644 index 0000000000..f89737e027 --- /dev/null +++ b/prepare/r-bioassayr/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bioassayR +_pkgver=1.32.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cross-target analysis of small molecule bioactivity' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-chemminer + r-dbi + r-rjson + r-rsqlite + r-xml +) +optdepends=( + r-biocstyle + r-biomart + r-cellhts2 + r-ggplot2 + r-knitcitations + r-knitr + r-knitrbootstrap + r-rcurl + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bioassayr/lilac.py b/prepare/r-bioassayr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bioassayr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bioassayr/lilac.yaml b/prepare/r-bioassayr/lilac.yaml new file mode 100644 index 0000000000..c74431045e --- /dev/null +++ b/prepare/r-bioassayr/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-chemminer +- r-dbi +- r-rjson +- r-rsqlite +- r-xml +update_on: +- regex: bioassayR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bioassayR diff --git a/prepare/r-biobase/PKGBUILD b/prepare/r-biobase/PKGBUILD new file mode 100644 index 0000000000..2302e084f6 --- /dev/null +++ b/prepare/r-biobase/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Biobase +_pkgver=2.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Biobase: Base functions for Bioconductor' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics +) +optdepends=( + r-all + r-golubesets + r-runit + r-tkwidgets + r-tools +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biobase/lilac.py b/prepare/r-biobase/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biobase/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biobase/lilac.yaml b/prepare/r-biobase/lilac.yaml new file mode 100644 index 0000000000..3295171afd --- /dev/null +++ b/prepare/r-biobase/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +update_on: +- regex: Biobase_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Biobase diff --git a/prepare/r-biobroom/PKGBUILD b/prepare/r-biobroom/PKGBUILD new file mode 100644 index 0000000000..ded2e1c71e --- /dev/null +++ b/prepare/r-biobroom/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biobroom +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Turn Bioconductor objects into tidy data frames' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-broom + r-dplyr + r-tidyr +) +optdepends=( + r-airway + r-data.table + r-deseq2 + r-edger + r-genomicranges + r-ggplot2 + r-knitr + r-limma + r-magrittr + r-msnbase + r-plyr + r-qvalue + r-rmarkdown + r-summarizedexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biobroom/lilac.py b/prepare/r-biobroom/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biobroom/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biobroom/lilac.yaml b/prepare/r-biobroom/lilac.yaml new file mode 100644 index 0000000000..a1d9b98d92 --- /dev/null +++ b/prepare/r-biobroom/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-broom +- r-dplyr +- r-tidyr +update_on: +- regex: biobroom_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biobroom diff --git a/prepare/r-biobtreer/PKGBUILD b/prepare/r-biobtreer/PKGBUILD new file mode 100644 index 0000000000..7cfb17cf06 --- /dev/null +++ b/prepare/r-biobtreer/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biobtreeR +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Using biobtree tool from R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-httpuv + r-httr + r-jsonlite + r-stringi +) +optdepends=( + r-biocstyle + r-knitr + r-markdown + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biobtreer/lilac.py b/prepare/r-biobtreer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biobtreer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biobtreer/lilac.yaml b/prepare/r-biobtreer/lilac.yaml new file mode 100644 index 0000000000..ab0f967c39 --- /dev/null +++ b/prepare/r-biobtreer/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-httpuv +- r-httr +- r-jsonlite +- r-stringi +update_on: +- regex: biobtreeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biobtreeR diff --git a/prepare/r-biocancer/PKGBUILD b/prepare/r-biocancer/PKGBUILD new file mode 100644 index 0000000000..7e3f1f0114 --- /dev/null +++ b/prepare/r-biocancer/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bioCancer +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive Multi-Omics Cancers Data Visualization and Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-algdesign + r-annotationdbi + r-biobase + r-cgdsr + r-clusterprofiler + r-diagrammer + r-dose + r-dplyr + r-dt + r-genetclassifier + r-go.db + r-htmlwidgets + r-import + r-org.bt.eg.db + r-org.hs.eg.db + r-plyr + r-radiant.data + r-reactome.db + r-reactomepa + r-shiny + r-shinythemes + r-tibble + r-visnetwork + r-xml +) +optdepends=( + r-biocstyle + r-knitr + r-prettydoc + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocancer/lilac.py b/prepare/r-biocancer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocancer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocancer/lilac.yaml b/prepare/r-biocancer/lilac.yaml new file mode 100644 index 0000000000..fbcd7fd465 --- /dev/null +++ b/prepare/r-biocancer/lilac.yaml @@ -0,0 +1,33 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-algdesign +- r-annotationdbi +- r-biobase +- r-cgdsr +- r-clusterprofiler +- r-diagrammer +- r-dose +- r-dplyr +- r-dt +- r-genetclassifier +- r-go.db +- r-htmlwidgets +- r-import +- r-org.bt.eg.db +- r-org.hs.eg.db +- r-plyr +- r-radiant.data +- r-reactome.db +- r-reactomepa +- r-shiny +- r-shinythemes +- r-tibble +- r-visnetwork +- r-xml +update_on: +- regex: bioCancer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bioCancer diff --git a/prepare/r-bioccheck/PKGBUILD b/prepare/r-bioccheck/PKGBUILD new file mode 100644 index 0000000000..7c1849d7cf --- /dev/null +++ b/prepare/r-bioccheck/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BiocCheck +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bioconductor-specific package checks' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocmanager + r-biocviews + r-graph + r-httr + r-knitr + r-optparse + r-stringdist +) +optdepends=( + r-biobase + r-biocgenerics + r-biocstyle + r-codetoolsbioc + r-devtools + r-rjsonio + r-rmarkdown + r-runit + r-usethis +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bioccheck/lilac.py b/prepare/r-bioccheck/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bioccheck/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bioccheck/lilac.yaml b/prepare/r-bioccheck/lilac.yaml new file mode 100644 index 0000000000..1d90bf0c56 --- /dev/null +++ b/prepare/r-bioccheck/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocmanager +- r-biocviews +- r-graph +- r-httr +- r-knitr +- r-optparse +- r-stringdist +update_on: +- regex: BiocCheck_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiocCheck diff --git a/prepare/r-biocdockermanager/PKGBUILD b/prepare/r-biocdockermanager/PKGBUILD new file mode 100644 index 0000000000..bf549f772a --- /dev/null +++ b/prepare/r-biocdockermanager/PKGBUILD @@ -0,0 +1,38 @@ +# system requirements: docker +# Maintainer: Guoyi Zhang + +_pkgname=BiocDockerManager +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Access Bioconductor docker images' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-dplyr + r-httr + r-memoise + r-readr + r-whisker +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocdockermanager/lilac.py b/prepare/r-biocdockermanager/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocdockermanager/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocdockermanager/lilac.yaml b/prepare/r-biocdockermanager/lilac.yaml new file mode 100644 index 0000000000..a0896dc03c --- /dev/null +++ b/prepare/r-biocdockermanager/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-httr +- r-memoise +- r-readr +- r-whisker +update_on: +- regex: BiocDockerManager_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiocDockerManager diff --git a/prepare/r-biocfilecache/PKGBUILD b/prepare/r-biocfilecache/PKGBUILD new file mode 100644 index 0000000000..c46e08e6ab --- /dev/null +++ b/prepare/r-biocfilecache/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BiocFileCache +_pkgver=2.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Manage Files Across Sessions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-curl + r-dbi + r-dbplyr + r-dplyr + r-filelock + r-httr + r-rappdirs + r-rsqlite +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-rtracklayer + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocfilecache/lilac.py b/prepare/r-biocfilecache/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocfilecache/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocfilecache/lilac.yaml b/prepare/r-biocfilecache/lilac.yaml new file mode 100644 index 0000000000..96eb932715 --- /dev/null +++ b/prepare/r-biocfilecache/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-dbi +- r-dbplyr +- r-dplyr +- r-filelock +- r-httr +- r-rappdirs +- r-rsqlite +update_on: +- regex: BiocFileCache_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiocFileCache diff --git a/prepare/r-biocgenerics/PKGBUILD b/prepare/r-biocgenerics/PKGBUILD new file mode 100644 index 0000000000..c92d5d2448 --- /dev/null +++ b/prepare/r-biocgenerics/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BiocGenerics +_pkgver=0.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='S4 generic functions used in Bioconductor' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-affy + r-affyplm + r-annotate + r-annotationdbi + r-biobase + r-biostrings + r-delayedarray + r-deseq2 + r-flowclust + r-genomicranges + r-iranges + r-msnbase + r-rsamtools + r-runit + r-s4vectors +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocgenerics/lilac.py b/prepare/r-biocgenerics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocgenerics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocgenerics/lilac.yaml b/prepare/r-biocgenerics/lilac.yaml new file mode 100644 index 0000000000..b74b3a2e27 --- /dev/null +++ b/prepare/r-biocgenerics/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: BiocGenerics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiocGenerics diff --git a/prepare/r-biocgraph/PKGBUILD b/prepare/r-biocgraph/PKGBUILD new file mode 100644 index 0000000000..fa620dcb01 --- /dev/null +++ b/prepare/r-biocgraph/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biocGraph +_pkgver=1.56.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Graph examples and use cases in Bioinformatics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-geneplotter + r-graph + r-rgraphviz +) +optdepends=( + r-fibroeset + r-geneplotter + r-hgu95av2.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocgraph/lilac.py b/prepare/r-biocgraph/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocgraph/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocgraph/lilac.yaml b/prepare/r-biocgraph/lilac.yaml new file mode 100644 index 0000000000..1c64b6661b --- /dev/null +++ b/prepare/r-biocgraph/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-geneplotter +- r-graph +- r-rgraphviz +update_on: +- regex: biocGraph_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biocGraph diff --git a/prepare/r-biocio/PKGBUILD b/prepare/r-biocio/PKGBUILD new file mode 100644 index 0000000000..6b6f5ca40b --- /dev/null +++ b/prepare/r-biocio/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BiocIO +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Standard Input and Output for Bioconductor Packages' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocio/lilac.py b/prepare/r-biocio/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocio/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocio/lilac.yaml b/prepare/r-biocio/lilac.yaml new file mode 100644 index 0000000000..fd24ae7649 --- /dev/null +++ b/prepare/r-biocio/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-s4vectors +update_on: +- regex: BiocIO_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiocIO diff --git a/prepare/r-biocmanager/PKGBUILD b/prepare/r-biocmanager/PKGBUILD new file mode 100644 index 0000000000..eb11359398 --- /dev/null +++ b/prepare/r-biocmanager/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BiocManager +_pkgver=1.30.16 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Access the Bioconductor Project Package Repository' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-biocversion + r-curl + r-knitr + r-remotes + r-rmarkdown + r-testthat + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocmanager/lilac.py b/prepare/r-biocmanager/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocmanager/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocmanager/lilac.yaml b/prepare/r-biocmanager/lilac.yaml new file mode 100644 index 0000000000..b570982228 --- /dev/null +++ b/prepare/r-biocmanager/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: BiocManager_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=BiocManager diff --git a/prepare/r-biocneighbors/PKGBUILD b/prepare/r-biocneighbors/PKGBUILD new file mode 100644 index 0000000000..632f461852 --- /dev/null +++ b/prepare/r-biocneighbors/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=BiocNeighbors +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Nearest Neighbor Detection for Bioconductor Packages' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-rcpp + r-rcpphnsw + r-s4vectors +) +optdepends=( + r-biocstyle + r-fnn + r-knitr + r-rcppannoy + r-rcpphnsw + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocneighbors/lilac.py b/prepare/r-biocneighbors/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocneighbors/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocneighbors/lilac.yaml b/prepare/r-biocneighbors/lilac.yaml new file mode 100644 index 0000000000..4c3ef848c6 --- /dev/null +++ b/prepare/r-biocneighbors/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-rcpp +- r-rcpphnsw +- r-s4vectors +update_on: +- regex: BiocNeighbors_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiocNeighbors diff --git a/prepare/r-bioconcotk/PKGBUILD b/prepare/r-bioconcotk/PKGBUILD new file mode 100644 index 0000000000..9cf414c629 --- /dev/null +++ b/prepare/r-bioconcotk/PKGBUILD @@ -0,0 +1,71 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BiocOncoTK +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bioconductor components for general cancer genomics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bigrquery + r-car + r-complexheatmap + r-curatedtcgadata + r-dbi + r-dplyr + r-dt + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggpubr + r-graph + r-httr + r-iranges + r-magrittr + r-plyr + r-rgraphviz + r-rjson + r-s4vectors + r-scales + r-shiny + r-summarizedexperiment +) +optdepends=( + r-annotationdbi + r-biobase + r-biocfilecache + r-biocstyle + r-dbplyr + r-ensdb.hsapiens.v75 + r-fdb.infiniummethylation.hg19 + r-genomeinfodb + r-knitr + r-multiassayexperiment + r-ontologyplot + r-ontoproc + r-org.hs.eg.db + r-pogos + r-reshape2 + r-restfulse + r-rhdf5client + r-rmarkdown + r-testthat + r-txdb.hsapiens.ucsc.hg18.knowngene + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bioconcotk/lilac.py b/prepare/r-bioconcotk/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bioconcotk/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bioconcotk/lilac.yaml b/prepare/r-bioconcotk/lilac.yaml new file mode 100644 index 0000000000..312aa1331e --- /dev/null +++ b/prepare/r-bioconcotk/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bigrquery +- r-car +- r-complexheatmap +- r-curatedtcgadata +- r-dbi +- r-dplyr +- r-dt +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-ggpubr +- r-graph +- r-httr +- r-iranges +- r-magrittr +- r-plyr +- r-rgraphviz +- r-rjson +- r-s4vectors +- r-scales +- r-shiny +- r-summarizedexperiment +update_on: +- regex: BiocOncoTK_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiocOncoTK diff --git a/prepare/r-biocor/PKGBUILD b/prepare/r-biocor/PKGBUILD new file mode 100644 index 0000000000..da91bca2f0 --- /dev/null +++ b/prepare/r-biocor/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BioCor +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functional similarities' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocparallel + r-gseabase +) +optdepends=( + r-airway + r-biocstyle + r-boot + r-deseq2 + r-gosemsim + r-hmisc + r-knitr + r-org.hs.eg.db + r-reactome.db + r-rmarkdown + r-spelling + r-targetscan.hs.eg.db + r-testthat + r-wgcna +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocor/lilac.py b/prepare/r-biocor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocor/lilac.yaml b/prepare/r-biocor/lilac.yaml new file mode 100644 index 0000000000..b69f7a67bb --- /dev/null +++ b/prepare/r-biocor/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-gseabase +update_on: +- regex: BioCor_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BioCor diff --git a/prepare/r-biocparallel/PKGBUILD b/prepare/r-biocparallel/PKGBUILD new file mode 100644 index 0000000000..1a1702201a --- /dev/null +++ b/prepare/r-biocparallel/PKGBUILD @@ -0,0 +1,52 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=BiocParallel +_pkgver=1.28.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bioconductor facilities for parallel evaluation' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bh + r-futile.logger + r-snow +) +optdepends=( + r-batchjobs + r-batchtools + r-bbmisc + r-biocgenerics + r-biocstyle + r-codetools + r-data.table + r-doparallel + r-foreach + r-genomicalignments + r-genomicranges + r-knitr + r-rmpi + r-rnaseqdata.hnrnpc.bam.chr14 + r-rsamtools + r-runit + r-shortread + r-tools + r-txdb.hsapiens.ucsc.hg19.knowngene + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocparallel/lilac.py b/prepare/r-biocparallel/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocparallel/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocparallel/lilac.yaml b/prepare/r-biocparallel/lilac.yaml new file mode 100644 index 0000000000..4c076999eb --- /dev/null +++ b/prepare/r-biocparallel/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-futile.logger +- r-snow +update_on: +- regex: BiocParallel_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiocParallel diff --git a/prepare/r-biocpkgtools/PKGBUILD b/prepare/r-biocpkgtools/PKGBUILD new file mode 100644 index 0000000000..cd5d774d69 --- /dev/null +++ b/prepare/r-biocpkgtools/PKGBUILD @@ -0,0 +1,64 @@ +# system requirements: mailsend-go +# Maintainer: Guoyi Zhang + +_pkgname=BiocPkgTools +_pkgver=1.12.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Collection of simple tools for learning about Bioc Packages' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocfilecache + r-biocmanager + r-biocviews + r-dplyr + r-dt + r-gh + r-graph + r-htmltools + r-htmlwidgets + r-httr + r-igraph + r-jsonlite + r-magrittr + r-rbgl + r-readr + r-rlang + r-rvest + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-xml2 +) +optdepends=( + r-biocstyle + r-blastula + r-clipr + r-diagrammer + r-kableextra + r-knitr + r-rmarkdown + r-snowballc + r-summarizedexperiment + r-testthat + r-tm + r-visnetwork +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocpkgtools/lilac.py b/prepare/r-biocpkgtools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocpkgtools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocpkgtools/lilac.yaml b/prepare/r-biocpkgtools/lilac.yaml new file mode 100644 index 0000000000..1aa5287c50 --- /dev/null +++ b/prepare/r-biocpkgtools/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-biocmanager +- r-biocviews +- r-dplyr +- r-dt +- r-gh +- r-graph +- r-htmltools +- r-htmlwidgets +- r-httr +- r-igraph +- r-jsonlite +- r-magrittr +- r-rbgl +- r-readr +- r-rlang +- r-rvest +- r-stringr +- r-tibble +- r-tidyr +- r-tidyselect +- r-xml2 +update_on: +- regex: BiocPkgTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiocPkgTools diff --git a/prepare/r-biocset/PKGBUILD b/prepare/r-biocset/PKGBUILD new file mode 100644 index 0000000000..f9e67ea6ba --- /dev/null +++ b/prepare/r-biocset/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BiocSet +_pkgver=1.8.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Representing Different Biological Sets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biocio + r-dplyr + r-keggrest + r-ontologyindex + r-plyr + r-rlang + r-s4vectors + r-tibble + r-tidyr +) +optdepends=( + r-airway + r-biocfilecache + r-biocstyle + r-deseq2 + r-go.db + r-gseabase + r-knitr + r-limma + r-org.hs.eg.db + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocset/lilac.py b/prepare/r-biocset/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocset/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocset/lilac.yaml b/prepare/r-biocset/lilac.yaml new file mode 100644 index 0000000000..70c97cbbda --- /dev/null +++ b/prepare/r-biocset/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocio +- r-dplyr +- r-keggrest +- r-ontologyindex +- r-plyr +- r-rlang +- r-s4vectors +- r-tibble +- r-tidyr +update_on: +- regex: BiocSet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiocSet diff --git a/prepare/r-biocsingular/PKGBUILD b/prepare/r-biocsingular/PKGBUILD new file mode 100644 index 0000000000..2393a39ece --- /dev/null +++ b/prepare/r-biocsingular/PKGBUILD @@ -0,0 +1,43 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=BiocSingular +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Singular Value Decomposition for Bioconductor Packages' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-beachmat + r-biocgenerics + r-biocparallel + r-delayedarray + r-irlba + r-rcpp + r-rsvd + r-s4vectors + r-scaledmatrix +) +optdepends=( + r-biocstyle + r-knitr + r-residualmatrix + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocsingular/lilac.py b/prepare/r-biocsingular/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocsingular/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocsingular/lilac.yaml b/prepare/r-biocsingular/lilac.yaml new file mode 100644 index 0000000000..8e5731b081 --- /dev/null +++ b/prepare/r-biocsingular/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beachmat +- r-biocgenerics +- r-biocparallel +- r-delayedarray +- r-irlba +- r-rcpp +- r-rsvd +- r-s4vectors +- r-scaledmatrix +update_on: +- regex: BiocSingular_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiocSingular diff --git a/prepare/r-biocsklearn/PKGBUILD b/prepare/r-biocsklearn/PKGBUILD new file mode 100644 index 0000000000..19a3d9246b --- /dev/null +++ b/prepare/r-biocsklearn/PKGBUILD @@ -0,0 +1,39 @@ +# system requirements: python (>= 2.7), sklearn, numpy, pandas, h5py +# Maintainer: Guoyi Zhang + +_pkgname=BiocSklearn +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='interface to python sklearn via Rstudio reticulate' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-basilisk + r-knitr + r-rcpp + r-reticulate + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-hdf5array + r-restfulse + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocsklearn/lilac.py b/prepare/r-biocsklearn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocsklearn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocsklearn/lilac.yaml b/prepare/r-biocsklearn/lilac.yaml new file mode 100644 index 0000000000..2e151fb5f8 --- /dev/null +++ b/prepare/r-biocsklearn/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-basilisk +- r-knitr +- r-rcpp +- r-reticulate +- r-summarizedexperiment +update_on: +- regex: BiocSklearn_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiocSklearn diff --git a/prepare/r-biocstyle/PKGBUILD b/prepare/r-biocstyle/PKGBUILD new file mode 100644 index 0000000000..7b01e7d085 --- /dev/null +++ b/prepare/r-biocstyle/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BiocStyle +_pkgver=2.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Standard styles for vignettes and other Bioconductor documents' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocmanager + r-bookdown + r-knitr + r-rmarkdown + r-yaml +) +optdepends=( + r-biocgenerics + r-htmltools + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocstyle/lilac.py b/prepare/r-biocstyle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocstyle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocstyle/lilac.yaml b/prepare/r-biocstyle/lilac.yaml new file mode 100644 index 0000000000..ec257d44aa --- /dev/null +++ b/prepare/r-biocstyle/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocmanager +- r-bookdown +- r-knitr +- r-rmarkdown +- r-yaml +update_on: +- regex: BiocStyle_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiocStyle diff --git a/prepare/r-biocthis/PKGBUILD b/prepare/r-biocthis/PKGBUILD new file mode 100644 index 0000000000..73beb536e8 --- /dev/null +++ b/prepare/r-biocthis/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biocthis +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automate package and project setup for Bioconductor packages' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocmanager + r-fs + r-glue + r-rlang + r-styler + r-usethis +) +optdepends=( + r-biocstyle + r-covr + r-devtools + r-knitr + r-pkgdown + r-refmanager + r-rmarkdown + r-sessioninfo + r-testthat + r-utils +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocthis/lilac.py b/prepare/r-biocthis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocthis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocthis/lilac.yaml b/prepare/r-biocthis/lilac.yaml new file mode 100644 index 0000000000..a1ee1e8df1 --- /dev/null +++ b/prepare/r-biocthis/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocmanager +- r-fs +- r-glue +- r-rlang +- r-styler +- r-usethis +update_on: +- regex: biocthis_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biocthis diff --git a/prepare/r-biocversion/PKGBUILD b/prepare/r-biocversion/PKGBUILD new file mode 100644 index 0000000000..12563eac89 --- /dev/null +++ b/prepare/r-biocversion/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BiocVersion +_pkgver=3.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Set the appropriate version of Bioconductor packages' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocversion/lilac.py b/prepare/r-biocversion/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocversion/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocversion/lilac.yaml b/prepare/r-biocversion/lilac.yaml new file mode 100644 index 0000000000..5761d51703 --- /dev/null +++ b/prepare/r-biocversion/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: BiocVersion_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiocVersion diff --git a/prepare/r-biocviews/PKGBUILD b/prepare/r-biocviews/PKGBUILD new file mode 100644 index 0000000000..8d0c5f676b --- /dev/null +++ b/prepare/r-biocviews/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biocViews +_pkgver=1.62.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Categorized views of R package repositories' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocmanager + r-graph + r-rbgl + r-rcurl + r-runit + r-xml +) +optdepends=( + r-biocgenerics + r-commonmark + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocviews/lilac.py b/prepare/r-biocviews/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocviews/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocviews/lilac.yaml b/prepare/r-biocviews/lilac.yaml new file mode 100644 index 0000000000..1b18bf342f --- /dev/null +++ b/prepare/r-biocviews/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocmanager +- r-graph +- r-rbgl +- r-rcurl +- r-runit +- r-xml +update_on: +- regex: biocViews_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biocViews diff --git a/prepare/r-biocworkflowtools/PKGBUILD b/prepare/r-biocworkflowtools/PKGBUILD new file mode 100644 index 0000000000..88cf3dc73f --- /dev/null +++ b/prepare/r-biocworkflowtools/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BiocWorkflowTools +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools to aid the development of Bioconductor Workflow packages' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocstyle + r-bookdown + r-git2r + r-httr + r-knitr + r-rmarkdown + r-rstudioapi + r-stringr + r-usethis +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biocworkflowtools/lilac.py b/prepare/r-biocworkflowtools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biocworkflowtools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biocworkflowtools/lilac.yaml b/prepare/r-biocworkflowtools/lilac.yaml new file mode 100644 index 0000000000..e54fcc6c79 --- /dev/null +++ b/prepare/r-biocworkflowtools/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocstyle +- r-bookdown +- r-git2r +- r-httr +- r-knitr +- r-rmarkdown +- r-rstudioapi +- r-stringr +- r-usethis +update_on: +- regex: BiocWorkflowTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiocWorkflowTools diff --git a/prepare/r-biodb/PKGBUILD b/prepare/r-biodb/PKGBUILD new file mode 100644 index 0000000000..08ff6b9b79 --- /dev/null +++ b/prepare/r-biodb/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biodb +_pkgver=1.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='biodb, a library and a development framework for connecting to chemical and biological databases' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-biocfilecache + r-chk + r-jsonlite + r-lgr + r-lifecycle + r-openssl + r-plyr + r-progress + r-r6 + r-rappdirs + r-rcpp + r-rcurl + r-rsqlite + r-stringr + r-testthat + r-withr + r-xml + r-yaml +) +optdepends=( + r-biocstyle + r-covr + r-devtools + r-git2r + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat + r-xml2 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biodb/lilac.py b/prepare/r-biodb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biodb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biodb/lilac.yaml b/prepare/r-biodb/lilac.yaml new file mode 100644 index 0000000000..40357186d4 --- /dev/null +++ b/prepare/r-biodb/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-chk +- r-jsonlite +- r-lgr +- r-lifecycle +- r-openssl +- r-plyr +- r-progress +- r-r6 +- r-rappdirs +- r-rcpp +- r-rcurl +- r-rsqlite +- r-stringr +- r-testthat +- r-withr +- r-xml +- r-yaml +update_on: +- regex: biodb_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biodb diff --git a/prepare/r-biodbchebi/PKGBUILD b/prepare/r-biodbchebi/PKGBUILD new file mode 100644 index 0000000000..c4346dd4e4 --- /dev/null +++ b/prepare/r-biodbchebi/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biodbChebi +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='biodbChebi, a library for connecting to the ChEBI Database' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-biodb + r-r6 +) +optdepends=( + r-biocstyle + r-devtools + r-knitr + r-lgr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biodbchebi/lilac.py b/prepare/r-biodbchebi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biodbchebi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biodbchebi/lilac.yaml b/prepare/r-biodbchebi/lilac.yaml new file mode 100644 index 0000000000..b87ed3181b --- /dev/null +++ b/prepare/r-biodbchebi/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biodb +- r-r6 +update_on: +- regex: biodbChebi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biodbChebi diff --git a/prepare/r-biodbhmdb/PKGBUILD b/prepare/r-biodbhmdb/PKGBUILD new file mode 100644 index 0000000000..61026eeef4 --- /dev/null +++ b/prepare/r-biodbhmdb/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biodbHmdb +_pkgver=1.0.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='biodbHmdb, a library for connecting to the HMDB Database' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-biodb + r-r6 + r-rcpp + r-testthat +) +optdepends=( + r-biocstyle + r-covr + r-devtools + r-knitr + r-lgr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biodbhmdb/lilac.py b/prepare/r-biodbhmdb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biodbhmdb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biodbhmdb/lilac.yaml b/prepare/r-biodbhmdb/lilac.yaml new file mode 100644 index 0000000000..f660d2d4f7 --- /dev/null +++ b/prepare/r-biodbhmdb/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biodb +- r-r6 +- r-rcpp +- r-testthat +update_on: +- regex: biodbHmdb_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biodbHmdb diff --git a/prepare/r-biodbkegg/PKGBUILD b/prepare/r-biodbkegg/PKGBUILD new file mode 100644 index 0000000000..66fd1d2f86 --- /dev/null +++ b/prepare/r-biodbkegg/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biodbKegg +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='biodbKegg, a library for connecting to the KEGG Database' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-biodb + r-chk + r-lifecycle + r-r6 +) +optdepends=( + r-biocstyle + r-devtools + r-igraph + r-knitr + r-lgr + r-magick + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biodbkegg/lilac.py b/prepare/r-biodbkegg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biodbkegg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biodbkegg/lilac.yaml b/prepare/r-biodbkegg/lilac.yaml new file mode 100644 index 0000000000..c83a79e934 --- /dev/null +++ b/prepare/r-biodbkegg/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biodb +- r-chk +- r-lifecycle +- r-r6 +update_on: +- regex: biodbKegg_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biodbKegg diff --git a/prepare/r-biodblipidmaps/PKGBUILD b/prepare/r-biodblipidmaps/PKGBUILD new file mode 100644 index 0000000000..87f37b5a3d --- /dev/null +++ b/prepare/r-biodblipidmaps/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biodbLipidmaps +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='biodbLipidmaps, a library for connecting to the Lipidmaps Structure database' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-biodb + r-lifecycle + r-r6 +) +optdepends=( + r-biocstyle + r-covr + r-devtools + r-knitr + r-lgr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biodblipidmaps/lilac.py b/prepare/r-biodblipidmaps/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biodblipidmaps/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biodblipidmaps/lilac.yaml b/prepare/r-biodblipidmaps/lilac.yaml new file mode 100644 index 0000000000..dbece0bf74 --- /dev/null +++ b/prepare/r-biodblipidmaps/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biodb +- r-lifecycle +- r-r6 +update_on: +- regex: biodbLipidmaps_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biodbLipidmaps diff --git a/prepare/r-biodbuniprot/PKGBUILD b/prepare/r-biodbuniprot/PKGBUILD new file mode 100644 index 0000000000..72753fab81 --- /dev/null +++ b/prepare/r-biodbuniprot/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biodbUniprot +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='biodbUniprot, a library for connecting to the Uniprot Database' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-biodb + r-r6 +) +optdepends=( + r-biocstyle + r-covr + r-devtools + r-knitr + r-lgr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biodbuniprot/lilac.py b/prepare/r-biodbuniprot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biodbuniprot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biodbuniprot/lilac.yaml b/prepare/r-biodbuniprot/lilac.yaml new file mode 100644 index 0000000000..08e48224ae --- /dev/null +++ b/prepare/r-biodbuniprot/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biodb +- r-r6 +update_on: +- regex: biodbUniprot_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biodbUniprot diff --git a/prepare/r-biodist/PKGBUILD b/prepare/r-biodist/PKGBUILD new file mode 100644 index 0000000000..75b5e74ce3 --- /dev/null +++ b/prepare/r-biodist/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bioDist +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Different distance measures' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase +) +optdepends=( + r-locfit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biodist/lilac.py b/prepare/r-biodist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biodist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biodist/lilac.yaml b/prepare/r-biodist/lilac.yaml new file mode 100644 index 0000000000..cb8760494d --- /dev/null +++ b/prepare/r-biodist/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: bioDist_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bioDist diff --git a/prepare/r-biomart/PKGBUILD b/prepare/r-biomart/PKGBUILD new file mode 100644 index 0000000000..ae4340696d --- /dev/null +++ b/prepare/r-biomart/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biomaRt +_pkgver=2.50.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interface to BioMart databases (i.e. Ensembl)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biocfilecache + r-digest + r-httr + r-progress + r-rappdirs + r-stringr + r-xml + r-xml2 +) +optdepends=( + r-biocstyle + r-knitr + r-mockery + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biomart/lilac.py b/prepare/r-biomart/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biomart/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biomart/lilac.yaml b/prepare/r-biomart/lilac.yaml new file mode 100644 index 0000000000..dfa1e059ce --- /dev/null +++ b/prepare/r-biomart/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocfilecache +- r-digest +- r-httr +- r-progress +- r-rappdirs +- r-stringr +- r-xml +- r-xml2 +update_on: +- regex: biomaRt_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biomaRt diff --git a/prepare/r-biomartr/PKGBUILD b/prepare/r-biomartr/PKGBUILD new file mode 100644 index 0000000000..eca7c2a699 --- /dev/null +++ b/prepare/r-biomartr/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biomartr +_pkgver=0.9.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genomic Data Retrieval' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-biostrings + r-curl + r-data.table + r-downloader + r-dplyr + r-fs + r-httr + r-jsonlite + r-philentropy + r-purrr + r-r.utils + r-rcurl + r-readr + r-stringr + r-tibble + r-xml +) +optdepends=( + r-devtools + r-knitr + r-magrittr + r-rmarkdown + r-seqinr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biomartr/lilac.py b/prepare/r-biomartr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biomartr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biomartr/lilac.yaml b/prepare/r-biomartr/lilac.yaml new file mode 100644 index 0000000000..c4847d714d --- /dev/null +++ b/prepare/r-biomartr/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-biostrings +- r-curl +- r-data.table +- r-downloader +- r-dplyr +- r-fs +- r-httr +- r-jsonlite +- r-philentropy +- r-purrr +- r-r.utils +- r-rcurl +- r-readr +- r-stringr +- r-tibble +- r-xml +update_on: +- regex: biomartr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=biomartr diff --git a/prepare/r-biomformat/PKGBUILD b/prepare/r-biomformat/PKGBUILD new file mode 100644 index 0000000000..ffc6e50002 --- /dev/null +++ b/prepare/r-biomformat/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biomformat +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An interface package for the BIOM file format' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-jsonlite + r-plyr + r-rhdf5 +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biomformat/lilac.py b/prepare/r-biomformat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biomformat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biomformat/lilac.yaml b/prepare/r-biomformat/lilac.yaml new file mode 100644 index 0000000000..a504754852 --- /dev/null +++ b/prepare/r-biomformat/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-jsonlite +- r-plyr +- r-rhdf5 +update_on: +- regex: biomformat_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biomformat diff --git a/prepare/r-biomm/PKGBUILD b/prepare/r-biomm/PKGBUILD new file mode 100644 index 0000000000..95e30d6c87 --- /dev/null +++ b/prepare/r-biomm/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BioMM +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-cmplot + r-e1071 + r-ggplot2 + r-glmnet + r-imager + r-nsprcomp + r-precrec + r-ranger + r-rms + r-topgo + r-vioplot + r-xlsx +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biomm/lilac.py b/prepare/r-biomm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biomm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biomm/lilac.yaml b/prepare/r-biomm/lilac.yaml new file mode 100644 index 0000000000..826c63cbec --- /dev/null +++ b/prepare/r-biomm/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-cmplot +- r-e1071 +- r-ggplot2 +- r-glmnet +- r-imager +- r-nsprcomp +- r-precrec +- r-ranger +- r-rms +- r-topgo +- r-vioplot +- r-xlsx +update_on: +- regex: BioMM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BioMM diff --git a/prepare/r-biomvcclass/PKGBUILD b/prepare/r-biomvcclass/PKGBUILD new file mode 100644 index 0000000000..5339d29879 --- /dev/null +++ b/prepare/r-biomvcclass/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BioMVCClass +_pkgver=1.62.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Model-View-Controller (MVC) Classes That Use Biobase' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-graph + r-mvcclass + r-rgraphviz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biomvcclass/lilac.py b/prepare/r-biomvcclass/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biomvcclass/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biomvcclass/lilac.yaml b/prepare/r-biomvcclass/lilac.yaml new file mode 100644 index 0000000000..9187fc44e9 --- /dev/null +++ b/prepare/r-biomvcclass/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-graph +- r-mvcclass +- r-rgraphviz +update_on: +- regex: BioMVCClass_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BioMVCClass diff --git a/prepare/r-biomvrcns/PKGBUILD b/prepare/r-biomvrcns/PKGBUILD new file mode 100644 index 0000000000..04d03083fd --- /dev/null +++ b/prepare/r-biomvrcns/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biomvRCNS +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Copy Number study and Segmentation for multivariate biological data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicranges + r-gviz + r-iranges + r-mvtnorm +) +optdepends=( + r-cluster + r-dynamictreecut + r-genomicfeatures + r-parallel + r-rsamtools + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biomvrcns/lilac.py b/prepare/r-biomvrcns/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biomvrcns/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biomvrcns/lilac.yaml b/prepare/r-biomvrcns/lilac.yaml new file mode 100644 index 0000000000..1e8b46cdb6 --- /dev/null +++ b/prepare/r-biomvrcns/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-gviz +- r-iranges +- r-mvtnorm +update_on: +- regex: biomvRCNS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biomvRCNS diff --git a/prepare/r-bionero/PKGBUILD b/prepare/r-bionero/PKGBUILD new file mode 100644 index 0000000000..5fbd87b87a --- /dev/null +++ b/prepare/r-bionero/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BioNERO +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Biological Network Reconstruction Omnibus' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-complexheatmap + r-deseq2 + r-dynamictreecut + r-genie3 + r-ggnetwork + r-ggnewscale + r-ggplot2 + r-ggpubr + r-igraph + r-intergraph + r-matrixstats + r-minet + r-netrep + r-networkd3 + r-rcolorbrewer + r-reshape2 + r-summarizedexperiment + r-sva + r-wgcna +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bionero/lilac.py b/prepare/r-bionero/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bionero/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bionero/lilac.yaml b/prepare/r-bionero/lilac.yaml new file mode 100644 index 0000000000..2ce2e60c71 --- /dev/null +++ b/prepare/r-bionero/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-complexheatmap +- r-deseq2 +- r-dynamictreecut +- r-genie3 +- r-ggnetwork +- r-ggnewscale +- r-ggplot2 +- r-ggpubr +- r-igraph +- r-intergraph +- r-matrixstats +- r-minet +- r-netrep +- r-networkd3 +- r-rcolorbrewer +- r-reshape2 +- r-summarizedexperiment +- r-sva +- r-wgcna +update_on: +- regex: BioNERO_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BioNERO diff --git a/prepare/r-bionet/PKGBUILD b/prepare/r-bionet/PKGBUILD new file mode 100644 index 0000000000..34087aa78a --- /dev/null +++ b/prepare/r-bionet/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BioNet +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Routines for the functional analysis of biological networks' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biobase + r-graph + r-igraph + r-rbgl +) +optdepends=( + r-all + r-dlbcl + r-genefilter + r-hgu95av2.db + r-impute + r-limma + r-rgl + r-xml + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bionet/lilac.py b/prepare/r-bionet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bionet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bionet/lilac.yaml b/prepare/r-bionet/lilac.yaml new file mode 100644 index 0000000000..69020da17b --- /dev/null +++ b/prepare/r-bionet/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-graph +- r-igraph +- r-rbgl +update_on: +- regex: BioNet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BioNet diff --git a/prepare/r-bionetstat/PKGBUILD b/prepare/r-bionetstat/PKGBUILD new file mode 100644 index 0000000000..1ee6fe7635 --- /dev/null +++ b/prepare/r-bionetstat/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BioNetStat +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Biological Network Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-dt + r-ggplot2 + r-hmisc + r-igraph + r-knitr + r-markdown + r-pathview + r-pheatmap + r-plyr + r-psych + r-rcolorbrewer + r-rjsonio + r-rmarkdown + r-shiny + r-shinybs + r-whisker + r-yaml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bionetstat/lilac.py b/prepare/r-bionetstat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bionetstat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bionetstat/lilac.yaml b/prepare/r-bionetstat/lilac.yaml new file mode 100644 index 0000000000..62fd917e07 --- /dev/null +++ b/prepare/r-bionetstat/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-dt +- r-ggplot2 +- r-hmisc +- r-igraph +- r-knitr +- r-markdown +- r-pathview +- r-pheatmap +- r-plyr +- r-psych +- r-rcolorbrewer +- r-rjsonio +- r-rmarkdown +- r-shiny +- r-shinybs +- r-whisker +- r-yaml +update_on: +- regex: BioNetStat_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BioNetStat diff --git a/prepare/r-bioplex/PKGBUILD b/prepare/r-bioplex/PKGBUILD new file mode 100644 index 0000000000..223c3c0f60 --- /dev/null +++ b/prepare/r-bioplex/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BioPlex +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R-side access to BioPlex protein-protein interaction data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocfilecache + r-geoquery + r-graph + r-summarizedexperiment +) +optdepends=( + r-annotationdbi + r-annotationhub + r-biocstyle + r-depmap + r-experimenthub + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bioplex/lilac.py b/prepare/r-bioplex/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bioplex/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bioplex/lilac.yaml b/prepare/r-bioplex/lilac.yaml new file mode 100644 index 0000000000..c0ca8cdd47 --- /dev/null +++ b/prepare/r-bioplex/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-geoquery +- r-graph +- r-summarizedexperiment +update_on: +- regex: BioPlex_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BioPlex diff --git a/prepare/r-bioqc/PKGBUILD b/prepare/r-bioqc/PKGBUILD new file mode 100644 index 0000000000..7e919dca58 --- /dev/null +++ b/prepare/r-bioqc/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BioQC +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detect tissue heterogeneity in expression profiles with gene sets' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-edger + r-rcpp +) +optdepends=( + r-covr + r-ggplot2 + r-gplots + r-gridextra + r-hgu133plus2.db + r-ineq + r-knitr + r-lattice + r-latticeextra + r-limma + r-org.hs.eg.db + r-plyr + r-rbenchmark + r-rcolorbrewer + r-reshape2 + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bioqc/lilac.py b/prepare/r-bioqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bioqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bioqc/lilac.yaml b/prepare/r-bioqc/lilac.yaml new file mode 100644 index 0000000000..940f866d4a --- /dev/null +++ b/prepare/r-bioqc/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-edger +- r-rcpp +update_on: +- regex: BioQC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BioQC diff --git a/prepare/r-biosigner/PKGBUILD b/prepare/r-biosigner/PKGBUILD new file mode 100644 index 0000000000..96d7658be3 --- /dev/null +++ b/prepare/r-biosigner/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biosigner +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Signature discovery from omics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CeCILL') +depends=( + r + r-biobase + r-e1071 + r-multidataset + r-randomforest + r-ropls +) +optdepends=( + r-biocgenerics + r-biocstyle + r-biomark + r-golubesets + r-hu6800.db + r-knitr + r-omicade4 + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biosigner/lilac.py b/prepare/r-biosigner/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biosigner/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biosigner/lilac.yaml b/prepare/r-biosigner/lilac.yaml new file mode 100644 index 0000000000..93529c3e28 --- /dev/null +++ b/prepare/r-biosigner/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-e1071 +- r-multidataset +- r-randomforest +- r-ropls +update_on: +- regex: biosigner_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biosigner diff --git a/prepare/r-biostrings/PKGBUILD b/prepare/r-biostrings/PKGBUILD new file mode 100644 index 0000000000..8f22b6d51c --- /dev/null +++ b/prepare/r-biostrings/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Biostrings +_pkgver=2.62.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Efficient manipulation of biological strings' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-crayon + r-genomeinfodb + r-iranges + r-s4vectors + r-xvector +) +optdepends=( + r-affy + r-affydata + r-bsgenome + r-bsgenome.celegans.ucsc.ce2 + r-bsgenome.dmelanogaster.ucsc.dm3 + r-bsgenome.hsapiens.ucsc.hg18 + r-drosophila2probe + r-genomicfeatures + r-hgu133aprobe + r-hgu95av2cdf + r-hgu95av2probe + r-rmpi + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biostrings/lilac.py b/prepare/r-biostrings/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biostrings/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biostrings/lilac.yaml b/prepare/r-biostrings/lilac.yaml new file mode 100644 index 0000000000..a3e9437cf8 --- /dev/null +++ b/prepare/r-biostrings/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-crayon +- r-genomeinfodb +- r-iranges +- r-s4vectors +- r-xvector +update_on: +- regex: Biostrings_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Biostrings diff --git a/prepare/r-biotip/PKGBUILD b/prepare/r-biotip/PKGBUILD new file mode 100644 index 0000000000..8081d235f0 --- /dev/null +++ b/prepare/r-biotip/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BioTIP +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='BioTIP: An R package for characterization of Biological Tipping-Point' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicranges + r-hmisc + r-igraph + r-psych + r-stringr +) +optdepends=( + r-base + r-ggplot2 + r-knitr + r-markdown + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biotip/lilac.py b/prepare/r-biotip/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biotip/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biotip/lilac.yaml b/prepare/r-biotip/lilac.yaml new file mode 100644 index 0000000000..35807564f2 --- /dev/null +++ b/prepare/r-biotip/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-hmisc +- r-igraph +- r-psych +- r-stringr +update_on: +- regex: BioTIP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BioTIP diff --git a/prepare/r-biotmle/PKGBUILD b/prepare/r-biotmle/PKGBUILD new file mode 100644 index 0000000000..2d1995d5ff --- /dev/null +++ b/prepare/r-biotmle/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biotmle +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Targeted Learning with Moderated Statistics for Biomarker Discovery' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-assertthat + r-biocgenerics + r-biocparallel + r-dplyr + r-drtmle + r-ggplot2 + r-ggsci + r-limma + r-s4vectors + r-summarizedexperiment + r-superheat + r-tibble +) +optdepends=( + r-arm + r-biocstyle + r-biotmledata + r-dbi + r-earth + r-knitr + r-matrix + r-ranger + r-rmarkdown + r-superlearner + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biotmle/lilac.py b/prepare/r-biotmle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biotmle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biotmle/lilac.yaml b/prepare/r-biotmle/lilac.yaml new file mode 100644 index 0000000000..95c1b329da --- /dev/null +++ b/prepare/r-biotmle/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biocgenerics +- r-biocparallel +- r-dplyr +- r-drtmle +- r-ggplot2 +- r-ggsci +- r-limma +- r-s4vectors +- r-summarizedexperiment +- r-superheat +- r-tibble +update_on: +- regex: biotmle_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biotmle diff --git a/prepare/r-biovizbase/PKGBUILD b/prepare/r-biovizbase/PKGBUILD new file mode 100644 index 0000000000..0f08f50f5b --- /dev/null +++ b/prepare/r-biovizbase/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biovizBase +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Basic graphic utilities for visualization of genomic data.' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-annotationfilter + r-biocgenerics + r-biostrings + r-dichromat + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-hmisc + r-iranges + r-rcolorbrewer + r-rlang + r-rsamtools + r-s4vectors + r-scales + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-bsgenome + r-bsgenome.hsapiens.ucsc.hg19 + r-ensdb.hsapiens.v75 + r-rtracklayer + r-runit + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biovizbase/lilac.py b/prepare/r-biovizbase/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biovizbase/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biovizbase/lilac.yaml b/prepare/r-biovizbase/lilac.yaml new file mode 100644 index 0000000000..017d961b5f --- /dev/null +++ b/prepare/r-biovizbase/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationfilter +- r-biocgenerics +- r-biostrings +- r-dichromat +- r-ensembldb +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-hmisc +- r-iranges +- r-rcolorbrewer +- r-rlang +- r-rsamtools +- r-s4vectors +- r-scales +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: biovizBase_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biovizBase diff --git a/prepare/r-birewire/PKGBUILD b/prepare/r-birewire/PKGBUILD new file mode 100644 index 0000000000..76d78a82d6 --- /dev/null +++ b/prepare/r-birewire/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BiRewire +_pkgver=3.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-igraph + r-slam + r-tsne +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-birewire/lilac.py b/prepare/r-birewire/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-birewire/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-birewire/lilac.yaml b/prepare/r-birewire/lilac.yaml new file mode 100644 index 0000000000..d33d6328fb --- /dev/null +++ b/prepare/r-birewire/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +- r-slam +- r-tsne +update_on: +- regex: BiRewire_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiRewire diff --git a/prepare/r-biscuiteer/PKGBUILD b/prepare/r-biscuiteer/PKGBUILD new file mode 100644 index 0000000000..73c7e41b62 --- /dev/null +++ b/prepare/r-biscuiteer/PKGBUILD @@ -0,0 +1,65 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biscuiteer +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Convenience Functions for Biscuit' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-biscuiteerdata + r-bsseq + r-data.table + r-delayedmatrixstats + r-dmrseq + r-genomeinfodb + r-genomicranges + r-gtools + r-hdf5array + r-homo.sapiens + r-impute + r-matrixstats + r-mus.musculus + r-qdnaseq + r-qualv + r-r.utils + r-readr + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-covr + r-dss + r-knitr + r-markdown + r-pkgdown + r-qdnaseq.hg19 + r-qdnaseq.mm10 + r-rlang + r-rmarkdown + r-roxygen2 + r-scmeth + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biscuiteer/lilac.py b/prepare/r-biscuiteer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biscuiteer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biscuiteer/lilac.yaml b/prepare/r-biscuiteer/lilac.yaml new file mode 100644 index 0000000000..f3c34aa649 --- /dev/null +++ b/prepare/r-biscuiteer/lilac.yaml @@ -0,0 +1,34 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-biscuiteerdata +- r-bsseq +- r-data.table +- r-delayedmatrixstats +- r-dmrseq +- r-genomeinfodb +- r-genomicranges +- r-gtools +- r-hdf5array +- r-homo.sapiens +- r-impute +- r-matrixstats +- r-mus.musculus +- r-qdnaseq +- r-qualv +- r-r.utils +- r-readr +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: biscuiteer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biscuiteer diff --git a/prepare/r-biscuiteerdata/PKGBUILD b/prepare/r-biscuiteerdata/PKGBUILD new file mode 100644 index 0000000000..9a03084263 --- /dev/null +++ b/prepare/r-biscuiteerdata/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biscuiteerData +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data Package for Biscuiteer' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationhub + r-curl + r-experimenthub +) +optdepends=( + r-knitr + r-markdown + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biscuiteerdata/lilac.py b/prepare/r-biscuiteerdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biscuiteerdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biscuiteerdata/lilac.yaml b/prepare/r-biscuiteerdata/lilac.yaml new file mode 100644 index 0000000000..0a6cba686d --- /dev/null +++ b/prepare/r-biscuiteerdata/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-curl +- r-experimenthub +update_on: +- regex: biscuiteerData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/biscuiteerData diff --git a/prepare/r-biseq/PKGBUILD b/prepare/r-biseq/PKGBUILD new file mode 100644 index 0000000000..610ff79178 --- /dev/null +++ b/prepare/r-biseq/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BiSeq +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Processing and analyzing bisulfite sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-betareg + r-biobase + r-biocgenerics + r-formula + r-genomeinfodb + r-genomicranges + r-globaltest + r-iranges + r-lokern + r-rtracklayer + r-s4vectors + r-summarizedexperiment +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biseq/lilac.py b/prepare/r-biseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biseq/lilac.yaml b/prepare/r-biseq/lilac.yaml new file mode 100644 index 0000000000..9f0bd91605 --- /dev/null +++ b/prepare/r-biseq/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-betareg +- r-biobase +- r-biocgenerics +- r-formula +- r-genomeinfodb +- r-genomicranges +- r-globaltest +- r-iranges +- r-lokern +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: BiSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BiSeq diff --git a/prepare/r-bitseq/PKGBUILD b/prepare/r-bitseq/PKGBUILD new file mode 100644 index 0000000000..cce29d4bc8 --- /dev/null +++ b/prepare/r-bitseq/PKGBUILD @@ -0,0 +1,34 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=BitSeq +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Transcript expression inference and differential expression analysis for RNA-seq data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-iranges + r-rhtslib + r-rsamtools + r-s4vectors +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bitseq/lilac.py b/prepare/r-bitseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bitseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bitseq/lilac.yaml b/prepare/r-bitseq/lilac.yaml new file mode 100644 index 0000000000..48677904f4 --- /dev/null +++ b/prepare/r-bitseq/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-iranges +- r-rhtslib +- r-rsamtools +- r-s4vectors +update_on: +- regex: BitSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BitSeq diff --git a/prepare/r-biwt/PKGBUILD b/prepare/r-biwt/PKGBUILD new file mode 100644 index 0000000000..7a2490ef57 --- /dev/null +++ b/prepare/r-biwt/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=biwt +_pkgver=1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions to compute the biweight mean vector and covariance & correlation matrices' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rrcov +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-biwt/lilac.py b/prepare/r-biwt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-biwt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-biwt/lilac.yaml b/prepare/r-biwt/lilac.yaml new file mode 100644 index 0000000000..626b13d146 --- /dev/null +++ b/prepare/r-biwt/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rrcov +update_on: +- regex: biwt_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=biwt diff --git a/prepare/r-blacksheepr/PKGBUILD b/prepare/r-blacksheepr/PKGBUILD new file mode 100644 index 0000000000..2f980f1606 --- /dev/null +++ b/prepare/r-blacksheepr/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=blacksheepr +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Outlier Analysis for pairwise differential comparison' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-circlize + r-complexheatmap + r-pasilla + r-rcolorbrewer + r-summarizedexperiment + r-viridis +) +optdepends=( + r-biocstyle + r-curl + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-blacksheepr/lilac.py b/prepare/r-blacksheepr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-blacksheepr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-blacksheepr/lilac.yaml b/prepare/r-blacksheepr/lilac.yaml new file mode 100644 index 0000000000..8e31597d92 --- /dev/null +++ b/prepare/r-blacksheepr/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circlize +- r-complexheatmap +- r-pasilla +- r-rcolorbrewer +- r-summarizedexperiment +- r-viridis +update_on: +- regex: blacksheepr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/blacksheepr diff --git a/prepare/r-bladderbatch/PKGBUILD b/prepare/r-bladderbatch/PKGBUILD new file mode 100644 index 0000000000..0d3656e0e6 --- /dev/null +++ b/prepare/r-bladderbatch/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bladderbatch +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bladder gene expression data illustrating batch effects' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bladderbatch/lilac.py b/prepare/r-bladderbatch/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bladderbatch/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bladderbatch/lilac.yaml b/prepare/r-bladderbatch/lilac.yaml new file mode 100644 index 0000000000..89ca402bf6 --- /dev/null +++ b/prepare/r-bladderbatch/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: bladderbatch_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bladderbatch diff --git a/prepare/r-blandaltmanleh/PKGBUILD b/prepare/r-blandaltmanleh/PKGBUILD new file mode 100644 index 0000000000..16893af7aa --- /dev/null +++ b/prepare/r-blandaltmanleh/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BlandAltmanLeh +_pkgver=0.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Plots (Slightly Extended) Bland-Altman Plots' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-ggextra + r-ggplot2 + r-knitr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-blandaltmanleh/lilac.py b/prepare/r-blandaltmanleh/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-blandaltmanleh/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-blandaltmanleh/lilac.yaml b/prepare/r-blandaltmanleh/lilac.yaml new file mode 100644 index 0000000000..1e12cad167 --- /dev/null +++ b/prepare/r-blandaltmanleh/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: BlandAltmanLeh_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=BlandAltmanLeh diff --git a/prepare/r-blima/PKGBUILD b/prepare/r-blima/PKGBUILD new file mode 100644 index 0000000000..662c492778 --- /dev/null +++ b/prepare/r-blima/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=blima +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-beadarray + r-biobase + r-biocgenerics + r-rcpp +) +optdepends=( + r-biocstyle + r-blimatestingdata + r-illuminahumanv4.db + r-knitr + r-lumi + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-blima/lilac.py b/prepare/r-blima/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-blima/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-blima/lilac.yaml b/prepare/r-blima/lilac.yaml new file mode 100644 index 0000000000..414084e3ae --- /dev/null +++ b/prepare/r-blima/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beadarray +- r-biobase +- r-biocgenerics +- r-rcpp +update_on: +- regex: blima_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/blima diff --git a/prepare/r-blma/PKGBUILD b/prepare/r-blma/PKGBUILD new file mode 100644 index 0000000000..ec3cc555cf --- /dev/null +++ b/prepare/r-blma/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BLMA +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='BLMA: A package for bi-level meta-analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-graph + r-gsa + r-limma + r-metafor + r-padog + r-rontotools +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-blma/lilac.py b/prepare/r-blma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-blma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-blma/lilac.yaml b/prepare/r-blma/lilac.yaml new file mode 100644 index 0000000000..db74565c51 --- /dev/null +++ b/prepare/r-blma/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-graph +- r-gsa +- r-limma +- r-metafor +- r-padog +- r-rontotools +update_on: +- regex: BLMA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BLMA diff --git a/prepare/r-blme/PKGBUILD b/prepare/r-blme/PKGBUILD new file mode 100644 index 0000000000..4e46c91535 --- /dev/null +++ b/prepare/r-blme/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=blme +_pkgver=1.0-5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian Linear Mixed-Effects Models' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-lme4 +) +optdepends=( + r-expint + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-blme/lilac.py b/prepare/r-blme/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-blme/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-blme/lilac.yaml b/prepare/r-blme/lilac.yaml new file mode 100644 index 0000000000..8180e396c5 --- /dev/null +++ b/prepare/r-blme/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lme4 +update_on: +- regex: blme_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=blme diff --git a/prepare/r-blockmodeling/PKGBUILD b/prepare/r-blockmodeling/PKGBUILD new file mode 100644 index 0000000000..9fe0deafbb --- /dev/null +++ b/prepare/r-blockmodeling/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=blockmodeling +_pkgver=1.0.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generalized and Classical Blockmodeling of Valued Networks' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-doparallel + r-dorng + r-foreach + r-sna +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-blockmodeling/lilac.py b/prepare/r-blockmodeling/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-blockmodeling/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-blockmodeling/lilac.yaml b/prepare/r-blockmodeling/lilac.yaml new file mode 100644 index 0000000000..94efaad082 --- /dev/null +++ b/prepare/r-blockmodeling/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: blockmodeling_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=blockmodeling diff --git a/prepare/r-bloodgen3module/PKGBUILD b/prepare/r-bloodgen3module/PKGBUILD new file mode 100644 index 0000000000..a22d43b163 --- /dev/null +++ b/prepare/r-bloodgen3module/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BloodGen3Module +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='This R package for performing module repertoire analyses and generating fingerprint representations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-circlize + r-complexheatmap + r-experimenthub + r-ggplot2 + r-gtools + r-limma + r-matrixstats + r-preprocesscore + r-randomcolor + r-reshape2 + r-summarizedexperiment + r-testthat + r-v8 +) +optdepends=( + r-biocgenerics + r-devtools + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bloodgen3module/lilac.py b/prepare/r-bloodgen3module/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bloodgen3module/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bloodgen3module/lilac.yaml b/prepare/r-bloodgen3module/lilac.yaml new file mode 100644 index 0000000000..d4d70f2d31 --- /dev/null +++ b/prepare/r-bloodgen3module/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circlize +- r-complexheatmap +- r-experimenthub +- r-ggplot2 +- r-gtools +- r-limma +- r-matrixstats +- r-preprocesscore +- r-randomcolor +- r-reshape2 +- r-summarizedexperiment +- r-testthat +- r-v8 +update_on: +- regex: BloodGen3Module_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BloodGen3Module diff --git a/prepare/r-bluster/PKGBUILD b/prepare/r-bluster/PKGBUILD new file mode 100644 index 0000000000..69c801d46b --- /dev/null +++ b/prepare/r-bluster/PKGBUILD @@ -0,0 +1,48 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=bluster +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clustering Algorithms for Bioconductor' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocneighbors + r-biocparallel + r-igraph + r-rcpp + r-s4vectors +) +optdepends=( + r-apcluster + r-biocstyle + r-dynamictreecut + r-knitr + r-kohonen + r-mbkmeans + r-pheatmap + r-rmarkdown + r-scater + r-scran + r-scrnaseq + r-scuttle + r-testthat + r-viridis +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bluster/lilac.py b/prepare/r-bluster/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bluster/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bluster/lilac.yaml b/prepare/r-bluster/lilac.yaml new file mode 100644 index 0000000000..010c944eeb --- /dev/null +++ b/prepare/r-bluster/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocneighbors +- r-biocparallel +- r-igraph +- r-rcpp +- r-s4vectors +update_on: +- regex: bluster_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bluster diff --git a/prepare/r-bma/PKGBUILD b/prepare/r-bma/PKGBUILD new file mode 100644 index 0000000000..442b139faf --- /dev/null +++ b/prepare/r-bma/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BMA +_pkgver=3.18.15 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian Model Averaging' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-inline + r-leaps + r-robustbase + r-rrcov +) +optdepends=( + r-mass +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bma/lilac.py b/prepare/r-bma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bma/lilac.yaml b/prepare/r-bma/lilac.yaml new file mode 100644 index 0000000000..fb06e5db23 --- /dev/null +++ b/prepare/r-bma/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-inline +- r-leaps +- r-robustbase +- r-rrcov +update_on: +- regex: BMA_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=BMA diff --git a/prepare/r-bmp/PKGBUILD b/prepare/r-bmp/PKGBUILD new file mode 100644 index 0000000000..fe7fb1cfa8 --- /dev/null +++ b/prepare/r-bmp/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bmp +_pkgver=0.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Read Windows Bitmap (BMP) Images' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-pixmap + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bmp/lilac.py b/prepare/r-bmp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bmp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bmp/lilac.yaml b/prepare/r-bmp/lilac.yaml new file mode 100644 index 0000000000..756249d4a2 --- /dev/null +++ b/prepare/r-bmp/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: bmp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bmp diff --git a/prepare/r-bnbc/PKGBUILD b/prepare/r-bnbc/PKGBUILD new file mode 100644 index 0000000000..c870195084 --- /dev/null +++ b/prepare/r-bnbc/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bnbc +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bandwise normalization and batch correction of Hi-C data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-data.table + r-ebimage + r-genomeinfodb + r-genomicranges + r-iranges + r-matrixstats + r-preprocesscore + r-rcpp + r-rhdf5 + r-s4vectors + r-summarizedexperiment + r-sva +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bnbc/lilac.py b/prepare/r-bnbc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bnbc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bnbc/lilac.yaml b/prepare/r-bnbc/lilac.yaml new file mode 100644 index 0000000000..15f52e57fc --- /dev/null +++ b/prepare/r-bnbc/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-data.table +- r-ebimage +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-matrixstats +- r-preprocesscore +- r-rcpp +- r-rhdf5 +- r-s4vectors +- r-summarizedexperiment +- r-sva +update_on: +- regex: bnbc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bnbc diff --git a/prepare/r-bnem/PKGBUILD b/prepare/r-bnem/PKGBUILD new file mode 100644 index 0000000000..db48e11a4e --- /dev/null +++ b/prepare/r-bnem/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bnem +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Training of logical models from indirect measurements of perturbation experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-binom + r-biobase + r-cellnoptr + r-epinem + r-flexclust + r-graph + r-limma + r-matrixstats + r-mnem + r-rcolorbrewer + r-rgraphviz + r-rmarkdown + r-snowfall + r-sva + r-vsn +) +optdepends=( + r-biocgenerics + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bnem/lilac.py b/prepare/r-bnem/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bnem/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bnem/lilac.yaml b/prepare/r-bnem/lilac.yaml new file mode 100644 index 0000000000..2f97257154 --- /dev/null +++ b/prepare/r-bnem/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-binom +- r-biobase +- r-cellnoptr +- r-epinem +- r-flexclust +- r-graph +- r-limma +- r-matrixstats +- r-mnem +- r-rcolorbrewer +- r-rgraphviz +- r-rmarkdown +- r-snowfall +- r-sva +- r-vsn +update_on: +- regex: bnem_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bnem diff --git a/prepare/r-bnlearn/PKGBUILD b/prepare/r-bnlearn/PKGBUILD new file mode 100644 index 0000000000..4073716158 --- /dev/null +++ b/prepare/r-bnlearn/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bnlearn +_pkgver=4.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian Network Structure Learning, Parameter Learning and Inference' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-gmp + r-grain + r-graph + r-igraph + r-lattice + r-parallel + r-rgraphviz + r-rmpfr + r-rocr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bnlearn/lilac.py b/prepare/r-bnlearn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bnlearn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bnlearn/lilac.yaml b/prepare/r-bnlearn/lilac.yaml new file mode 100644 index 0000000000..8e6e9461b1 --- /dev/null +++ b/prepare/r-bnlearn/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: bnlearn_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bnlearn diff --git a/prepare/r-bnstruct/PKGBUILD b/prepare/r-bnstruct/PKGBUILD new file mode 100644 index 0000000000..5a9f8b7a75 --- /dev/null +++ b/prepare/r-bnstruct/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bnstruct +_pkgver=1.0.12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian Network Structure Learning from Data with Missing Values' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bitops + r-igraph +) +optdepends=( + r-graph + r-knitr + r-qgraph + r-rgraphviz + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bnstruct/lilac.py b/prepare/r-bnstruct/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bnstruct/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bnstruct/lilac.yaml b/prepare/r-bnstruct/lilac.yaml new file mode 100644 index 0000000000..3b112211ed --- /dev/null +++ b/prepare/r-bnstruct/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bitops +- r-igraph +update_on: +- regex: bnstruct_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bnstruct diff --git a/prepare/r-bookdown/PKGBUILD b/prepare/r-bookdown/PKGBUILD new file mode 100644 index 0000000000..ff711eade5 --- /dev/null +++ b/prepare/r-bookdown/PKGBUILD @@ -0,0 +1,52 @@ +# system requirements: Pandoc (>= 1.17.2) +# Maintainer: Guoyi Zhang + +_pkgname=bookdown +_pkgver=0.24 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Authoring Books and Technical Documents with R Markdown' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-htmltools + r-jquerylib + r-knitr + r-rmarkdown + r-tinytex + r-xfun + r-yaml +) +optdepends=( + r-bslib + r-downlit + r-htmlwidgets + r-jsonlite + r-miniui + r-rsconnect + r-rstudioapi + r-servr + r-shiny + r-testit + r-testthat + r-tibble + r-tufte + r-webshot + r-withr + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bookdown/lilac.py b/prepare/r-bookdown/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bookdown/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bookdown/lilac.yaml b/prepare/r-bookdown/lilac.yaml new file mode 100644 index 0000000000..531e6b89b7 --- /dev/null +++ b/prepare/r-bookdown/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-jquerylib +- r-knitr +- r-rmarkdown +- r-tinytex +- r-xfun +- r-yaml +update_on: +- regex: bookdown_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bookdown diff --git a/prepare/r-boolnet/PKGBUILD b/prepare/r-boolnet/PKGBUILD new file mode 100644 index 0000000000..fcbce90e9c --- /dev/null +++ b/prepare/r-boolnet/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BoolNet +_pkgver=2.1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Construction, Simulation and Analysis of Boolean Networks' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-igraph + r-xml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-boolnet/lilac.py b/prepare/r-boolnet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-boolnet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-boolnet/lilac.yaml b/prepare/r-boolnet/lilac.yaml new file mode 100644 index 0000000000..84719314b5 --- /dev/null +++ b/prepare/r-boolnet/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +- r-xml +update_on: +- regex: BoolNet_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=BoolNet diff --git a/prepare/r-bootstrap/PKGBUILD b/prepare/r-bootstrap/PKGBUILD new file mode 100644 index 0000000000..b718462f15 --- /dev/null +++ b/prepare/r-bootstrap/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bootstrap +_pkgver=2019.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for the Book "An Introduction to the Bootstrap"' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bootstrap/lilac.py b/prepare/r-bootstrap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bootstrap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bootstrap/lilac.yaml b/prepare/r-bootstrap/lilac.yaml new file mode 100644 index 0000000000..d2f814c2ec --- /dev/null +++ b/prepare/r-bootstrap/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: bootstrap_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bootstrap diff --git a/prepare/r-bprmeth/PKGBUILD b/prepare/r-bprmeth/PKGBUILD new file mode 100644 index 0000000000..443af52325 --- /dev/null +++ b/prepare/r-bprmeth/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BPRMeth +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Model higher-order methylation profiles' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-biocstyle + r-cowplot + r-data.table + r-doparallel + r-e1071 + r-earth + r-foreach + r-genomicranges + r-ggplot2 + r-iranges + r-kernlab + r-magrittr + r-matrixcalc + r-mvtnorm + r-randomforest + r-rcpp + r-rcpparmadillo + r-s4vectors + r-truncnorm +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bprmeth/lilac.py b/prepare/r-bprmeth/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bprmeth/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bprmeth/lilac.yaml b/prepare/r-bprmeth/lilac.yaml new file mode 100644 index 0000000000..fd72ca8b9a --- /dev/null +++ b/prepare/r-bprmeth/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biocstyle +- r-cowplot +- r-data.table +- r-doparallel +- r-e1071 +- r-earth +- r-foreach +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-kernlab +- r-magrittr +- r-matrixcalc +- r-mvtnorm +- r-randomforest +- r-rcpp +- r-rcpparmadillo +- r-s4vectors +- r-truncnorm +update_on: +- regex: BPRMeth_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BPRMeth diff --git a/prepare/r-brain/PKGBUILD b/prepare/r-brain/PKGBUILD new file mode 100644 index 0000000000..6eb2e1d2c0 --- /dev/null +++ b/prepare/r-brain/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BRAIN +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Baffling Recursive Algorithm for Isotope distributioN calculations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-polynomf +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-brain/lilac.py b/prepare/r-brain/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-brain/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-brain/lilac.yaml b/prepare/r-brain/lilac.yaml new file mode 100644 index 0000000000..44da3d0e3a --- /dev/null +++ b/prepare/r-brain/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-polynomf +update_on: +- regex: BRAIN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BRAIN diff --git a/prepare/r-brainflowprobes/PKGBUILD b/prepare/r-brainflowprobes/PKGBUILD new file mode 100644 index 0000000000..27265347d2 --- /dev/null +++ b/prepare/r-brainflowprobes/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=brainflowprobes +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Plots and annotation for choosing BrainFlow target probe sequence' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-bsgenome.hsapiens.ucsc.hg19 + r-bumphunter + r-cowplot + r-derfinder + r-derfinderplot + r-genomicranges + r-genomicstate + r-ggplot2 + r-rcolorbrewer +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-refmanager + r-rmarkdown + r-sessioninfo + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-brainflowprobes/lilac.py b/prepare/r-brainflowprobes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-brainflowprobes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-brainflowprobes/lilac.yaml b/prepare/r-brainflowprobes/lilac.yaml new file mode 100644 index 0000000000..30f6c2cca9 --- /dev/null +++ b/prepare/r-brainflowprobes/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome.hsapiens.ucsc.hg19 +- r-bumphunter +- r-cowplot +- r-derfinder +- r-derfinderplot +- r-genomicranges +- r-genomicstate +- r-ggplot2 +- r-rcolorbrewer +update_on: +- regex: brainflowprobes_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/brainflowprobes diff --git a/prepare/r-brainsaber/PKGBUILD b/prepare/r-brainsaber/PKGBUILD new file mode 100644 index 0000000000..d1ae5b1941 --- /dev/null +++ b/prepare/r-brainsaber/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BrainSABER +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Brain Span Atlas in Biobase Expressionset R toolset' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocfilecache + r-biomart + r-data.table + r-lsa + r-s4vectors + r-shiny + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-complexheatmap + r-fastcluster + r-heatmaply + r-knitr + r-plotly + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-brainsaber/lilac.py b/prepare/r-brainsaber/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-brainsaber/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-brainsaber/lilac.yaml b/prepare/r-brainsaber/lilac.yaml new file mode 100644 index 0000000000..9637b8ce5e --- /dev/null +++ b/prepare/r-brainsaber/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-biomart +- r-data.table +- r-lsa +- r-s4vectors +- r-shiny +- r-summarizedexperiment +update_on: +- regex: BrainSABER_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BrainSABER diff --git a/prepare/r-brainstars/PKGBUILD b/prepare/r-brainstars/PKGBUILD new file mode 100644 index 0000000000..c98eb6e301 --- /dev/null +++ b/prepare/r-brainstars/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BrainStars +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='query gene expression data and plots from BrainStars' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-curl + r-biobase + r-rjsonio +) +makedepends=( + git + tar +) +source=("git+https://git.bioconductor.org/packages/${_pkgname}.git") +sha256sums=('SKIP') + +build() { + tar -zcvf ${_pkgname}.tar.gz ${_pkgname} + R CMD INSTALL ${_pkgname}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: + diff --git a/prepare/r-brainstars/lilac.py b/prepare/r-brainstars/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-brainstars/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-brainstars/lilac.yaml b/prepare/r-brainstars/lilac.yaml new file mode 100644 index 0000000000..f605367a9f --- /dev/null +++ b/prepare/r-brainstars/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-biobase +- r-rjsonio +update_on: +- regex: Version(\d+.\d+.\d+) + source: regex + url: https://bioconductor.org/packages/BrainStars diff --git a/prepare/r-branchpointer/PKGBUILD b/prepare/r-branchpointer/PKGBUILD new file mode 100644 index 0000000000..4c0a77a6cf --- /dev/null +++ b/prepare/r-branchpointer/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=branchpointer +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Prediction of intronic splicing branchpoints' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-biomart + r-biostrings + r-bsgenome.hsapiens.ucsc.hg38 + r-caret + r-cowplot + r-data.table + r-gbm + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-kernlab + r-plyr + r-rtracklayer + r-s4vectors + r-stringr +) +optdepends=( + r-biocstyle + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-branchpointer/lilac.py b/prepare/r-branchpointer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-branchpointer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-branchpointer/lilac.yaml b/prepare/r-branchpointer/lilac.yaml new file mode 100644 index 0000000000..b5520c2e9b --- /dev/null +++ b/prepare/r-branchpointer/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-biostrings +- r-bsgenome.hsapiens.ucsc.hg38 +- r-caret +- r-cowplot +- r-data.table +- r-gbm +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-kernlab +- r-plyr +- r-rtracklayer +- r-s4vectors +- r-stringr +update_on: +- regex: branchpointer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/branchpointer diff --git a/prepare/r-breakpointr/PKGBUILD b/prepare/r-breakpointr/PKGBUILD new file mode 100644 index 0000000000..5d00a566ea --- /dev/null +++ b/prepare/r-breakpointr/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=breakpointR +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Find breakpoints in Strand-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-biocgenerics + r-breakpointrdata + r-cowplot + r-doparallel + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-gtools + r-iranges + r-rsamtools + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-breakpointr/lilac.py b/prepare/r-breakpointr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-breakpointr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-breakpointr/lilac.yaml b/prepare/r-breakpointr/lilac.yaml new file mode 100644 index 0000000000..8cf03acbe9 --- /dev/null +++ b/prepare/r-breakpointr/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-breakpointrdata +- r-cowplot +- r-doparallel +- r-foreach +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-gtools +- r-iranges +- r-rsamtools +- r-s4vectors +update_on: +- regex: breakpointR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/breakpointR diff --git a/prepare/r-breakpointrdata/PKGBUILD b/prepare/r-breakpointrdata/PKGBUILD new file mode 100644 index 0000000000..1ee60f62d4 --- /dev/null +++ b/prepare/r-breakpointrdata/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=breakpointRdata +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Strand-seq data for demonstration purposes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r +) +optdepends=( + r-biocstyle + r-knitr +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-breakpointrdata/lilac.py b/prepare/r-breakpointrdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-breakpointrdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-breakpointrdata/lilac.yaml b/prepare/r-breakpointrdata/lilac.yaml new file mode 100644 index 0000000000..7806801912 --- /dev/null +++ b/prepare/r-breakpointrdata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: breakpointRdata_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/breakpointRdata diff --git a/prepare/r-breastcancervdx/PKGBUILD b/prepare/r-breastcancervdx/PKGBUILD new file mode 100644 index 0000000000..04bbd19ed3 --- /dev/null +++ b/prepare/r-breastcancervdx/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=breastCancerVDX +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX).' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-biobase + r-genefu + r-survcomp +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-breastcancervdx/lilac.py b/prepare/r-breastcancervdx/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-breastcancervdx/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-breastcancervdx/lilac.yaml b/prepare/r-breastcancervdx/lilac.yaml new file mode 100644 index 0000000000..0161f60805 --- /dev/null +++ b/prepare/r-breastcancervdx/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: breastCancerVDX_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/breastCancerVDX diff --git a/prepare/r-brendadb/PKGBUILD b/prepare/r-brendadb/PKGBUILD new file mode 100644 index 0000000000..51d2d6c2df --- /dev/null +++ b/prepare/r-brendadb/PKGBUILD @@ -0,0 +1,49 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=brendaDb +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The BRENDA Enzyme Database' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocfilecache + r-biocparallel + r-crayon + r-curl + r-dplyr + r-magrittr + r-purrr + r-rappdirs + r-rcpp + r-rlang + r-stringr + r-tibble + r-tidyr + r-xml2 +) +optdepends=( + r-biocstyle + r-devtools + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-brendadb/lilac.py b/prepare/r-brendadb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-brendadb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-brendadb/lilac.yaml b/prepare/r-brendadb/lilac.yaml new file mode 100644 index 0000000000..65b99843f4 --- /dev/null +++ b/prepare/r-brendadb/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-biocparallel +- r-crayon +- r-curl +- r-dplyr +- r-magrittr +- r-purrr +- r-rappdirs +- r-rcpp +- r-rlang +- r-stringr +- r-tibble +- r-tidyr +- r-xml2 +update_on: +- regex: brendaDb_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/brendaDb diff --git a/prepare/r-brew/PKGBUILD b/prepare/r-brew/PKGBUILD new file mode 100644 index 0000000000..9b05a87994 --- /dev/null +++ b/prepare/r-brew/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=brew +_pkgver=1.0-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Templating Framework for Report Generation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-brew/lilac.py b/prepare/r-brew/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-brew/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-brew/lilac.yaml b/prepare/r-brew/lilac.yaml new file mode 100644 index 0000000000..a1951a4fcb --- /dev/null +++ b/prepare/r-brew/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: brew_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=brew diff --git a/prepare/r-brgenomics/PKGBUILD b/prepare/r-brgenomics/PKGBUILD new file mode 100644 index 0000000000..eeb26e9849 --- /dev/null +++ b/prepare/r-brgenomics/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BRGenomics +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for the Efficient Analysis of High-Resolution Genomics Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-deseq2 + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-apeglm + r-biocstyle + r-biostrings + r-ggplot2 + r-knitr + r-remotes + r-reshape2 + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-brgenomics/lilac.py b/prepare/r-brgenomics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-brgenomics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-brgenomics/lilac.yaml b/prepare/r-brgenomics/lilac.yaml new file mode 100644 index 0000000000..d5fbe5c16f --- /dev/null +++ b/prepare/r-brgenomics/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-deseq2 +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: BRGenomics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BRGenomics diff --git a/prepare/r-brglm/PKGBUILD b/prepare/r-brglm/PKGBUILD new file mode 100644 index 0000000000..95b9818215 --- /dev/null +++ b/prepare/r-brglm/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=brglm +_pkgver=0.7.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bias Reduction in Binomial-Response Generalized Linear Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-profilemodel +) +optdepends=( + r-mass +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-brglm/lilac.py b/prepare/r-brglm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-brglm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-brglm/lilac.yaml b/prepare/r-brglm/lilac.yaml new file mode 100644 index 0000000000..7bde40777f --- /dev/null +++ b/prepare/r-brglm/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-profilemodel +update_on: +- regex: brglm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=brglm diff --git a/prepare/r-bridge/PKGBUILD b/prepare/r-bridge/PKGBUILD new file mode 100644 index 0000000000..eb13f4aca5 --- /dev/null +++ b/prepare/r-bridge/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bridge +_pkgver=1.58.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian Robust Inference for Differential Gene Expression' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rama +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bridge/lilac.py b/prepare/r-bridge/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bridge/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bridge/lilac.yaml b/prepare/r-bridge/lilac.yaml new file mode 100644 index 0000000000..3eb51ff0e7 --- /dev/null +++ b/prepare/r-bridge/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rama +update_on: +- regex: bridge_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bridge diff --git a/prepare/r-bridgedbr/PKGBUILD b/prepare/r-bridgedbr/PKGBUILD new file mode 100644 index 0000000000..bc11886fc4 --- /dev/null +++ b/prepare/r-bridgedbr/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BridgeDbR +_pkgver=2.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Code for using BridgeDb identifier mapping framework from within R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-curl + r-rjava +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bridgedbr/lilac.py b/prepare/r-bridgedbr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bridgedbr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bridgedbr/lilac.yaml b/prepare/r-bridgedbr/lilac.yaml new file mode 100644 index 0000000000..2f5ecfeeca --- /dev/null +++ b/prepare/r-bridgedbr/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-rjava +update_on: +- regex: BridgeDbR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BridgeDbR diff --git a/prepare/r-brio/PKGBUILD b/prepare/r-brio/PKGBUILD new file mode 100644 index 0000000000..09ce4a8039 --- /dev/null +++ b/prepare/r-brio/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=brio +_pkgver=1.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Basic R Input Output' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-brio/lilac.py b/prepare/r-brio/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-brio/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-brio/lilac.yaml b/prepare/r-brio/lilac.yaml new file mode 100644 index 0000000000..da71bddd0b --- /dev/null +++ b/prepare/r-brio/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: brio_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=brio diff --git a/prepare/r-broom.mixed/PKGBUILD b/prepare/r-broom.mixed/PKGBUILD new file mode 100644 index 0000000000..d4c1200580 --- /dev/null +++ b/prepare/r-broom.mixed/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=broom.mixed +_pkgver=0.2.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tidying Methods for Mixed Models' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-broom + r-coda + r-dplyr + r-purrr + r-stringr + r-tibble + r-tidyr +) +optdepends=( + r-brms + r-dotwhisker + r-gamlss + r-gamlss.data + r-ggplot2 + r-glmmadaptive + r-glmmadmb + r-glmmtmb + r-knitr + r-lme4 + r-lmertest + r-matrix + r-mcmcglmm + r-mgcv + r-pander + r-pbkrtest + r-r2jags + r-rmarkdown + r-rstan + r-rstanarm + r-testthat + r-tmb +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-broom.mixed/lilac.py b/prepare/r-broom.mixed/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-broom.mixed/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-broom.mixed/lilac.yaml b/prepare/r-broom.mixed/lilac.yaml new file mode 100644 index 0000000000..af36e0f06c --- /dev/null +++ b/prepare/r-broom.mixed/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-broom +- r-coda +- r-dplyr +- r-purrr +- r-stringr +- r-tibble +- r-tidyr +update_on: +- regex: broom.mixed_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=broom.mixed diff --git a/prepare/r-broom/PKGBUILD b/prepare/r-broom/PKGBUILD new file mode 100644 index 0000000000..f67f95241d --- /dev/null +++ b/prepare/r-broom/PKGBUILD @@ -0,0 +1,123 @@ +# Maintainer: Guoyi Zhang + +_pkgname=broom +_pkgver=0.7.11 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Convert Statistical Objects into Tidy Tibbles' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-backports + r-dplyr + r-ellipsis + r-generics + r-ggplot2 + r-glue + r-purrr + r-rlang + r-stringr + r-tibble + r-tidyr +) +optdepends=( + r-aer + r-akima + r-auc + r-bbmle + r-betareg + r-biglm + r-bingroup + r-boot + r-btergm + r-car + r-caret + r-cluster + r-cmprsk + r-coda + r-covr + r-drc + r-e1071 + r-emmeans + r-epir + r-ergm + r-fixest + r-gam + r-gee + r-geepack + r-glmnet + r-glmnetutils + r-gmm + r-hmisc + r-irlba + r-joinerml + r-kendall + r-knitr + r-ks + r-lahman + r-lavaan + r-leaps + r-lfe + r-lm.beta + r-lme4 + r-lmodel2 + r-lmtest + r-lsmeans + r-maps + r-maptools + r-margins + r-mass + r-matrix + r-mclust + r-mediation + r-metafor + r-mfx + r-mgcv + r-mlogit + r-modeldata + r-modeltests + r-muhaz + r-multcomp + r-network + r-nnet + r-orcutt + r-ordinal + r-plm + r-polca + r-psych + r-quantreg + r-rgeos + r-rmarkdown + r-robust + r-robustbase + r-rsample + r-sandwich + r-sp + r-spatialreg + r-spdep + r-speedglm + r-spelling + r-survey + r-survival + r-systemfit + r-testthat + r-tseries + r-vars + r-zoo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-broom/lilac.py b/prepare/r-broom/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-broom/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-broom/lilac.yaml b/prepare/r-broom/lilac.yaml new file mode 100644 index 0000000000..2307434a83 --- /dev/null +++ b/prepare/r-broom/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-backports +- r-dplyr +- r-ellipsis +- r-generics +- r-ggplot2 +- r-glue +- r-purrr +- r-rlang +- r-stringr +- r-tibble +- r-tidyr +update_on: +- regex: broom_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=broom diff --git a/prepare/r-browserviz/PKGBUILD b/prepare/r-browserviz/PKGBUILD new file mode 100644 index 0000000000..891f8f5770 --- /dev/null +++ b/prepare/r-browserviz/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BrowserViz +_pkgver=2.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='BrowserViz: interactive R/browser graphics using websockets and JSON' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-httpuv + r-jsonlite +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-browserviz/lilac.py b/prepare/r-browserviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-browserviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-browserviz/lilac.yaml b/prepare/r-browserviz/lilac.yaml new file mode 100644 index 0000000000..8137f34c67 --- /dev/null +++ b/prepare/r-browserviz/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-httpuv +- r-jsonlite +update_on: +- regex: BrowserViz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BrowserViz diff --git a/prepare/r-bs4dash/PKGBUILD b/prepare/r-bs4dash/PKGBUILD new file mode 100644 index 0000000000..d5f46da74f --- /dev/null +++ b/prepare/r-bs4dash/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bs4Dash +_pkgver=2.0.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="A 'Bootstrap 4' Version of 'shinydashboard'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bslib + r-fresh + r-htmltools + r-httpuv + r-httr + r-jsonlite + r-lifecycle + r-shiny + r-waiter +) +optdepends=( + r-covr + r-dt + r-echarts4r + r-golem + r-knitr + r-rmarkdown + r-testthat + r-thematic +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bs4dash/lilac.py b/prepare/r-bs4dash/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bs4dash/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bs4dash/lilac.yaml b/prepare/r-bs4dash/lilac.yaml new file mode 100644 index 0000000000..88cedc7a3a --- /dev/null +++ b/prepare/r-bs4dash/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bslib +- r-fresh +- r-htmltools +- r-httpuv +- r-httr +- r-jsonlite +- r-lifecycle +- r-shiny +- r-waiter +update_on: +- regex: bs4Dash_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bs4Dash diff --git a/prepare/r-bsgenome.celegans.ucsc.ce2/PKGBUILD b/prepare/r-bsgenome.celegans.ucsc.ce2/PKGBUILD new file mode 100644 index 0000000000..fe9fb30872 --- /dev/null +++ b/prepare/r-bsgenome.celegans.ucsc.ce2/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BSgenome.Celegans.UCSC.ce2 +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Full genome sequences for Caenorhabditis elegans (UCSC version ce2)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bsgenome +) +optdepends=( + r-genomicfeatures +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bsgenome.celegans.ucsc.ce2/lilac.py b/prepare/r-bsgenome.celegans.ucsc.ce2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bsgenome.celegans.ucsc.ce2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bsgenome.celegans.ucsc.ce2/lilac.yaml b/prepare/r-bsgenome.celegans.ucsc.ce2/lilac.yaml new file mode 100644 index 0000000000..db011e66d3 --- /dev/null +++ b/prepare/r-bsgenome.celegans.ucsc.ce2/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +update_on: +- regex: BSgenome.Celegans.UCSC.ce2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BSgenome.Celegans.UCSC.ce2 diff --git a/prepare/r-bsgenome.drerio.ucsc.danrer7/PKGBUILD b/prepare/r-bsgenome.drerio.ucsc.danrer7/PKGBUILD new file mode 100644 index 0000000000..878623ea0f --- /dev/null +++ b/prepare/r-bsgenome.drerio.ucsc.danrer7/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BSgenome.Drerio.UCSC.danRer7 +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Full genome sequences for Danio rerio (UCSC version danRer7)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bsgenome +) +optdepends=( + r-genomicfeatures +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bsgenome.drerio.ucsc.danrer7/lilac.py b/prepare/r-bsgenome.drerio.ucsc.danrer7/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bsgenome.drerio.ucsc.danrer7/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bsgenome.drerio.ucsc.danrer7/lilac.yaml b/prepare/r-bsgenome.drerio.ucsc.danrer7/lilac.yaml new file mode 100644 index 0000000000..901e5e7009 --- /dev/null +++ b/prepare/r-bsgenome.drerio.ucsc.danrer7/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +update_on: +- regex: BSgenome.Drerio.UCSC.danRer7_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer7 diff --git a/prepare/r-bsgenome.ecoli.ncbi.20080805/PKGBUILD b/prepare/r-bsgenome.ecoli.ncbi.20080805/PKGBUILD new file mode 100644 index 0000000000..1f28b62355 --- /dev/null +++ b/prepare/r-bsgenome.ecoli.ncbi.20080805/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BSgenome.Ecoli.NCBI.20080805 +_pkgver=1.3.1000 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Escherichia coli full genomes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bsgenome +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bsgenome.ecoli.ncbi.20080805/lilac.py b/prepare/r-bsgenome.ecoli.ncbi.20080805/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bsgenome.ecoli.ncbi.20080805/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bsgenome.ecoli.ncbi.20080805/lilac.yaml b/prepare/r-bsgenome.ecoli.ncbi.20080805/lilac.yaml new file mode 100644 index 0000000000..0f9fcaa172 --- /dev/null +++ b/prepare/r-bsgenome.ecoli.ncbi.20080805/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +update_on: +- regex: BSgenome.Ecoli.NCBI.20080805_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BSgenome.Ecoli.NCBI.20080805 diff --git a/prepare/r-bsgenome.hsapiens.ucsc.hg18/PKGBUILD b/prepare/r-bsgenome.hsapiens.ucsc.hg18/PKGBUILD new file mode 100644 index 0000000000..11ee3bb11a --- /dev/null +++ b/prepare/r-bsgenome.hsapiens.ucsc.hg18/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BSgenome.Hsapiens.UCSC.hg18 +_pkgver=1.3.1000 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Full genome sequences for Homo sapiens (UCSC version hg18)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bsgenome +) +optdepends=( + r-txdb.hsapiens.ucsc.hg18.knowngene +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bsgenome.hsapiens.ucsc.hg18/lilac.py b/prepare/r-bsgenome.hsapiens.ucsc.hg18/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bsgenome.hsapiens.ucsc.hg18/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bsgenome.hsapiens.ucsc.hg18/lilac.yaml b/prepare/r-bsgenome.hsapiens.ucsc.hg18/lilac.yaml new file mode 100644 index 0000000000..cd071d761f --- /dev/null +++ b/prepare/r-bsgenome.hsapiens.ucsc.hg18/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +update_on: +- regex: BSgenome.Hsapiens.UCSC.hg18_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg18 diff --git a/prepare/r-bsgenome.hsapiens.ucsc.hg19/PKGBUILD b/prepare/r-bsgenome.hsapiens.ucsc.hg19/PKGBUILD new file mode 100644 index 0000000000..b4a37cc7ba --- /dev/null +++ b/prepare/r-bsgenome.hsapiens.ucsc.hg19/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BSgenome.Hsapiens.UCSC.hg19 +_pkgver=1.4.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bsgenome +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bsgenome.hsapiens.ucsc.hg19/lilac.py b/prepare/r-bsgenome.hsapiens.ucsc.hg19/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bsgenome.hsapiens.ucsc.hg19/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bsgenome.hsapiens.ucsc.hg19/lilac.yaml b/prepare/r-bsgenome.hsapiens.ucsc.hg19/lilac.yaml new file mode 100644 index 0000000000..7e22403b8f --- /dev/null +++ b/prepare/r-bsgenome.hsapiens.ucsc.hg19/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +update_on: +- regex: BSgenome.Hsapiens.UCSC.hg19_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19 diff --git a/prepare/r-bsgenome.hsapiens.ucsc.hg38/PKGBUILD b/prepare/r-bsgenome.hsapiens.ucsc.hg38/PKGBUILD new file mode 100644 index 0000000000..914c43c5b6 --- /dev/null +++ b/prepare/r-bsgenome.hsapiens.ucsc.hg38/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BSgenome.Hsapiens.UCSC.hg38 +_pkgver=1.4.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p13)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bsgenome +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bsgenome.hsapiens.ucsc.hg38/lilac.py b/prepare/r-bsgenome.hsapiens.ucsc.hg38/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bsgenome.hsapiens.ucsc.hg38/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bsgenome.hsapiens.ucsc.hg38/lilac.yaml b/prepare/r-bsgenome.hsapiens.ucsc.hg38/lilac.yaml new file mode 100644 index 0000000000..5a156f778c --- /dev/null +++ b/prepare/r-bsgenome.hsapiens.ucsc.hg38/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +update_on: +- regex: BSgenome.Hsapiens.UCSC.hg38_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38 diff --git a/prepare/r-bsgenome.mmusculus.ucsc.mm10/PKGBUILD b/prepare/r-bsgenome.mmusculus.ucsc.mm10/PKGBUILD new file mode 100644 index 0000000000..aac10b5dc6 --- /dev/null +++ b/prepare/r-bsgenome.mmusculus.ucsc.mm10/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BSgenome.Mmusculus.UCSC.mm10 +_pkgver=1.4.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Full genome sequences for Mus musculus (UCSC version mm10, based on GRCm38.p6)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bsgenome +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bsgenome.mmusculus.ucsc.mm10/lilac.py b/prepare/r-bsgenome.mmusculus.ucsc.mm10/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bsgenome.mmusculus.ucsc.mm10/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bsgenome.mmusculus.ucsc.mm10/lilac.yaml b/prepare/r-bsgenome.mmusculus.ucsc.mm10/lilac.yaml new file mode 100644 index 0000000000..f03d42aa7d --- /dev/null +++ b/prepare/r-bsgenome.mmusculus.ucsc.mm10/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +update_on: +- regex: BSgenome.Mmusculus.UCSC.mm10_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10 diff --git a/prepare/r-bsgenome.mmusculus.ucsc.mm9/PKGBUILD b/prepare/r-bsgenome.mmusculus.ucsc.mm9/PKGBUILD new file mode 100644 index 0000000000..4f8e358ada --- /dev/null +++ b/prepare/r-bsgenome.mmusculus.ucsc.mm9/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BSgenome.Mmusculus.UCSC.mm9 +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Full genome sequences for Mus musculus (UCSC version mm9)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bsgenome +) +optdepends=( + r-txdb.mmusculus.ucsc.mm9.knowngene +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bsgenome.mmusculus.ucsc.mm9/lilac.py b/prepare/r-bsgenome.mmusculus.ucsc.mm9/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bsgenome.mmusculus.ucsc.mm9/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bsgenome.mmusculus.ucsc.mm9/lilac.yaml b/prepare/r-bsgenome.mmusculus.ucsc.mm9/lilac.yaml new file mode 100644 index 0000000000..44c1f6bfe8 --- /dev/null +++ b/prepare/r-bsgenome.mmusculus.ucsc.mm9/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +update_on: +- regex: BSgenome.Mmusculus.UCSC.mm9_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9 diff --git a/prepare/r-bsgenome/PKGBUILD b/prepare/r-bsgenome/PKGBUILD new file mode 100644 index 0000000000..d53bbdc785 --- /dev/null +++ b/prepare/r-bsgenome/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BSgenome +_pkgver=1.62.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Software infrastructure for efficient representation of full genomes and their SNPs' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biostrings + r-genomeinfodb + r-genomicranges + r-iranges + r-matrixstats + r-rsamtools + r-rtracklayer + r-s4vectors + r-xvector +) +optdepends=( + r-biobase + r-biocmanager + r-bsgenome.celegans.ucsc.ce2 + r-bsgenome.hsapiens.ncbi.grch38 + r-bsgenome.hsapiens.ucsc.hg38 + r-bsgenome.hsapiens.ucsc.hg38.masked + r-bsgenome.mmusculus.ucsc.mm10 + r-bsgenome.rnorvegicus.ucsc.rn5 + r-bsgenome.scerevisiae.ucsc.saccer1 + r-hgu95av2probe + r-runit + r-snplocs.hsapiens.dbsnp144.grch38 + r-txdb.hsapiens.ucsc.hg38.knowngene + r-txdb.mmusculus.ucsc.mm10.knowngene + r-xtrasnplocs.hsapiens.dbsnp144.grch38 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bsgenome/lilac.py b/prepare/r-bsgenome/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bsgenome/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bsgenome/lilac.yaml b/prepare/r-bsgenome/lilac.yaml new file mode 100644 index 0000000000..f08bbf9bf4 --- /dev/null +++ b/prepare/r-bsgenome/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-matrixstats +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-xvector +update_on: +- regex: BSgenome_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BSgenome diff --git a/prepare/r-bslib/PKGBUILD b/prepare/r-bslib/PKGBUILD new file mode 100644 index 0000000000..d4eb6ecfad --- /dev/null +++ b/prepare/r-bslib/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bslib +_pkgver=0.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmltools + r-jquerylib + r-jsonlite + r-rlang + r-sass +) +optdepends=( + r-curl + r-knitr + r-magrittr + r-rappdirs + r-rmarkdown + r-shiny + r-testthat + r-thematic + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bslib/lilac.py b/prepare/r-bslib/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bslib/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bslib/lilac.yaml b/prepare/r-bslib/lilac.yaml new file mode 100644 index 0000000000..6358d696b6 --- /dev/null +++ b/prepare/r-bslib/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-jquerylib +- r-jsonlite +- r-rlang +- r-sass +update_on: +- regex: bslib_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bslib diff --git a/prepare/r-bsplus/PKGBUILD b/prepare/r-bsplus/PKGBUILD new file mode 100644 index 0000000000..23dce12970 --- /dev/null +++ b/prepare/r-bsplus/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bsplus +_pkgver=0.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Adds Functionality to the R Markdown + Shiny Bootstrap Framework' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-glue + r-htmltools + r-jsonlite + r-lubridate + r-magrittr + r-purrr + r-rmarkdown + r-stringr +) +optdepends=( + r-covr + r-knitr + r-markdown + r-shiny + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bsplus/lilac.py b/prepare/r-bsplus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bsplus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bsplus/lilac.yaml b/prepare/r-bsplus/lilac.yaml new file mode 100644 index 0000000000..c133465599 --- /dev/null +++ b/prepare/r-bsplus/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-glue +- r-htmltools +- r-jsonlite +- r-lubridate +- r-magrittr +- r-purrr +- r-rmarkdown +- r-stringr +update_on: +- regex: bsplus_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=bsplus diff --git a/prepare/r-bsseq/PKGBUILD b/prepare/r-bsseq/PKGBUILD new file mode 100644 index 0000000000..d6aa1e1d2e --- /dev/null +++ b/prepare/r-bsseq/PKGBUILD @@ -0,0 +1,63 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=bsseq +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analyze, manage and store bisulfite sequencing data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-beachmat + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-data.table + r-delayedarray + r-delayedmatrixstats + r-genomeinfodb + r-genomicranges + r-gtools + r-hdf5array + r-iranges + r-limma + r-locfit + r-permute + r-r.utils + r-rcpp + r-rhdf5 + r-s4vectors + r-scales + r-summarizedexperiment +) +optdepends=( + r-batchjobs + r-beachmat + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg38 + r-bsseqdata + r-doparallel + r-knitr + r-matrix + r-rmarkdown + r-rtracklayer + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bsseq/lilac.py b/prepare/r-bsseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bsseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bsseq/lilac.yaml b/prepare/r-bsseq/lilac.yaml new file mode 100644 index 0000000000..73da8bed53 --- /dev/null +++ b/prepare/r-bsseq/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beachmat +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-data.table +- r-delayedarray +- r-delayedmatrixstats +- r-genomeinfodb +- r-genomicranges +- r-gtools +- r-hdf5array +- r-iranges +- r-limma +- r-locfit +- r-permute +- r-r.utils +- r-rcpp +- r-rhdf5 +- r-s4vectors +- r-scales +- r-summarizedexperiment +update_on: +- regex: bsseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bsseq diff --git a/prepare/r-bubbletree/PKGBUILD b/prepare/r-bubbletree/PKGBUILD new file mode 100644 index 0000000000..0ee297a15c --- /dev/null +++ b/prepare/r-bubbletree/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BubbleTree +_pkgver=2.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-biocgenerics + r-biocstyle + r-biovizbase + r-dplyr + r-e1071 + r-genomicranges + r-ggplot2 + r-gridextra + r-gtable + r-gtools + r-iranges + r-limma + r-magrittr + r-plyr + r-rcolorbrewer + r-writexls +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bubbletree/lilac.py b/prepare/r-bubbletree/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bubbletree/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bubbletree/lilac.yaml b/prepare/r-bubbletree/lilac.yaml new file mode 100644 index 0000000000..260e570f23 --- /dev/null +++ b/prepare/r-bubbletree/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocstyle +- r-biovizbase +- r-dplyr +- r-e1071 +- r-genomicranges +- r-ggplot2 +- r-gridextra +- r-gtable +- r-gtools +- r-iranges +- r-limma +- r-magrittr +- r-plyr +- r-rcolorbrewer +- r-writexls +update_on: +- regex: BubbleTree_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BubbleTree diff --git a/prepare/r-bufferedmatrix/PKGBUILD b/prepare/r-bufferedmatrix/PKGBUILD new file mode 100644 index 0000000000..624371eeb9 --- /dev/null +++ b/prepare/r-bufferedmatrix/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BufferedMatrix +_pkgver=1.58.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A matrix data storage object held in temporary files' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bufferedmatrix/lilac.py b/prepare/r-bufferedmatrix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bufferedmatrix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bufferedmatrix/lilac.yaml b/prepare/r-bufferedmatrix/lilac.yaml new file mode 100644 index 0000000000..73af77e28a --- /dev/null +++ b/prepare/r-bufferedmatrix/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: BufferedMatrix_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BufferedMatrix diff --git a/prepare/r-bufferedmatrixmethods/PKGBUILD b/prepare/r-bufferedmatrixmethods/PKGBUILD new file mode 100644 index 0000000000..45a3fedc33 --- /dev/null +++ b/prepare/r-bufferedmatrixmethods/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BufferedMatrixMethods +_pkgver=1.58.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Microarray Data related methods that utlize BufferedMatrix objects' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bufferedmatrix +) +optdepends=( + r-affy + r-affyio +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bufferedmatrixmethods/lilac.py b/prepare/r-bufferedmatrixmethods/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bufferedmatrixmethods/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bufferedmatrixmethods/lilac.yaml b/prepare/r-bufferedmatrixmethods/lilac.yaml new file mode 100644 index 0000000000..b6b265b181 --- /dev/null +++ b/prepare/r-bufferedmatrixmethods/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bufferedmatrix +update_on: +- regex: BufferedMatrixMethods_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BufferedMatrixMethods diff --git a/prepare/r-bugsigdbr/PKGBUILD b/prepare/r-bugsigdbr/PKGBUILD new file mode 100644 index 0000000000..6824be3ac0 --- /dev/null +++ b/prepare/r-bugsigdbr/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bugsigdbr +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R-side access to published microbial signatures from BugSigDB' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocfilecache + r-vroom +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bugsigdbr/lilac.py b/prepare/r-bugsigdbr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bugsigdbr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bugsigdbr/lilac.yaml b/prepare/r-bugsigdbr/lilac.yaml new file mode 100644 index 0000000000..444d95d549 --- /dev/null +++ b/prepare/r-bugsigdbr/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-vroom +update_on: +- regex: bugsigdbr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bugsigdbr diff --git a/prepare/r-bumhmm/PKGBUILD b/prepare/r-bumhmm/PKGBUILD new file mode 100644 index 0000000000..2a7c83f7f4 --- /dev/null +++ b/prepare/r-bumhmm/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BUMHMM +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Computational pipeline for computing probability of modification from structure probing experiment data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-devtools + r-gtools + r-iranges + r-stringi + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bumhmm/lilac.py b/prepare/r-bumhmm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bumhmm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bumhmm/lilac.yaml b/prepare/r-bumhmm/lilac.yaml new file mode 100644 index 0000000000..6ba5527c5d --- /dev/null +++ b/prepare/r-bumhmm/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-devtools +- r-gtools +- r-iranges +- r-stringi +- r-summarizedexperiment +update_on: +- regex: BUMHMM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BUMHMM diff --git a/prepare/r-bumphunter/PKGBUILD b/prepare/r-bumphunter/PKGBUILD new file mode 100644 index 0000000000..c1250a2dff --- /dev/null +++ b/prepare/r-bumphunter/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=bumphunter +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bump Hunter' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biocgenerics + r-dorng + r-foreach + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-iterators + r-limma + r-locfit + r-matrixstats + r-s4vectors +) +optdepends=( + r-doparallel + r-org.hs.eg.db + r-runit + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bumphunter/lilac.py b/prepare/r-bumphunter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bumphunter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bumphunter/lilac.yaml b/prepare/r-bumphunter/lilac.yaml new file mode 100644 index 0000000000..3e53b84446 --- /dev/null +++ b/prepare/r-bumphunter/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-dorng +- r-foreach +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-iterators +- r-limma +- r-locfit +- r-matrixstats +- r-s4vectors +update_on: +- regex: bumphunter_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/bumphunter diff --git a/prepare/r-bumpymatrix/PKGBUILD b/prepare/r-bumpymatrix/PKGBUILD new file mode 100644 index 0000000000..7db17f4976 --- /dev/null +++ b/prepare/r-bumpymatrix/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BumpyMatrix +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bumpy Matrix of Non-Scalar Objects' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-iranges + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bumpymatrix/lilac.py b/prepare/r-bumpymatrix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bumpymatrix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bumpymatrix/lilac.yaml b/prepare/r-bumpymatrix/lilac.yaml new file mode 100644 index 0000000000..922829ee22 --- /dev/null +++ b/prepare/r-bumpymatrix/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-iranges +- r-s4vectors +update_on: +- regex: BumpyMatrix_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BumpyMatrix diff --git a/prepare/r-bus/PKGBUILD b/prepare/r-bus/PKGBUILD new file mode 100644 index 0000000000..72cbd016a3 --- /dev/null +++ b/prepare/r-bus/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BUS +_pkgver=1.50.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene network reconstruction' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-infotheo + r-minet +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bus/lilac.py b/prepare/r-bus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bus/lilac.yaml b/prepare/r-bus/lilac.yaml new file mode 100644 index 0000000000..8d4706c5e6 --- /dev/null +++ b/prepare/r-bus/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-infotheo +- r-minet +update_on: +- regex: BUS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BUS diff --git a/prepare/r-buscorrect/PKGBUILD b/prepare/r-buscorrect/PKGBUILD new file mode 100644 index 0000000000..d3a612a515 --- /dev/null +++ b/prepare/r-buscorrect/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BUScorrect +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Batch Effects Correction with Unknown Subtypes' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-gplots + r-summarizedexperiment +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-buscorrect/lilac.py b/prepare/r-buscorrect/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-buscorrect/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-buscorrect/lilac.yaml b/prepare/r-buscorrect/lilac.yaml new file mode 100644 index 0000000000..98a88029eb --- /dev/null +++ b/prepare/r-buscorrect/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gplots +- r-summarizedexperiment +update_on: +- regex: BUScorrect_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BUScorrect diff --git a/prepare/r-busparse/PKGBUILD b/prepare/r-busparse/PKGBUILD new file mode 100644 index 0000000000..78c7955152 --- /dev/null +++ b/prepare/r-busparse/PKGBUILD @@ -0,0 +1,62 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=BUSpaRse +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='kallisto | bustools R utilities' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-annotationdbi + r-annotationfilter + r-bh + r-biocgenerics + r-biomart + r-biostrings + r-bsgenome + r-dplyr + r-ensembldb + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-magrittr + r-plyranges + r-rcpp + r-rcpparmadillo + r-rcppprogress + r-s4vectors + r-stringr + r-tibble + r-tidyr + r-zeallot +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg38 + r-ensdb.hsapiens.v86 + r-knitr + r-rmarkdown + r-tenxbusdata + r-testthat + r-txdb.hsapiens.ucsc.hg38.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-busparse/lilac.py b/prepare/r-busparse/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-busparse/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-busparse/lilac.yaml b/prepare/r-busparse/lilac.yaml new file mode 100644 index 0000000000..06eaef310d --- /dev/null +++ b/prepare/r-busparse/lilac.yaml @@ -0,0 +1,33 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationfilter +- r-bh +- r-biocgenerics +- r-biomart +- r-biostrings +- r-bsgenome +- r-dplyr +- r-ensembldb +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-magrittr +- r-plyranges +- r-rcpp +- r-rcpparmadillo +- r-rcppprogress +- r-s4vectors +- r-stringr +- r-tibble +- r-tidyr +- r-zeallot +update_on: +- regex: BUSpaRse_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BUSpaRse diff --git a/prepare/r-busseq/PKGBUILD b/prepare/r-busseq/PKGBUILD new file mode 100644 index 0000000000..366ab29837 --- /dev/null +++ b/prepare/r-busseq/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BUSseq +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Batch Effect Correction with Unknow Subtypes for scRNA-seq data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-gplots + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-busseq/lilac.py b/prepare/r-busseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-busseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-busseq/lilac.yaml b/prepare/r-busseq/lilac.yaml new file mode 100644 index 0000000000..af03b7a28b --- /dev/null +++ b/prepare/r-busseq/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gplots +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: BUSseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/BUSseq diff --git a/prepare/r-bwstest/PKGBUILD b/prepare/r-bwstest/PKGBUILD new file mode 100644 index 0000000000..bfd5f129aa --- /dev/null +++ b/prepare/r-bwstest/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=BWStest +_pkgver=0.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Baumgartner Weiss Schindler Test of Equal Distributions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-memoise + r-rcpp +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-bwstest/lilac.py b/prepare/r-bwstest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-bwstest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-bwstest/lilac.yaml b/prepare/r-bwstest/lilac.yaml new file mode 100644 index 0000000000..d7633ceb4d --- /dev/null +++ b/prepare/r-bwstest/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-memoise +- r-rcpp +update_on: +- regex: BWStest_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=BWStest diff --git a/prepare/r-c3net/PKGBUILD b/prepare/r-c3net/PKGBUILD new file mode 100644 index 0000000000..f6360391fa --- /dev/null +++ b/prepare/r-c3net/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=c3net +_pkgver=1.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Infering large-scale gene networks with C3NET' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-igraph +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-c3net/lilac.py b/prepare/r-c3net/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-c3net/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-c3net/lilac.yaml b/prepare/r-c3net/lilac.yaml new file mode 100644 index 0000000000..cffb396969 --- /dev/null +++ b/prepare/r-c3net/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +update_on: +- regex: c3net_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=c3net diff --git a/prepare/r-c50/PKGBUILD b/prepare/r-c50/PKGBUILD new file mode 100644 index 0000000000..b80e76bb66 --- /dev/null +++ b/prepare/r-c50/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=C50 +_pkgver=0.1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='C5.0 Decision Trees and Rule-Based Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-cubist + r-partykit +) +optdepends=( + r-covr + r-knitr + r-modeldata + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-c50/lilac.py b/prepare/r-c50/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-c50/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-c50/lilac.yaml b/prepare/r-c50/lilac.yaml new file mode 100644 index 0000000000..1100ed3538 --- /dev/null +++ b/prepare/r-c50/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cubist +- r-partykit +update_on: +- regex: C50_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=C50 diff --git a/prepare/r-caen/PKGBUILD b/prepare/r-caen/PKGBUILD new file mode 100644 index 0000000000..766d57ff8a --- /dev/null +++ b/prepare/r-caen/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CAEN +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Category encoding method for selecting feature genes for the classification of single-cell RNA-seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-poiclaclu + r-summarizedexperiment +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-caen/lilac.py b/prepare/r-caen/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-caen/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-caen/lilac.yaml b/prepare/r-caen/lilac.yaml new file mode 100644 index 0000000000..173ab8570d --- /dev/null +++ b/prepare/r-caen/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-poiclaclu +- r-summarizedexperiment +update_on: +- regex: CAEN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CAEN diff --git a/prepare/r-cafe/PKGBUILD b/prepare/r-cafe/PKGBUILD new file mode 100644 index 0000000000..26ca517b10 --- /dev/null +++ b/prepare/r-cafe/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CAFE +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Chromosmal Aberrations Finder in Expression data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-annotate + r-biobase + r-biovizbase + r-genomicranges + r-ggbio + r-ggplot2 + r-gridextra + r-iranges +) +optdepends=( + r-biocgenerics + r-biocstyle + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cafe/lilac.py b/prepare/r-cafe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cafe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cafe/lilac.yaml b/prepare/r-cafe/lilac.yaml new file mode 100644 index 0000000000..271f60238d --- /dev/null +++ b/prepare/r-cafe/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-annotate +- r-biobase +- r-biovizbase +- r-genomicranges +- r-ggbio +- r-ggplot2 +- r-gridextra +- r-iranges +update_on: +- regex: CAFE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CAFE diff --git a/prepare/r-cagefightr/PKGBUILD b/prepare/r-cagefightr/PKGBUILD new file mode 100644 index 0000000000..8ef5b7ffed --- /dev/null +++ b/prepare/r-cagefightr/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CAGEfightR +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicfiles + r-genomicinteractions + r-genomicranges + r-gviz + r-interactionset + r-iranges + r-pryr + r-rtracklayer + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-org.mm.eg.db + r-rmarkdown + r-txdb.mmusculus.ucsc.mm9.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cagefightr/lilac.py b/prepare/r-cagefightr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cagefightr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cagefightr/lilac.yaml b/prepare/r-cagefightr/lilac.yaml new file mode 100644 index 0000000000..99ab97d9d1 --- /dev/null +++ b/prepare/r-cagefightr/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biocgenerics +- r-biocparallel +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicfiles +- r-genomicinteractions +- r-genomicranges +- r-gviz +- r-interactionset +- r-iranges +- r-pryr +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: CAGEfightR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CAGEfightR diff --git a/prepare/r-cageminer/PKGBUILD b/prepare/r-cageminer/PKGBUILD new file mode 100644 index 0000000000..2ce4cfe1f5 --- /dev/null +++ b/prepare/r-cageminer/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cageminer +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Candidate Gene Miner' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bionero + r-genomeinfodb + r-genomicranges + r-ggbio + r-ggplot2 + r-ggtext + r-iranges + r-reshape2 +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-summarizedexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cageminer/lilac.py b/prepare/r-cageminer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cageminer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cageminer/lilac.yaml b/prepare/r-cageminer/lilac.yaml new file mode 100644 index 0000000000..35aa8f1e14 --- /dev/null +++ b/prepare/r-cageminer/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bionero +- r-genomeinfodb +- r-genomicranges +- r-ggbio +- r-ggplot2 +- r-ggtext +- r-iranges +- r-reshape2 +update_on: +- regex: cageminer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cageminer diff --git a/prepare/r-cager/PKGBUILD b/prepare/r-cager/PKGBUILD new file mode 100644 index 0000000000..8af3bb6cc8 --- /dev/null +++ b/prepare/r-cager/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CAGEr +_pkgver=2.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-bsgenome + r-data.table + r-delayedarray + r-delayedmatrixstats + r-formula.tools + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-gtools + r-iranges + r-memoise + r-multiassayexperiment + r-plyr + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors + r-som + r-stringdist + r-stringi + r-summarizedexperiment + r-vegan + r-vgam +) +optdepends=( + r-biocstyle + r-bsgenome.drerio.ucsc.danrer7 + r-deseq2 + r-fantom3and4cage + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cager/lilac.py b/prepare/r-cager/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cager/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cager/lilac.yaml b/prepare/r-cager/lilac.yaml new file mode 100644 index 0000000000..a203766289 --- /dev/null +++ b/prepare/r-cager/lilac.yaml @@ -0,0 +1,35 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-bsgenome +- r-data.table +- r-delayedarray +- r-delayedmatrixstats +- r-formula.tools +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-gtools +- r-iranges +- r-memoise +- r-multiassayexperiment +- r-plyr +- r-reshape2 +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-som +- r-stringdist +- r-stringi +- r-summarizedexperiment +- r-vegan +- r-vgam +update_on: +- regex: CAGEr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CAGEr diff --git a/prepare/r-cairo/PKGBUILD b/prepare/r-cairo/PKGBUILD new file mode 100644 index 0000000000..bd352f3795 --- /dev/null +++ b/prepare/r-cairo/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: cairo (>= 1.2 http://www.cairographics.org/) +# Maintainer: Guoyi Zhang + +_pkgname=Cairo +_pkgver=1.5-14 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Graphics Device using Cairo Graphics Library for Creating High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and Win32) Output' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-fastrweb + r-png +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cairo/lilac.py b/prepare/r-cairo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cairo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cairo/lilac.yaml b/prepare/r-cairo/lilac.yaml new file mode 100644 index 0000000000..c8fb9f4e9c --- /dev/null +++ b/prepare/r-cairo/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Cairo_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Cairo diff --git a/prepare/r-calibrate/PKGBUILD b/prepare/r-calibrate/PKGBUILD new file mode 100644 index 0000000000..80ba124a40 --- /dev/null +++ b/prepare/r-calibrate/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=calibrate +_pkgver=1.7.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Calibration of Scatterplot and Biplot Axes' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-calibrate/lilac.py b/prepare/r-calibrate/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-calibrate/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-calibrate/lilac.yaml b/prepare/r-calibrate/lilac.yaml new file mode 100644 index 0000000000..e7680da0ea --- /dev/null +++ b/prepare/r-calibrate/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: calibrate_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=calibrate diff --git a/prepare/r-callr/PKGBUILD b/prepare/r-callr/PKGBUILD new file mode 100644 index 0000000000..7680df5f7e --- /dev/null +++ b/prepare/r-callr/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=callr +_pkgver=3.7.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Call R from R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-processx + r-r6 +) +optdepends=( + r-cli + r-covr + r-ps + r-rprojroot + r-spelling + r-testthat + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-callr/lilac.py b/prepare/r-callr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-callr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-callr/lilac.yaml b/prepare/r-callr/lilac.yaml new file mode 100644 index 0000000000..26da2af724 --- /dev/null +++ b/prepare/r-callr/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-processx +- r-r6 +update_on: +- regex: callr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=callr diff --git a/prepare/r-calm/PKGBUILD b/prepare/r-calm/PKGBUILD new file mode 100644 index 0000000000..beff6788f6 --- /dev/null +++ b/prepare/r-calm/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=calm +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Covariate Assisted Large-scale Multiple testing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-calm/lilac.py b/prepare/r-calm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-calm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-calm/lilac.yaml b/prepare/r-calm/lilac.yaml new file mode 100644 index 0000000000..778b589e68 --- /dev/null +++ b/prepare/r-calm/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: calm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/calm diff --git a/prepare/r-camera/PKGBUILD b/prepare/r-camera/PKGBUILD new file mode 100644 index 0000000000..a2bd5d1e81 --- /dev/null +++ b/prepare/r-camera/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CAMERA +_pkgver=1.50.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Collection of annotation related methods for mass spectrometry data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-graph + r-hmisc + r-igraph + r-rbgl + r-xcms +) +optdepends=( + r-biocgenerics + r-faahko + r-rmpi + r-runit + r-snow +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-camera/lilac.py b/prepare/r-camera/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-camera/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-camera/lilac.yaml b/prepare/r-camera/lilac.yaml new file mode 100644 index 0000000000..cc954f27f8 --- /dev/null +++ b/prepare/r-camera/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-graph +- r-hmisc +- r-igraph +- r-rbgl +- r-xcms +update_on: +- regex: CAMERA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CAMERA diff --git a/prepare/r-cancer/PKGBUILD b/prepare/r-cancer/PKGBUILD new file mode 100644 index 0000000000..e3fe63863c --- /dev/null +++ b/prepare/r-cancer/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=canceR +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-cgdsr + r-circlize + r-formula + r-genetclassifier + r-gseabase + r-phenotest + r-plyr + r-runit + r-tcltk2 + r-tkrplot +) +optdepends=( + r-r.rsp + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cancer/lilac.py b/prepare/r-cancer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cancer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cancer/lilac.yaml b/prepare/r-cancer/lilac.yaml new file mode 100644 index 0000000000..69ab18e545 --- /dev/null +++ b/prepare/r-cancer/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-cgdsr +- r-circlize +- r-formula +- r-genetclassifier +- r-gseabase +- r-phenotest +- r-plyr +- r-runit +- r-tcltk2 +- r-tkrplot +update_on: +- regex: canceR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/canceR diff --git a/prepare/r-cancerclass/PKGBUILD b/prepare/r-cancerclass/PKGBUILD new file mode 100644 index 0000000000..ccbfec9ed9 --- /dev/null +++ b/prepare/r-cancerclass/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cancerclass +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Development and validation of diagnostic tests from high-dimensional molecular data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-binom + r-biobase +) +optdepends=( + r-cancerdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cancerclass/lilac.py b/prepare/r-cancerclass/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cancerclass/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cancerclass/lilac.yaml b/prepare/r-cancerclass/lilac.yaml new file mode 100644 index 0000000000..55861bc11b --- /dev/null +++ b/prepare/r-cancerclass/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-binom +- r-biobase +update_on: +- regex: cancerclass_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cancerclass diff --git a/prepare/r-cancerinsilico/PKGBUILD b/prepare/r-cancerinsilico/PKGBUILD new file mode 100644 index 0000000000..f252d4727b --- /dev/null +++ b/prepare/r-cancerinsilico/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CancerInSilico +_pkgver=2.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R interface for computational modeling of tumor progression' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bh + r-rcpp +) +optdepends=( + r-biocstyle + r-gplots + r-knitr + r-rgl + r-rmarkdown + r-rtsne + r-testthat + r-viridis +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cancerinsilico/lilac.py b/prepare/r-cancerinsilico/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cancerinsilico/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cancerinsilico/lilac.yaml b/prepare/r-cancerinsilico/lilac.yaml new file mode 100644 index 0000000000..b259802ad7 --- /dev/null +++ b/prepare/r-cancerinsilico/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-rcpp +update_on: +- regex: CancerInSilico_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CancerInSilico diff --git a/prepare/r-cancersubtypes/PKGBUILD b/prepare/r-cancersubtypes/PKGBUILD new file mode 100644 index 0000000000..df5fbfbeb9 --- /dev/null +++ b/prepare/r-cancersubtypes/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CancerSubtypes +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cancer subtypes identification, validation and visualization based on multiple genomic data sets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-consensusclusterplus + r-icluster + r-impute + r-limma + r-nmf + r-sigclust +) +optdepends=( + r-biocgenerics + r-knitr + r-rmarkdown + r-rtcga.mrna +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cancersubtypes/lilac.py b/prepare/r-cancersubtypes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cancersubtypes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cancersubtypes/lilac.yaml b/prepare/r-cancersubtypes/lilac.yaml new file mode 100644 index 0000000000..e9566b3309 --- /dev/null +++ b/prepare/r-cancersubtypes/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-consensusclusterplus +- r-icluster +- r-impute +- r-limma +- r-nmf +- r-sigclust +update_on: +- regex: CancerSubtypes_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CancerSubtypes diff --git a/prepare/r-cand/PKGBUILD b/prepare/r-cand/PKGBUILD new file mode 100644 index 0000000000..629d6a8a0a --- /dev/null +++ b/prepare/r-cand/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CAnD +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Perform Chromosomal Ancestry Differences (CAnD) Analyses' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ggplot2 + r-reshape +) +optdepends=( + r-biocgenerics + r-biocstyle + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cand/lilac.py b/prepare/r-cand/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cand/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cand/lilac.yaml b/prepare/r-cand/lilac.yaml new file mode 100644 index 0000000000..eebae957d4 --- /dev/null +++ b/prepare/r-cand/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-reshape +update_on: +- regex: CAnD_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CAnD diff --git a/prepare/r-caomicsv/PKGBUILD b/prepare/r-caomicsv/PKGBUILD new file mode 100644 index 0000000000..5631a77ea5 --- /dev/null +++ b/prepare/r-caomicsv/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=caOmicsV +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization of multi-dimentional cancer genomics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bc3net + r-igraph +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-caomicsv/lilac.py b/prepare/r-caomicsv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-caomicsv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-caomicsv/lilac.yaml b/prepare/r-caomicsv/lilac.yaml new file mode 100644 index 0000000000..49e7b7f8fb --- /dev/null +++ b/prepare/r-caomicsv/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bc3net +- r-igraph +update_on: +- regex: caOmicsV_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/caOmicsV diff --git a/prepare/r-capushe/PKGBUILD b/prepare/r-capushe/PKGBUILD new file mode 100644 index 0000000000..333cff1e6d --- /dev/null +++ b/prepare/r-capushe/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=capushe +_pkgver=1.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CAlibrating Penalities Using Slope HEuristics' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-capushe/lilac.py b/prepare/r-capushe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-capushe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-capushe/lilac.yaml b/prepare/r-capushe/lilac.yaml new file mode 100644 index 0000000000..a95f74975c --- /dev/null +++ b/prepare/r-capushe/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: capushe_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=capushe diff --git a/prepare/r-car/PKGBUILD b/prepare/r-car/PKGBUILD new file mode 100644 index 0000000000..a7dc15a9e6 --- /dev/null +++ b/prepare/r-car/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=car +_pkgver=3.0-12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Companion to Applied Regression' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-cardata + r-lme4 + r-maptools + r-pbkrtest + r-quantreg +) +optdepends=( + r-alr4 + r-boot + r-coxme + r-effects + r-knitr + r-leaps + r-lmtest + r-matrix + r-matrixmodels + r-rgl + r-rio + r-sandwich + r-sparsem + r-survey + r-survival +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-car/lilac.py b/prepare/r-car/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-car/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-car/lilac.yaml b/prepare/r-car/lilac.yaml new file mode 100644 index 0000000000..3d10f63171 --- /dev/null +++ b/prepare/r-car/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-cardata +- r-lme4 +- r-maptools +- r-pbkrtest +- r-quantreg +update_on: +- regex: car_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=car diff --git a/prepare/r-cardata/PKGBUILD b/prepare/r-cardata/PKGBUILD new file mode 100644 index 0000000000..b917d44bd3 --- /dev/null +++ b/prepare/r-cardata/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=carData +_pkgver=3.0-5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Companion to Applied Regression Data Sets' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-car +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cardata/lilac.py b/prepare/r-cardata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cardata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cardata/lilac.yaml b/prepare/r-cardata/lilac.yaml new file mode 100644 index 0000000000..637fcc1cae --- /dev/null +++ b/prepare/r-cardata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: carData_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=carData diff --git a/prepare/r-cardinal/PKGBUILD b/prepare/r-cardinal/PKGBUILD new file mode 100644 index 0000000000..d1f5293df4 --- /dev/null +++ b/prepare/r-cardinal/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Cardinal +_pkgver=2.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A mass spectrometry imaging toolbox for statistical analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-dplyr + r-ebimage + r-irlba + r-magrittr + r-matter + r-mclust + r-protgenerics + r-s4vectors + r-signal + r-sp + r-viridislite +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cardinal/lilac.py b/prepare/r-cardinal/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cardinal/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cardinal/lilac.yaml b/prepare/r-cardinal/lilac.yaml new file mode 100644 index 0000000000..38a27ea6f6 --- /dev/null +++ b/prepare/r-cardinal/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-dplyr +- r-ebimage +- r-irlba +- r-magrittr +- r-matter +- r-mclust +- r-protgenerics +- r-s4vectors +- r-signal +- r-sp +- r-viridislite +update_on: +- regex: Cardinal_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Cardinal diff --git a/prepare/r-caret/PKGBUILD b/prepare/r-caret/PKGBUILD new file mode 100644 index 0000000000..bd77d7e617 --- /dev/null +++ b/prepare/r-caret/PKGBUILD @@ -0,0 +1,69 @@ +# Maintainer: Guoyi Zhang + +_pkgname=caret +_pkgver=6.0-90 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Classification and Regression Training' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-e1071 + r-foreach + r-ggplot2 + r-modelmetrics + r-plyr + r-proc + r-recipes + r-reshape2 + r-withr +) +optdepends=( + r-bradleyterry2 + r-covr + r-cubist + r-dplyr + r-earth + r-ellipse + r-fastica + r-gam + r-ipred + r-kernlab + r-klar + r-knitr + r-mass + r-matrix + r-mda + r-mgcv + r-mlbench + r-mlmetrics + r-nnet + r-pamr + r-party + r-pls + r-proxy + r-randomforest + r-rann + r-rmarkdown + r-rpart + r-spls + r-subselect + r-superpc + r-testthat + r-themis +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-caret/lilac.py b/prepare/r-caret/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-caret/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-caret/lilac.yaml b/prepare/r-caret/lilac.yaml new file mode 100644 index 0000000000..3429c81dc8 --- /dev/null +++ b/prepare/r-caret/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-e1071 +- r-foreach +- r-ggplot2 +- r-modelmetrics +- r-plyr +- r-proc +- r-recipes +- r-reshape2 +- r-withr +update_on: +- regex: caret_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=caret diff --git a/prepare/r-caretensemble/PKGBUILD b/prepare/r-caretensemble/PKGBUILD new file mode 100644 index 0000000000..47ae0002e2 --- /dev/null +++ b/prepare/r-caretensemble/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=caretEnsemble +_pkgver=2.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Ensembles of Caret Models' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-caret + r-data.table + r-digest + r-ggplot2 + r-gridextra + r-pbapply + r-plyr +) +optdepends=( + r-catools + r-e1071 + r-gbm + r-glmnet + r-ipred + r-kernlab + r-klar + r-knitr + r-lintr + r-mass + r-mlbench + r-nnet + r-proc + r-randomforest + r-rmarkdown + r-rpart + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-caretensemble/lilac.py b/prepare/r-caretensemble/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-caretensemble/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-caretensemble/lilac.yaml b/prepare/r-caretensemble/lilac.yaml new file mode 100644 index 0000000000..f8233556b8 --- /dev/null +++ b/prepare/r-caretensemble/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-caret +- r-data.table +- r-digest +- r-ggplot2 +- r-gridextra +- r-pbapply +- r-plyr +update_on: +- regex: caretEnsemble_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=caretEnsemble diff --git a/prepare/r-carnival/PKGBUILD b/prepare/r-carnival/PKGBUILD new file mode 100644 index 0000000000..74a27f2fc4 --- /dev/null +++ b/prepare/r-carnival/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CARNIVAL +_pkgver=2.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-igraph + r-lpsolve + r-readr + r-rjson + r-rmarkdown + r-stringr +) +optdepends=( + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-carnival/lilac.py b/prepare/r-carnival/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-carnival/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-carnival/lilac.yaml b/prepare/r-carnival/lilac.yaml new file mode 100644 index 0000000000..5369ec3312 --- /dev/null +++ b/prepare/r-carnival/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-igraph +- r-lpsolve +- r-readr +- r-rjson +- r-rmarkdown +- r-stringr +update_on: +- regex: CARNIVAL_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CARNIVAL diff --git a/prepare/r-casper/PKGBUILD b/prepare/r-casper/PKGBUILD new file mode 100644 index 0000000000..0e4b596af0 --- /dev/null +++ b/prepare/r-casper/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=casper +_pkgver=2.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Characterization of Alternative Splicing based on Paired-End Reads' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-coda + r-ebarrays + r-gaga + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-gtools + r-iranges + r-limma + r-rsamtools + r-rtracklayer + r-s4vectors + r-sqldf + r-vgam +) +optdepends=( + r-parallel +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-casper/lilac.py b/prepare/r-casper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-casper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-casper/lilac.yaml b/prepare/r-casper/lilac.yaml new file mode 100644 index 0000000000..482eef69ec --- /dev/null +++ b/prepare/r-casper/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-coda +- r-ebarrays +- r-gaga +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-gtools +- r-iranges +- r-limma +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-sqldf +- r-vgam +update_on: +- regex: casper_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/casper diff --git a/prepare/r-catalyst/PKGBUILD b/prepare/r-catalyst/PKGBUILD new file mode 100644 index 0000000000..1f75480694 --- /dev/null +++ b/prepare/r-catalyst/PKGBUILD @@ -0,0 +1,62 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CATALYST +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cytometry dATa anALYSis Tools' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-circlize + r-complexheatmap + r-consensusclusterplus + r-cowplot + r-data.table + r-dplyr + r-drc + r-flowcore + r-flowsom + r-ggplot2 + r-ggrepel + r-ggridges + r-gridextra + r-magrittr + r-matrixstats + r-nnls + r-purrr + r-rcolorbrewer + r-reshape2 + r-rtsne + r-s4vectors + r-scales + r-scater + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-diffcyt + r-flowworkspace + r-ggcyto + r-knitr + r-opencyto + r-rmarkdown + r-testthat + r-uwot +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-catalyst/lilac.py b/prepare/r-catalyst/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-catalyst/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-catalyst/lilac.yaml b/prepare/r-catalyst/lilac.yaml new file mode 100644 index 0000000000..b66743b5b5 --- /dev/null +++ b/prepare/r-catalyst/lilac.yaml @@ -0,0 +1,34 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circlize +- r-complexheatmap +- r-consensusclusterplus +- r-cowplot +- r-data.table +- r-dplyr +- r-drc +- r-flowcore +- r-flowsom +- r-ggplot2 +- r-ggrepel +- r-ggridges +- r-gridextra +- r-magrittr +- r-matrixstats +- r-nnls +- r-purrr +- r-rcolorbrewer +- r-reshape2 +- r-rtsne +- r-s4vectors +- r-scales +- r-scater +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: CATALYST_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CATALYST diff --git a/prepare/r-catdata/PKGBUILD b/prepare/r-catdata/PKGBUILD new file mode 100644 index 0000000000..73e1d94e42 --- /dev/null +++ b/prepare/r-catdata/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=catdata +_pkgver=1.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Categorical Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-class + r-e1071 + r-ecdat + r-flexmix + r-gamboost + r-gee + r-geepack + r-glmmml + r-glmnet + r-lme4 + r-lpsolve + r-mboost + r-mgcv + r-mlogit + r-nnet + r-ordinal + r-party + r-penalized + r-pscl + r-qvcalc + r-rms + r-rpart + r-vcdextra + r-vgam +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-catdata/lilac.py b/prepare/r-catdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-catdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-catdata/lilac.yaml b/prepare/r-catdata/lilac.yaml new file mode 100644 index 0000000000..946b893372 --- /dev/null +++ b/prepare/r-catdata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: catdata_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=catdata diff --git a/prepare/r-category/PKGBUILD b/prepare/r-category/PKGBUILD new file mode 100644 index 0000000000..f12811ddbd --- /dev/null +++ b/prepare/r-category/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Category +_pkgver=2.60.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Category Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-genefilter + r-graph + r-gseabase + r-rbgl +) +optdepends=( + r-all + r-ebarrays + r-geneplotter + r-go.db + r-gostats + r-hgu95av2.db + r-karyoploter + r-keggrest + r-lattice + r-limma + r-org.sc.sgd.db + r-rcolorbrewer + r-rgraphviz + r-runit + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-category/lilac.py b/prepare/r-category/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-category/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-category/lilac.yaml b/prepare/r-category/lilac.yaml new file mode 100644 index 0000000000..20af28ca59 --- /dev/null +++ b/prepare/r-category/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-dbi +- r-genefilter +- r-graph +- r-gseabase +- r-rbgl +update_on: +- regex: Category_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Category diff --git a/prepare/r-categorycompare/PKGBUILD b/prepare/r-categorycompare/PKGBUILD new file mode 100644 index 0000000000..cbbe07c686 --- /dev/null +++ b/prepare/r-categorycompare/PKGBUILD @@ -0,0 +1,50 @@ +# system requirements: Cytoscape (>= 3.6.1) (if used for visualization ofresults, heavily suggested) +# Maintainer: Guoyi Zhang + +_pkgname=categoryCompare +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Meta-analysis of high-throughput experiments using feature annotations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-category + r-colorspace + r-gostats + r-graph + r-gseabase + r-hwriter + r-rcy3 +) +optdepends=( + r-affy + r-estrogen + r-genefilter + r-go.db + r-hgu95av2.db + r-keggrest + r-knitr + r-limma + r-org.hs.eg.db + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-categorycompare/lilac.py b/prepare/r-categorycompare/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-categorycompare/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-categorycompare/lilac.yaml b/prepare/r-categorycompare/lilac.yaml new file mode 100644 index 0000000000..c28427141d --- /dev/null +++ b/prepare/r-categorycompare/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-category +- r-colorspace +- r-gostats +- r-graph +- r-gseabase +- r-hwriter +- r-rcy3 +update_on: +- regex: categoryCompare_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/categoryCompare diff --git a/prepare/r-catencoders/PKGBUILD b/prepare/r-catencoders/PKGBUILD new file mode 100644 index 0000000000..172fa28db8 --- /dev/null +++ b/prepare/r-catencoders/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CatEncoders +_pkgver=0.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Encoders for Categorical Variables' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-data.table +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-catencoders/lilac.py b/prepare/r-catencoders/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-catencoders/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-catencoders/lilac.yaml b/prepare/r-catencoders/lilac.yaml new file mode 100644 index 0000000000..d2b15e6277 --- /dev/null +++ b/prepare/r-catencoders/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +update_on: +- regex: CatEncoders_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=CatEncoders diff --git a/prepare/r-catnet/PKGBUILD b/prepare/r-catnet/PKGBUILD new file mode 100644 index 0000000000..5aeca5f0c0 --- /dev/null +++ b/prepare/r-catnet/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=catnet +_pkgver=1.15.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Categorical Bayesian Network Inference' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-catnet/lilac.py b/prepare/r-catnet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-catnet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-catnet/lilac.yaml b/prepare/r-catnet/lilac.yaml new file mode 100644 index 0000000000..b800756dda --- /dev/null +++ b/prepare/r-catnet/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: catnet_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=catnet diff --git a/prepare/r-catools/PKGBUILD b/prepare/r-catools/PKGBUILD new file mode 100644 index 0000000000..18c40c94ce --- /dev/null +++ b/prepare/r-catools/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=caTools +_pkgver=1.18.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bitops +) +optdepends=( + r-mass + r-rpart +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-catools/lilac.py b/prepare/r-catools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-catools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-catools/lilac.yaml b/prepare/r-catools/lilac.yaml new file mode 100644 index 0000000000..b8b8c4836f --- /dev/null +++ b/prepare/r-catools/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bitops +update_on: +- regex: caTools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=caTools diff --git a/prepare/r-causalr/PKGBUILD b/prepare/r-causalr/PKGBUILD new file mode 100644 index 0000000000..99c936287f --- /dev/null +++ b/prepare/r-causalr/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CausalR +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Causal network analysis methods' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-igraph +) +optdepends=( + r-biocgenerics + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-causalr/lilac.py b/prepare/r-causalr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-causalr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-causalr/lilac.yaml b/prepare/r-causalr/lilac.yaml new file mode 100644 index 0000000000..0517f143ba --- /dev/null +++ b/prepare/r-causalr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +update_on: +- regex: CausalR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CausalR diff --git a/prepare/r-cba/PKGBUILD b/prepare/r-cba/PKGBUILD new file mode 100644 index 0000000000..2e661bbdc2 --- /dev/null +++ b/prepare/r-cba/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cba +_pkgver=0.2-21 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clustering for Business Analytics' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-proxy +) +optdepends=( + r-colorspace + r-gclus +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cba/lilac.py b/prepare/r-cba/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cba/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cba/lilac.yaml b/prepare/r-cba/lilac.yaml new file mode 100644 index 0000000000..fe50f451eb --- /dev/null +++ b/prepare/r-cba/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-proxy +update_on: +- regex: cba_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=cba diff --git a/prepare/r-cbaf/PKGBUILD b/prepare/r-cbaf/PKGBUILD new file mode 100644 index 0000000000..8733ad11c2 --- /dev/null +++ b/prepare/r-cbaf/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cbaf +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automated functions for comparing various omic data from cbioportal.org' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocfilecache + r-cgdsr + r-genefilter + r-gplots + r-openxlsx + r-rcolorbrewer +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cbaf/lilac.py b/prepare/r-cbaf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cbaf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cbaf/lilac.yaml b/prepare/r-cbaf/lilac.yaml new file mode 100644 index 0000000000..cfb4d8cc46 --- /dev/null +++ b/prepare/r-cbaf/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-cgdsr +- r-genefilter +- r-gplots +- r-openxlsx +- r-rcolorbrewer +update_on: +- regex: cbaf_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cbaf diff --git a/prepare/r-cbioportaldata/PKGBUILD b/prepare/r-cbioportaldata/PKGBUILD new file mode 100644 index 0000000000..b1455bb65c --- /dev/null +++ b/prepare/r-cbioportaldata/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cBioPortalData +_pkgver=2.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Exposes and makes available data from the cBioPortal web resources' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-anvil + r-biocfilecache + r-digest + r-dplyr + r-genomeinfodb + r-genomicranges + r-httr + r-iranges + r-multiassayexperiment + r-raggedexperiment + r-readr + r-rtcgatoolbox + r-s4vectors + r-summarizedexperiment + r-tcgautils + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-survival + r-survminer + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cbioportaldata/lilac.py b/prepare/r-cbioportaldata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cbioportaldata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cbioportaldata/lilac.yaml b/prepare/r-cbioportaldata/lilac.yaml new file mode 100644 index 0000000000..9d3ed4a4a3 --- /dev/null +++ b/prepare/r-cbioportaldata/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-anvil +- r-biocfilecache +- r-digest +- r-dplyr +- r-genomeinfodb +- r-genomicranges +- r-httr +- r-iranges +- r-multiassayexperiment +- r-raggedexperiment +- r-readr +- r-rtcgatoolbox +- r-s4vectors +- r-summarizedexperiment +- r-tcgautils +- r-tibble +- r-tidyr +update_on: +- regex: cBioPortalData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cBioPortalData diff --git a/prepare/r-cbpmanager/PKGBUILD b/prepare/r-cbpmanager/PKGBUILD new file mode 100644 index 0000000000..fd81ac6475 --- /dev/null +++ b/prepare/r-cbpmanager/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cbpManager +_pkgver=1.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-basilisk + r-dplyr + r-dt + r-htmltools + r-jsonlite + r-magrittr + r-markdown + r-plyr + r-rapportools + r-reticulate + r-rintrojs + r-shiny + r-shinybs + r-shinycssloaders + r-shinydashboard + r-vroom +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cbpmanager/lilac.py b/prepare/r-cbpmanager/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cbpmanager/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cbpmanager/lilac.yaml b/prepare/r-cbpmanager/lilac.yaml new file mode 100644 index 0000000000..9401da9ecb --- /dev/null +++ b/prepare/r-cbpmanager/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-basilisk +- r-dplyr +- r-dt +- r-htmltools +- r-jsonlite +- r-magrittr +- r-markdown +- r-plyr +- r-rapportools +- r-reticulate +- r-rintrojs +- r-shiny +- r-shinybs +- r-shinycssloaders +- r-shinydashboard +- r-vroom +update_on: +- regex: cbpManager_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cbpManager diff --git a/prepare/r-ccapp/PKGBUILD b/prepare/r-ccapp/PKGBUILD new file mode 100644 index 0000000000..b1465a3571 --- /dev/null +++ b/prepare/r-ccapp/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ccaPP +_pkgver=0.3.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='(Robust) Canonical Correlation Analysis via Projection Pursuit' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-pcapp + r-rcpp + r-rcpparmadillo + r-robustbase +) +optdepends=( + r-knitr + r-mvtnorm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ccapp/lilac.py b/prepare/r-ccapp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ccapp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ccapp/lilac.yaml b/prepare/r-ccapp/lilac.yaml new file mode 100644 index 0000000000..a197e3029a --- /dev/null +++ b/prepare/r-ccapp/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-pcapp +- r-rcpp +- r-rcpparmadillo +- r-robustbase +update_on: +- regex: ccaPP_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ccaPP diff --git a/prepare/r-ccdata/PKGBUILD b/prepare/r-ccdata/PKGBUILD new file mode 100644 index 0000000000..2daf62cdc6 --- /dev/null +++ b/prepare/r-ccdata/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ccdata +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data for Combination Connectivity Mapping (ccmap) Package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ccdata/lilac.py b/prepare/r-ccdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ccdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ccdata/lilac.yaml b/prepare/r-ccdata/lilac.yaml new file mode 100644 index 0000000000..2bfa9cf744 --- /dev/null +++ b/prepare/r-ccdata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ccdata_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ccdata diff --git a/prepare/r-ccdralgorithm/PKGBUILD b/prepare/r-ccdralgorithm/PKGBUILD new file mode 100644 index 0000000000..0f5002c39e --- /dev/null +++ b/prepare/r-ccdralgorithm/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ccdrAlgorithm +_pkgver=0.0.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CCDr Algorithm for Learning Sparse Gaussian Bayesian Networks' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-sparsebnutils +) +optdepends=( + r-graph + r-igraph + r-matrix + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ccdralgorithm/lilac.py b/prepare/r-ccdralgorithm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ccdralgorithm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ccdralgorithm/lilac.yaml b/prepare/r-ccdralgorithm/lilac.yaml new file mode 100644 index 0000000000..d3d9b29048 --- /dev/null +++ b/prepare/r-ccdralgorithm/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-sparsebnutils +update_on: +- regex: ccdrAlgorithm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ccdrAlgorithm diff --git a/prepare/r-ccfindr/PKGBUILD b/prepare/r-ccfindr/PKGBUILD new file mode 100644 index 0000000000..9103e10ba6 --- /dev/null +++ b/prepare/r-ccfindr/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ccfindR +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cancer Clone Finder' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-gtools + r-irlba + r-rcolorbrewer + r-rcpp + r-rcppeigen + r-rdpack + r-rmpi + r-rtsne + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ccfindr/lilac.py b/prepare/r-ccfindr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ccfindr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ccfindr/lilac.yaml b/prepare/r-ccfindr/lilac.yaml new file mode 100644 index 0000000000..daf361b616 --- /dev/null +++ b/prepare/r-ccfindr/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-gtools +- r-irlba +- r-rcolorbrewer +- r-rcpp +- r-rcppeigen +- r-rdpack +- r-rmpi +- r-rtsne +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: ccfindR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ccfindR diff --git a/prepare/r-ccmap/PKGBUILD b/prepare/r-ccmap/PKGBUILD new file mode 100644 index 0000000000..b1868923dd --- /dev/null +++ b/prepare/r-ccmap/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ccmap +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Combination Connectivity Mapping' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-biocmanager + r-ccdata + r-data.table + r-doparallel + r-foreach + r-lsa + r-xgboost +) +optdepends=( + r-crossmeta + r-knitr + r-lydata + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ccmap/lilac.py b/prepare/r-ccmap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ccmap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ccmap/lilac.yaml b/prepare/r-ccmap/lilac.yaml new file mode 100644 index 0000000000..4b313c6049 --- /dev/null +++ b/prepare/r-ccmap/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocmanager +- r-ccdata +- r-data.table +- r-doparallel +- r-foreach +- r-lsa +- r-xgboost +update_on: +- regex: ccmap_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ccmap diff --git a/prepare/r-ccp/PKGBUILD b/prepare/r-ccp/PKGBUILD new file mode 100644 index 0000000000..6f25b1d60f --- /dev/null +++ b/prepare/r-ccp/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CCP +_pkgver=1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Significance Tests for Canonical Correlation Analysis (CCA)' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ccp/lilac.py b/prepare/r-ccp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ccp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ccp/lilac.yaml b/prepare/r-ccp/lilac.yaml new file mode 100644 index 0000000000..bc06979cd7 --- /dev/null +++ b/prepare/r-ccp/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: CCP_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=CCP diff --git a/prepare/r-ccpromise/PKGBUILD b/prepare/r-ccpromise/PKGBUILD new file mode 100644 index 0000000000..0c43091584 --- /dev/null +++ b/prepare/r-ccpromise/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CCPROMISE +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-ccp + r-gseabase + r-promise +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ccpromise/lilac.py b/prepare/r-ccpromise/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ccpromise/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ccpromise/lilac.yaml b/prepare/r-ccpromise/lilac.yaml new file mode 100644 index 0000000000..b2a9105b97 --- /dev/null +++ b/prepare/r-ccpromise/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-ccp +- r-gseabase +- r-promise +update_on: +- regex: CCPROMISE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CCPROMISE diff --git a/prepare/r-ccrepe/PKGBUILD b/prepare/r-ccrepe/PKGBUILD new file mode 100644 index 0000000000..0117647314 --- /dev/null +++ b/prepare/r-ccrepe/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ccrepe +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ccrepe_and_nc.score' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-infotheo +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ccrepe/lilac.py b/prepare/r-ccrepe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ccrepe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ccrepe/lilac.yaml b/prepare/r-ccrepe/lilac.yaml new file mode 100644 index 0000000000..061a70ac33 --- /dev/null +++ b/prepare/r-ccrepe/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-infotheo +update_on: +- regex: ccrepe_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ccrepe diff --git a/prepare/r-cctensor/PKGBUILD b/prepare/r-cctensor/PKGBUILD new file mode 100644 index 0000000000..46d4c8b5cf --- /dev/null +++ b/prepare/r-cctensor/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ccTensor +_pkgver=1.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CUR/CX Tensor Decomposition' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-fields + r-igraph + r-rtensor +) +optdepends=( + r-nntensor + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cctensor/lilac.py b/prepare/r-cctensor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cctensor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cctensor/lilac.yaml b/prepare/r-cctensor/lilac.yaml new file mode 100644 index 0000000000..164563c1a0 --- /dev/null +++ b/prepare/r-cctensor/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fields +- r-igraph +- r-rtensor +update_on: +- regex: ccTensor_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ccTensor diff --git a/prepare/r-cdft/PKGBUILD b/prepare/r-cdft/PKGBUILD new file mode 100644 index 0000000000..515bdd4c2f --- /dev/null +++ b/prepare/r-cdft/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CDFt +_pkgver=1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Downscaling and Bias Correction via Non-Parametric CDF-Transform' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cdft/lilac.py b/prepare/r-cdft/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cdft/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cdft/lilac.yaml b/prepare/r-cdft/lilac.yaml new file mode 100644 index 0000000000..c0f31634b6 --- /dev/null +++ b/prepare/r-cdft/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: CDFt_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=CDFt diff --git a/prepare/r-celaref/PKGBUILD b/prepare/r-celaref/PKGBUILD new file mode 100644 index 0000000000..db7f150b18 --- /dev/null +++ b/prepare/r-celaref/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=celaref +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Single-cell RNAseq cell cluster labelling by reference' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-delayedarray + r-dplyr + r-ggplot2 + r-magrittr + r-mast + r-readr + r-rlang + r-s4vectors + r-summarizedexperiment + r-tibble +) +optdepends=( + r-experimenthub + r-knitr + r-limma + r-parallel + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-celaref/lilac.py b/prepare/r-celaref/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-celaref/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-celaref/lilac.yaml b/prepare/r-celaref/lilac.yaml new file mode 100644 index 0000000000..9500255acd --- /dev/null +++ b/prepare/r-celaref/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-delayedarray +- r-dplyr +- r-ggplot2 +- r-magrittr +- r-mast +- r-readr +- r-rlang +- r-s4vectors +- r-summarizedexperiment +- r-tibble +update_on: +- regex: celaref_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/celaref diff --git a/prepare/r-celda/PKGBUILD b/prepare/r-celda/PKGBUILD new file mode 100644 index 0000000000..0370d1fdb5 --- /dev/null +++ b/prepare/r-celda/PKGBUILD @@ -0,0 +1,70 @@ +# Maintainer: Guoyi Zhang + +_pkgname=celda +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CEllular Latent Dirichlet Allocation' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-circlize + r-complexheatmap + r-data.table + r-dbscan + r-delayedarray + r-digest + r-doparallel + r-enrichr + r-foreach + r-ggplot2 + r-ggrepel + r-gtable + r-matrixstats + r-mcmcprecision + r-multipanelfigure + r-plyr + r-rcolorbrewer + r-rcpp + r-rcppeigen + r-reshape2 + r-rtsne + r-s4vectors + r-scales + r-scater + r-scran + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-uwot + r-withr +) +optdepends=( + r-biocmanager + r-biocstyle + r-biomart + r-covr + r-knitr + r-m3dexampledata + r-rmarkdown + r-roxygen2 + r-singlecelltk + r-tenxpbmcdata + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-celda/lilac.py b/prepare/r-celda/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-celda/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-celda/lilac.yaml b/prepare/r-celda/lilac.yaml new file mode 100644 index 0000000000..9601fbcba1 --- /dev/null +++ b/prepare/r-celda/lilac.yaml @@ -0,0 +1,39 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circlize +- r-complexheatmap +- r-data.table +- r-dbscan +- r-delayedarray +- r-digest +- r-doparallel +- r-enrichr +- r-foreach +- r-ggplot2 +- r-ggrepel +- r-gtable +- r-matrixstats +- r-mcmcprecision +- r-multipanelfigure +- r-plyr +- r-rcolorbrewer +- r-rcpp +- r-rcppeigen +- r-reshape2 +- r-rtsne +- r-s4vectors +- r-scales +- r-scater +- r-scran +- r-singlecellexperiment +- r-stringr +- r-summarizedexperiment +- r-uwot +- r-withr +update_on: +- regex: celda_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/celda diff --git a/prepare/r-celestial/PKGBUILD b/prepare/r-celestial/PKGBUILD new file mode 100644 index 0000000000..4672385f81 --- /dev/null +++ b/prepare/r-celestial/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=celestial +_pkgver=1.4.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Collection of Common Astronomical Conversion Routines and Functions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-nistunits + r-pracma + r-rann +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-celestial/lilac.py b/prepare/r-celestial/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-celestial/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-celestial/lilac.yaml b/prepare/r-celestial/lilac.yaml new file mode 100644 index 0000000000..2b186a5649 --- /dev/null +++ b/prepare/r-celestial/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-nistunits +- r-pracma +- r-rann +update_on: +- regex: celestial_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=celestial diff --git a/prepare/r-cellarepertorium/PKGBUILD b/prepare/r-cellarepertorium/PKGBUILD new file mode 100644 index 0000000000..d0d855f292 --- /dev/null +++ b/prepare/r-cellarepertorium/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CellaRepertorium +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-dplyr + r-forcats + r-progress + r-purrr + r-rcpp + r-reshape2 + r-rlang + r-s4vectors + r-stringr + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-broom + r-broom.mixed + r-cowplot + r-ggdendro + r-ggplot2 + r-ggraph + r-igraph + r-knitr + r-lme4 + r-rcolorbrewer + r-readr + r-rmarkdown + r-scater + r-singlecellexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cellarepertorium/lilac.py b/prepare/r-cellarepertorium/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cellarepertorium/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cellarepertorium/lilac.yaml b/prepare/r-cellarepertorium/lilac.yaml new file mode 100644 index 0000000000..a4682e7c24 --- /dev/null +++ b/prepare/r-cellarepertorium/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-dplyr +- r-forcats +- r-progress +- r-purrr +- r-rcpp +- r-reshape2 +- r-rlang +- r-s4vectors +- r-stringr +- r-tibble +- r-tidyr +update_on: +- regex: CellaRepertorium_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CellaRepertorium diff --git a/prepare/r-cellbarcode/PKGBUILD b/prepare/r-cellbarcode/PKGBUILD new file mode 100644 index 0000000000..d9fa121d4d --- /dev/null +++ b/prepare/r-cellbarcode/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CellBarcode +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cellular DNA Barcode Analysis toolkit' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biostrings + r-ckmeans.1d.dp + r-data.table + r-egg + r-ggplot2 + r-magrittr + r-plyr + r-rcpp + r-s4vectors + r-shortread + r-stringr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cellbarcode/lilac.py b/prepare/r-cellbarcode/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cellbarcode/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cellbarcode/lilac.yaml b/prepare/r-cellbarcode/lilac.yaml new file mode 100644 index 0000000000..9b26d36f37 --- /dev/null +++ b/prepare/r-cellbarcode/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-ckmeans.1d.dp +- r-data.table +- r-egg +- r-ggplot2 +- r-magrittr +- r-plyr +- r-rcpp +- r-s4vectors +- r-shortread +- r-stringr +update_on: +- regex: CellBarcode_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CellBarcode diff --git a/prepare/r-cellbaser/PKGBUILD b/prepare/r-cellbaser/PKGBUILD new file mode 100644 index 0000000000..24e7ab834c --- /dev/null +++ b/prepare/r-cellbaser/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cellbaseR +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Querying annotation data from the high performance Cellbase web' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Apache') +depends=( + r + r-biocparallel + r-data.table + r-doparallel + r-foreach + r-httr + r-jsonlite + r-pbapply + r-r.utils + r-rsamtools + r-tidyr +) +optdepends=( + r-biocstyle + r-gviz + r-knitr + r-rmarkdown + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cellbaser/lilac.py b/prepare/r-cellbaser/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cellbaser/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cellbaser/lilac.yaml b/prepare/r-cellbaser/lilac.yaml new file mode 100644 index 0000000000..163b4d2b79 --- /dev/null +++ b/prepare/r-cellbaser/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-data.table +- r-doparallel +- r-foreach +- r-httr +- r-jsonlite +- r-pbapply +- r-r.utils +- r-rsamtools +- r-tidyr +update_on: +- regex: cellbaseR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cellbaseR diff --git a/prepare/r-cellbench/PKGBUILD b/prepare/r-cellbench/PKGBUILD new file mode 100644 index 0000000000..5fb45ce814 --- /dev/null +++ b/prepare/r-cellbench/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CellBench +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Construct Benchmarks for Single Cell Analysis Methods' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocfilecache + r-biocgenerics + r-biocparallel + r-dplyr + r-glue + r-lubridate + r-magrittr + r-memoise + r-purrr + r-rappdirs + r-rlang + r-singlecellexperiment + r-tibble + r-tidyr + r-tidyselect +) +optdepends=( + r-biocstyle + r-covr + r-ggplot2 + r-knitr + r-limma + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cellbench/lilac.py b/prepare/r-cellbench/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cellbench/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cellbench/lilac.yaml b/prepare/r-cellbench/lilac.yaml new file mode 100644 index 0000000000..ef6c7cdac0 --- /dev/null +++ b/prepare/r-cellbench/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-biocgenerics +- r-biocparallel +- r-dplyr +- r-glue +- r-lubridate +- r-magrittr +- r-memoise +- r-purrr +- r-rappdirs +- r-rlang +- r-singlecellexperiment +- r-tibble +- r-tidyr +- r-tidyselect +update_on: +- regex: CellBench_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CellBench diff --git a/prepare/r-celldex/PKGBUILD b/prepare/r-celldex/PKGBUILD new file mode 100644 index 0000000000..fe06f0de3c --- /dev/null +++ b/prepare/r-celldex/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=celldex +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Reference Index for Cell Types' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-annotationhub + r-delayedarray + r-delayedmatrixstats + r-experimenthub + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-dt + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-celldex/lilac.py b/prepare/r-celldex/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-celldex/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-celldex/lilac.yaml b/prepare/r-celldex/lilac.yaml new file mode 100644 index 0000000000..aa7c8b0a2c --- /dev/null +++ b/prepare/r-celldex/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-delayedarray +- r-delayedmatrixstats +- r-experimenthub +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: celldex_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/celldex diff --git a/prepare/r-cellhts2/PKGBUILD b/prepare/r-cellhts2/PKGBUILD new file mode 100644 index 0000000000..e548fec924 --- /dev/null +++ b/prepare/r-cellhts2/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cellHTS2 +_pkgver=2.58.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of cell-based screens - revised version of cellHTS' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-category + r-genefilter + r-gseabase + r-hwriter + r-locfit + r-rcolorbrewer + r-splots + r-vsn +) +optdepends=( + r-ggplot2 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cellhts2/lilac.py b/prepare/r-cellhts2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cellhts2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cellhts2/lilac.yaml b/prepare/r-cellhts2/lilac.yaml new file mode 100644 index 0000000000..a30a4538df --- /dev/null +++ b/prepare/r-cellhts2/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-category +- r-genefilter +- r-gseabase +- r-hwriter +- r-locfit +- r-rcolorbrewer +- r-splots +- r-vsn +update_on: +- regex: cellHTS2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cellHTS2 diff --git a/prepare/r-cellid/PKGBUILD b/prepare/r-cellid/PKGBUILD new file mode 100644 index 0000000000..7152f54183 --- /dev/null +++ b/prepare/r-cellid/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CelliD +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-data.table + r-fastmatch + r-fgsea + r-ggplot2 + r-glue + r-irlba + r-matrixstats + r-pbapply + r-rcpp + r-rcpparmadillo + r-reticulate + r-rtsne + r-scater + r-seurat + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-tictoc + r-umap +) +optdepends=( + r-biocstyle + r-destiny + r-ggpubr + r-ggrepel + r-knitr + r-rmarkdown + r-testthat + r-tidyverse +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cellid/lilac.py b/prepare/r-cellid/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cellid/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cellid/lilac.yaml b/prepare/r-cellid/lilac.yaml new file mode 100644 index 0000000000..bb9c3c7251 --- /dev/null +++ b/prepare/r-cellid/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-data.table +- r-fastmatch +- r-fgsea +- r-ggplot2 +- r-glue +- r-irlba +- r-matrixstats +- r-pbapply +- r-rcpp +- r-rcpparmadillo +- r-reticulate +- r-rtsne +- r-scater +- r-seurat +- r-singlecellexperiment +- r-stringr +- r-summarizedexperiment +- r-tictoc +- r-umap +update_on: +- regex: CelliD_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CelliD diff --git a/prepare/r-cellity/PKGBUILD b/prepare/r-cellity/PKGBUILD new file mode 100644 index 0000000000..71d405d904 --- /dev/null +++ b/prepare/r-cellity/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cellity +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quality Control for Single-Cell RNA-seq Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-e1071 + r-ggplot2 + r-mvoutlier + r-org.hs.eg.db + r-org.mm.eg.db + r-robustbase + r-topgo +) +optdepends=( + r-biocstyle + r-caret + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cellity/lilac.py b/prepare/r-cellity/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cellity/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cellity/lilac.yaml b/prepare/r-cellity/lilac.yaml new file mode 100644 index 0000000000..d6e38d3102 --- /dev/null +++ b/prepare/r-cellity/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-e1071 +- r-ggplot2 +- r-mvoutlier +- r-org.hs.eg.db +- r-org.mm.eg.db +- r-robustbase +- r-topgo +update_on: +- regex: cellity_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cellity diff --git a/prepare/r-cellmapper/PKGBUILD b/prepare/r-cellmapper/PKGBUILD new file mode 100644 index 0000000000..d41a7b018c --- /dev/null +++ b/prepare/r-cellmapper/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CellMapper +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Predict genes expressed selectively in specific cell types' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-s4vectors +) +optdepends=( + r-all + r-biobase + r-biocstyle + r-cellmapperdata + r-experimenthub + r-humanaffydata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cellmapper/lilac.py b/prepare/r-cellmapper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cellmapper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cellmapper/lilac.yaml b/prepare/r-cellmapper/lilac.yaml new file mode 100644 index 0000000000..413d838b11 --- /dev/null +++ b/prepare/r-cellmapper/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-s4vectors +update_on: +- regex: CellMapper_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CellMapper diff --git a/prepare/r-cellmigration/PKGBUILD b/prepare/r-cellmigration/PKGBUILD new file mode 100644 index 0000000000..beedc4008a --- /dev/null +++ b/prepare/r-cellmigration/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cellmigRation +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Track Cells, Analyze Cell Trajectories and Compute Migration Statistics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-doparallel + r-factominer + r-fme + r-foreach + r-hmisc + r-matrixstats + r-reshape2 + r-sp + r-spatialtools + r-tiff + r-vioplot +) +optdepends=( + r-biocgenerics + r-biocmanager + r-dplyr + r-ggplot2 + r-kableextra + r-knitr + r-rgl + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cellmigration/lilac.py b/prepare/r-cellmigration/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cellmigration/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cellmigration/lilac.yaml b/prepare/r-cellmigration/lilac.yaml new file mode 100644 index 0000000000..26a3d5841a --- /dev/null +++ b/prepare/r-cellmigration/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-factominer +- r-fme +- r-foreach +- r-hmisc +- r-matrixstats +- r-reshape2 +- r-sp +- r-spatialtools +- r-tiff +- r-vioplot +update_on: +- regex: cellmigRation_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cellmigRation diff --git a/prepare/r-cellmixs/PKGBUILD b/prepare/r-cellmixs/PKGBUILD new file mode 100644 index 0000000000..57186cee32 --- /dev/null +++ b/prepare/r-cellmixs/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CellMixS +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Evaluate Cellspecific Mixing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocneighbors + r-biocparallel + r-cowplot + r-dplyr + r-ggplot2 + r-ggridges + r-ksamples + r-magrittr + r-purrr + r-scater + r-singlecellexperiment + r-summarizedexperiment + r-tidyr + r-viridis +) +optdepends=( + r-biocstyle + r-knitr + r-limma + r-rmarkdown + r-rtsne + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cellmixs/lilac.py b/prepare/r-cellmixs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cellmixs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cellmixs/lilac.yaml b/prepare/r-cellmixs/lilac.yaml new file mode 100644 index 0000000000..e49323a442 --- /dev/null +++ b/prepare/r-cellmixs/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocneighbors +- r-biocparallel +- r-cowplot +- r-dplyr +- r-ggplot2 +- r-ggridges +- r-ksamples +- r-magrittr +- r-purrr +- r-scater +- r-singlecellexperiment +- r-summarizedexperiment +- r-tidyr +- r-viridis +update_on: +- regex: CellMixS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CellMixS diff --git a/prepare/r-cellnoptr/PKGBUILD b/prepare/r-cellnoptr/PKGBUILD new file mode 100644 index 0000000000..800da88df1 --- /dev/null +++ b/prepare/r-cellnoptr/PKGBUILD @@ -0,0 +1,48 @@ +# system requirements: Graphviz version >= 2.2 +# Maintainer: Guoyi Zhang + +_pkgname=CellNOptR +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-graph + r-hash + r-igraph + r-rbgl + r-rcurl + r-rgraphviz + r-stringi + r-stringr + r-xml +) +optdepends=( + r-biocgenerics + r-data.table + r-doparallel + r-dplyr + r-foreach + r-plyr + r-readr + r-runit + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cellnoptr/lilac.py b/prepare/r-cellnoptr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cellnoptr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cellnoptr/lilac.yaml b/prepare/r-cellnoptr/lilac.yaml new file mode 100644 index 0000000000..29dbbc2fe6 --- /dev/null +++ b/prepare/r-cellnoptr/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-graph +- r-hash +- r-igraph +- r-rbgl +- r-rcurl +- r-rgraphviz +- r-stringi +- r-stringr +- r-xml +update_on: +- regex: CellNOptR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CellNOptR diff --git a/prepare/r-cellranger/PKGBUILD b/prepare/r-cellranger/PKGBUILD new file mode 100644 index 0000000000..fc7b322bb8 --- /dev/null +++ b/prepare/r-cellranger/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cellranger +_pkgver=1.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Translate Spreadsheet Cell Ranges to Rows and Columns' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-rematch + r-tibble +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cellranger/lilac.py b/prepare/r-cellranger/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cellranger/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cellranger/lilac.yaml b/prepare/r-cellranger/lilac.yaml new file mode 100644 index 0000000000..c764360b16 --- /dev/null +++ b/prepare/r-cellranger/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rematch +- r-tibble +update_on: +- regex: cellranger_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=cellranger diff --git a/prepare/r-cellscape/PKGBUILD b/prepare/r-cellscape/PKGBUILD new file mode 100644 index 0000000000..4d6e2b57e5 --- /dev/null +++ b/prepare/r-cellscape/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cellscape +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Explores single cell copy number profiles in the context of a single cell tree' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-gtools + r-htmlwidgets + r-jsonlite + r-plyr + r-reshape2 + r-stringr +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cellscape/lilac.py b/prepare/r-cellscape/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cellscape/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cellscape/lilac.yaml b/prepare/r-cellscape/lilac.yaml new file mode 100644 index 0000000000..ea15a34d58 --- /dev/null +++ b/prepare/r-cellscape/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-gtools +- r-htmlwidgets +- r-jsonlite +- r-plyr +- r-reshape2 +- r-stringr +update_on: +- regex: cellscape_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cellscape diff --git a/prepare/r-cellscore/PKGBUILD b/prepare/r-cellscore/PKGBUILD new file mode 100644 index 0000000000..2a02133790 --- /dev/null +++ b/prepare/r-cellscore/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CellScore +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tool for Evaluation of Cell Identity from Transcription Profiles' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-gplots + r-lsa + r-rcolorbrewer + r-squash +) +optdepends=( + r-hgu133plus2cellscore + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cellscore/lilac.py b/prepare/r-cellscore/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cellscore/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cellscore/lilac.yaml b/prepare/r-cellscore/lilac.yaml new file mode 100644 index 0000000000..314e1bdf3d --- /dev/null +++ b/prepare/r-cellscore/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-gplots +- r-lsa +- r-rcolorbrewer +- r-squash +update_on: +- regex: CellScore_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CellScore diff --git a/prepare/r-celltrails/PKGBUILD b/prepare/r-celltrails/PKGBUILD new file mode 100644 index 0000000000..8d70917ef8 --- /dev/null +++ b/prepare/r-celltrails/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CellTrails +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Reconstruction, visualization and analysis of branching trajectories' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-cba + r-dendextend + r-dtw + r-envstats + r-ggplot2 + r-ggrepel + r-igraph + r-maptree + r-reshape2 + r-rtsne + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-annotationdbi + r-destiny + r-knitr + r-org.mm.eg.db + r-rmarkdown + r-runit + r-scater + r-scran +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-celltrails/lilac.py b/prepare/r-celltrails/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-celltrails/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-celltrails/lilac.yaml b/prepare/r-celltrails/lilac.yaml new file mode 100644 index 0000000000..b377d8d5a7 --- /dev/null +++ b/prepare/r-celltrails/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-cba +- r-dendextend +- r-dtw +- r-envstats +- r-ggplot2 +- r-ggrepel +- r-igraph +- r-maptree +- r-reshape2 +- r-rtsne +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: CellTrails_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CellTrails diff --git a/prepare/r-celltree/PKGBUILD b/prepare/r-celltree/PKGBUILD new file mode 100644 index 0000000000..480856ae32 --- /dev/null +++ b/prepare/r-celltree/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cellTree +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-gplots + r-igraph + r-maptpx + r-slam + r-topgo + r-topicmodels + r-xtable +) +optdepends=( + r-biobase + r-biocstyle + r-biomart + r-hsmmsinglecell + r-knitr + r-org.hs.eg.db + r-tools +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-celltree/lilac.py b/prepare/r-celltree/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-celltree/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-celltree/lilac.yaml b/prepare/r-celltree/lilac.yaml new file mode 100644 index 0000000000..7f3bf84c83 --- /dev/null +++ b/prepare/r-celltree/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gplots +- r-igraph +- r-maptpx +- r-slam +- r-topgo +- r-topicmodels +- r-xtable +update_on: +- regex: cellTree_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cellTree diff --git a/prepare/r-cemitool/PKGBUILD b/prepare/r-cemitool/PKGBUILD new file mode 100644 index 0000000000..bccb197d90 --- /dev/null +++ b/prepare/r-cemitool/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CEMiTool +_pkgver=1.18.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Co-expression Modules identification Tool' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-clusterprofiler + r-data.table + r-dplyr + r-dt + r-fastcluster + r-fgsea + r-ggdendro + r-ggplot2 + r-ggpmisc + r-ggrepel + r-ggthemes + r-gridextra + r-gtable + r-htmltools + r-igraph + r-intergraph + r-knitr + r-matrixstats + r-network + r-pracma + r-rmarkdown + r-scales + r-sna + r-stringr + r-wgcna +) +optdepends=( + r-biocmanager + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cemitool/lilac.py b/prepare/r-cemitool/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cemitool/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cemitool/lilac.yaml b/prepare/r-cemitool/lilac.yaml new file mode 100644 index 0000000000..736e8ab512 --- /dev/null +++ b/prepare/r-cemitool/lilac.yaml @@ -0,0 +1,34 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clusterprofiler +- r-data.table +- r-dplyr +- r-dt +- r-fastcluster +- r-fgsea +- r-ggdendro +- r-ggplot2 +- r-ggpmisc +- r-ggrepel +- r-ggthemes +- r-gridextra +- r-gtable +- r-htmltools +- r-igraph +- r-intergraph +- r-knitr +- r-matrixstats +- r-network +- r-pracma +- r-rmarkdown +- r-scales +- r-sna +- r-stringr +- r-wgcna +update_on: +- regex: CEMiTool_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CEMiTool diff --git a/prepare/r-censcyt/PKGBUILD b/prepare/r-censcyt/PKGBUILD new file mode 100644 index 0000000000..1d2f920649 --- /dev/null +++ b/prepare/r-censcyt/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=censcyt +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential abundance analysis with a right censored covariate in high-dimensional cytometry' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocparallel + r-broom.mixed + r-diffcyt + r-dirmult + r-dplyr + r-edger + r-fitdistrplus + r-lme4 + r-magrittr + r-mice + r-multcomp + r-purrr + r-rlang + r-s4vectors + r-stringr + r-summarizedexperiment + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-ggplot2 + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-censcyt/lilac.py b/prepare/r-censcyt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-censcyt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-censcyt/lilac.yaml b/prepare/r-censcyt/lilac.yaml new file mode 100644 index 0000000000..4172f81eb0 --- /dev/null +++ b/prepare/r-censcyt/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-broom.mixed +- r-diffcyt +- r-dirmult +- r-dplyr +- r-edger +- r-fitdistrplus +- r-lme4 +- r-magrittr +- r-mice +- r-multcomp +- r-purrr +- r-rlang +- r-s4vectors +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-tidyr +update_on: +- regex: censcyt_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/censcyt diff --git a/prepare/r-cepo/PKGBUILD b/prepare/r-cepo/PKGBUILD new file mode 100644 index 0000000000..16ff29b1ba --- /dev/null +++ b/prepare/r-cepo/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Cepo +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cepo for the identification of differentially stable genes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocparallel + r-delayedarray + r-delayedmatrixstats + r-ggplot2 + r-gseabase + r-hdf5array + r-patchwork + r-reshape2 + r-rlang + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-covr + r-escape + r-fgsea + r-knitr + r-patchwork + r-pheatmap + r-rmarkdown + r-scater + r-scmerge + r-testthat + r-upsetr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cepo/lilac.py b/prepare/r-cepo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cepo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cepo/lilac.yaml b/prepare/r-cepo/lilac.yaml new file mode 100644 index 0000000000..e62f8ee5d7 --- /dev/null +++ b/prepare/r-cepo/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-delayedarray +- r-delayedmatrixstats +- r-ggplot2 +- r-gseabase +- r-hdf5array +- r-patchwork +- r-reshape2 +- r-rlang +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: Cepo_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Cepo diff --git a/prepare/r-cernanetsim/PKGBUILD b/prepare/r-cernanetsim/PKGBUILD new file mode 100644 index 0000000000..175429900b --- /dev/null +++ b/prepare/r-cernanetsim/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ceRNAnetsim +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-furrr + r-future + r-ggplot2 + r-ggraph + r-igraph + r-purrr + r-rlang + r-tibble + r-tidygraph + r-tidyr +) +optdepends=( + r-covr + r-knitr + r-png + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cernanetsim/lilac.py b/prepare/r-cernanetsim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cernanetsim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cernanetsim/lilac.yaml b/prepare/r-cernanetsim/lilac.yaml new file mode 100644 index 0000000000..b49d198cb6 --- /dev/null +++ b/prepare/r-cernanetsim/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-furrr +- r-future +- r-ggplot2 +- r-ggraph +- r-igraph +- r-purrr +- r-rlang +- r-tibble +- r-tidygraph +- r-tidyr +update_on: +- regex: ceRNAnetsim_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ceRNAnetsim diff --git a/prepare/r-cetf/PKGBUILD b/prepare/r-cetf/PKGBUILD new file mode 100644 index 0000000000..f5d3794451 --- /dev/null +++ b/prepare/r-cetf/PKGBUILD @@ -0,0 +1,54 @@ +# system requirements: libcurl4-openssl-dev, libxml2-dev, libssl-dev,gfortran, build-essential, libz-dev, zlib1g-dev +# Maintainer: Guoyi Zhang + +_pkgname=CeTF +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-circlize + r-clusterprofiler + r-complexheatmap + r-deseq2 + r-dplyr + r-genomictools + r-genomictools.filehandler + r-ggally + r-ggnetwork + r-ggplot2 + r-ggpubr + r-ggrepel + r-igraph + r-network + r-rcpp + r-rcpparmadillo + r-rcy3 + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-airway + r-kableextra + r-knitr + r-org.hs.eg.db + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cetf/lilac.py b/prepare/r-cetf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cetf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cetf/lilac.yaml b/prepare/r-cetf/lilac.yaml new file mode 100644 index 0000000000..9c59384758 --- /dev/null +++ b/prepare/r-cetf/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circlize +- r-clusterprofiler +- r-complexheatmap +- r-deseq2 +- r-dplyr +- r-genomictools +- r-genomictools.filehandler +- r-ggally +- r-ggnetwork +- r-ggplot2 +- r-ggpubr +- r-ggrepel +- r-igraph +- r-network +- r-rcpp +- r-rcpparmadillo +- r-rcy3 +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: CeTF_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CeTF diff --git a/prepare/r-cexor/PKGBUILD b/prepare/r-cexor/PKGBUILD new file mode 100644 index 0000000000..47c362e4e0 --- /dev/null +++ b/prepare/r-cexor/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CexoR +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomation + r-genomeinfodb + r-genomicranges + r-idr + r-iranges + r-rcolorbrewer + r-rsamtools + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cexor/lilac.py b/prepare/r-cexor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cexor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cexor/lilac.yaml b/prepare/r-cexor/lilac.yaml new file mode 100644 index 0000000000..204bfc8912 --- /dev/null +++ b/prepare/r-cexor/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomation +- r-genomeinfodb +- r-genomicranges +- r-idr +- r-iranges +- r-rcolorbrewer +- r-rsamtools +- r-rtracklayer +- r-s4vectors +update_on: +- regex: CexoR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CexoR diff --git a/prepare/r-cfassay/PKGBUILD b/prepare/r-cfassay/PKGBUILD new file mode 100644 index 0000000000..8939faa084 --- /dev/null +++ b/prepare/r-cfassay/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CFAssay +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical analysis for the Colony Formation Assay' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cfassay/lilac.py b/prepare/r-cfassay/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cfassay/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cfassay/lilac.yaml b/prepare/r-cfassay/lilac.yaml new file mode 100644 index 0000000000..d9f95ed2c6 --- /dev/null +++ b/prepare/r-cfassay/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: CFAssay_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CFAssay diff --git a/prepare/r-cfdnapro/PKGBUILD b/prepare/r-cfdnapro/PKGBUILD new file mode 100644 index 0000000000..7d865c57ac --- /dev/null +++ b/prepare/r-cfdnapro/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cfDNAPro +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='cfDNAPro Helps Characterise and Visualise Whole Genome Sequencing Data from Liquid Biopsy' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-ggplot2 + r-magrittr + r-quantmod + r-rlang + r-rsamtools + r-stringr +) +optdepends=( + r-biocstyle + r-devtools + r-ggpubr + r-knitr + r-rmarkdown + r-scales + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cfdnapro/lilac.py b/prepare/r-cfdnapro/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cfdnapro/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cfdnapro/lilac.yaml b/prepare/r-cfdnapro/lilac.yaml new file mode 100644 index 0000000000..f01df99af0 --- /dev/null +++ b/prepare/r-cfdnapro/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-magrittr +- r-quantmod +- r-rlang +- r-rsamtools +- r-stringr +update_on: +- regex: cfDNAPro_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cfDNAPro diff --git a/prepare/r-cgdsr/PKGBUILD b/prepare/r-cgdsr/PKGBUILD new file mode 100644 index 0000000000..06b9ee334f --- /dev/null +++ b/prepare/r-cgdsr/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cgdsr +_pkgver=1.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R-Based API for Accessing the MSKCC Cancer Genomics Data Server (CGDS)' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-httr + r-r.methodss3 + r-r.oo +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cgdsr/lilac.py b/prepare/r-cgdsr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cgdsr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cgdsr/lilac.yaml b/prepare/r-cgdsr/lilac.yaml new file mode 100644 index 0000000000..5f0fb3008f --- /dev/null +++ b/prepare/r-cgdsr/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-httr +- r-r.methodss3 +- r-r.oo +update_on: +- regex: cgdsr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=cgdsr diff --git a/prepare/r-cgen/PKGBUILD b/prepare/r-cgen/PKGBUILD new file mode 100644 index 0000000000..e5e58151c1 --- /dev/null +++ b/prepare/r-cgen/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CGEN +_pkgver=3.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package for analysis of case-control studies in genetic epidemiology' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-mvtnorm +) +optdepends=( + r-cluster +) +makedepends=( + gcc-fortran +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cgen/lilac.py b/prepare/r-cgen/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cgen/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cgen/lilac.yaml b/prepare/r-cgen/lilac.yaml new file mode 100644 index 0000000000..3ce62cbe30 --- /dev/null +++ b/prepare/r-cgen/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mvtnorm +update_on: +- regex: CGEN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CGEN diff --git a/prepare/r-cghbase/PKGBUILD b/prepare/r-cghbase/PKGBUILD new file mode 100644 index 0000000000..767668c71d --- /dev/null +++ b/prepare/r-cghbase/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CGHbase +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CGHbase: Base functions and classes for arrayCGH data analysis.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-marray +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cghbase/lilac.py b/prepare/r-cghbase/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cghbase/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cghbase/lilac.yaml b/prepare/r-cghbase/lilac.yaml new file mode 100644 index 0000000000..3eb59e9a65 --- /dev/null +++ b/prepare/r-cghbase/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-marray +update_on: +- regex: CGHbase_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CGHbase diff --git a/prepare/r-cghcall/PKGBUILD b/prepare/r-cghcall/PKGBUILD new file mode 100644 index 0000000000..e90963f8d2 --- /dev/null +++ b/prepare/r-cghcall/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CGHcall +_pkgver=2.56.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Calling aberrations for array CGH tumor profiles.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-cghbase + r-dnacopy + r-impute + r-snowfall +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cghcall/lilac.py b/prepare/r-cghcall/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cghcall/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cghcall/lilac.yaml b/prepare/r-cghcall/lilac.yaml new file mode 100644 index 0000000000..8413c83bdc --- /dev/null +++ b/prepare/r-cghcall/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-cghbase +- r-dnacopy +- r-impute +- r-snowfall +update_on: +- regex: CGHcall_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CGHcall diff --git a/prepare/r-cghmcr/PKGBUILD b/prepare/r-cghmcr/PKGBUILD new file mode 100644 index 0000000000..c3c07a79ab --- /dev/null +++ b/prepare/r-cghmcr/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cghMCR +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Find chromosome regions showing common gains/losses' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biocgenerics + r-cntools + r-dnacopy + r-limma +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cghmcr/lilac.py b/prepare/r-cghmcr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cghmcr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cghmcr/lilac.yaml b/prepare/r-cghmcr/lilac.yaml new file mode 100644 index 0000000000..e8afb02d4b --- /dev/null +++ b/prepare/r-cghmcr/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-cntools +- r-dnacopy +- r-limma +update_on: +- regex: cghMCR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cghMCR diff --git a/prepare/r-cghnormaliter/PKGBUILD b/prepare/r-cghnormaliter/PKGBUILD new file mode 100644 index 0000000000..6c6f1d2ab4 --- /dev/null +++ b/prepare/r-cghnormaliter/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CGHnormaliter +_pkgver=1.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Normalization of array CGH data with imbalanced aberrations.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-cghbase + r-cghcall +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cghnormaliter/lilac.py b/prepare/r-cghnormaliter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cghnormaliter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cghnormaliter/lilac.yaml b/prepare/r-cghnormaliter/lilac.yaml new file mode 100644 index 0000000000..c15b371309 --- /dev/null +++ b/prepare/r-cghnormaliter/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-cghbase +- r-cghcall +update_on: +- regex: CGHnormaliter_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CGHnormaliter diff --git a/prepare/r-cghregions/PKGBUILD b/prepare/r-cghregions/PKGBUILD new file mode 100644 index 0000000000..d0da788f12 --- /dev/null +++ b/prepare/r-cghregions/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CGHregions +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dimension Reduction for Array CGH Data with Minimal Information Loss.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-cghbase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cghregions/lilac.py b/prepare/r-cghregions/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cghregions/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cghregions/lilac.yaml b/prepare/r-cghregions/lilac.yaml new file mode 100644 index 0000000000..7c4020c4a8 --- /dev/null +++ b/prepare/r-cghregions/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-cghbase +update_on: +- regex: CGHregions_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CGHregions diff --git a/prepare/r-champ/PKGBUILD b/prepare/r-champ/PKGBUILD new file mode 100644 index 0000000000..c5eadef993 --- /dev/null +++ b/prepare/r-champ/PKGBUILD @@ -0,0 +1,69 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ChAMP +_pkgver=2.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bumphunter + r-champdata + r-combinat + r-dendextend + r-dmrcate + r-dnacopy + r-doparallel + r-dt + r-genomicranges + r-ggplot2 + r-globaltest + r-goseq + r-hmisc + r-illumina450probevariants.db + r-illuminahumanmethylation450kmanifest + r-illuminahumanmethylationepicanno.ilm10b4.hg19 + r-illuminahumanmethylationepicmanifest + r-illuminaio + r-impute + r-isva + r-kpmt + r-limma + r-marray + r-matrixstats + r-minfi + r-missmethyl + r-plotly + r-plyr + r-preprocesscore + r-prettydoc + r-quadprog + r-qvalue + r-rcolorbrewer + r-rmarkdown + r-rpmm + r-shiny + r-shinythemes + r-sva + r-watermelon +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-champ/lilac.py b/prepare/r-champ/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-champ/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-champ/lilac.yaml b/prepare/r-champ/lilac.yaml new file mode 100644 index 0000000000..1cad85f05a --- /dev/null +++ b/prepare/r-champ/lilac.yaml @@ -0,0 +1,48 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bumphunter +- r-champdata +- r-combinat +- r-dendextend +- r-dmrcate +- r-dnacopy +- r-doparallel +- r-dt +- r-genomicranges +- r-ggplot2 +- r-globaltest +- r-goseq +- r-hmisc +- r-illumina450probevariants.db +- r-illuminahumanmethylation450kmanifest +- r-illuminahumanmethylationepicanno.ilm10b4.hg19 +- r-illuminahumanmethylationepicmanifest +- r-illuminaio +- r-impute +- r-isva +- r-kpmt +- r-limma +- r-marray +- r-matrixstats +- r-minfi +- r-missmethyl +- r-plotly +- r-plyr +- r-preprocesscore +- r-prettydoc +- r-quadprog +- r-qvalue +- r-rcolorbrewer +- r-rmarkdown +- r-rpmm +- r-shiny +- r-shinythemes +- r-sva +- r-watermelon +update_on: +- regex: ChAMP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChAMP diff --git a/prepare/r-champdata/PKGBUILD b/prepare/r-champdata/PKGBUILD new file mode 100644 index 0000000000..a75ad24348 --- /dev/null +++ b/prepare/r-champdata/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ChAMPdata +_pkgver=2.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data Packages for ChAMP package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-genomicranges +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-champdata/lilac.py b/prepare/r-champdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-champdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-champdata/lilac.yaml b/prepare/r-champdata/lilac.yaml new file mode 100644 index 0000000000..472db9b911 --- /dev/null +++ b/prepare/r-champdata/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomicranges +update_on: +- regex: ChAMPdata_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChAMPdata diff --git a/prepare/r-changepoint/PKGBUILD b/prepare/r-changepoint/PKGBUILD new file mode 100644 index 0000000000..43fa0b16ee --- /dev/null +++ b/prepare/r-changepoint/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=changepoint +_pkgver=2.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methods for Changepoint Detection' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-zoo +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-changepoint/lilac.py b/prepare/r-changepoint/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-changepoint/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-changepoint/lilac.yaml b/prepare/r-changepoint/lilac.yaml new file mode 100644 index 0000000000..8a68d83dac --- /dev/null +++ b/prepare/r-changepoint/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-zoo +update_on: +- regex: changepoint_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=changepoint diff --git a/prepare/r-checkmate/PKGBUILD b/prepare/r-checkmate/PKGBUILD new file mode 100644 index 0000000000..9fde2bf3eb --- /dev/null +++ b/prepare/r-checkmate/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=checkmate +_pkgver=2.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast and Versatile Argument Checks' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-backports +) +optdepends=( + r-data.table + r-devtools + r-fastmatch + r-ggplot2 + r-knitr + r-magrittr + r-microbenchmark + r-r6 + r-rmarkdown + r-testthat + r-tibble + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-checkmate/lilac.py b/prepare/r-checkmate/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-checkmate/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-checkmate/lilac.yaml b/prepare/r-checkmate/lilac.yaml new file mode 100644 index 0000000000..d1520ef061 --- /dev/null +++ b/prepare/r-checkmate/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-backports +update_on: +- regex: checkmate_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=checkmate diff --git a/prepare/r-chemmineob/PKGBUILD b/prepare/r-chemmineob/PKGBUILD new file mode 100644 index 0000000000..1c2ded984a --- /dev/null +++ b/prepare/r-chemmineob/PKGBUILD @@ -0,0 +1,41 @@ +# system requirements: OpenBabel (>= 3.0.0) with headers(http://openbabel.org). Eigen3 with headers. +# Maintainer: Guoyi Zhang + +_pkgname=ChemmineOB +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R interface to a subset of OpenBabel functionalities' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-bh + r-biocgenerics + r-rcpp + r-zlibbioc +) +optdepends=( + r-biocmanager + r-biocstyle + r-chemminer + r-chemminer + r-knitr + r-knitrbootstrap + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chemmineob/lilac.py b/prepare/r-chemmineob/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chemmineob/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chemmineob/lilac.yaml b/prepare/r-chemmineob/lilac.yaml new file mode 100644 index 0000000000..23c28ace40 --- /dev/null +++ b/prepare/r-chemmineob/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-biocgenerics +- r-rcpp +- r-zlibbioc +update_on: +- regex: ChemmineOB_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChemmineOB diff --git a/prepare/r-chemminer/PKGBUILD b/prepare/r-chemminer/PKGBUILD new file mode 100644 index 0000000000..c2a5bd40de --- /dev/null +++ b/prepare/r-chemminer/PKGBUILD @@ -0,0 +1,59 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=ChemmineR +_pkgver=3.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cheminformatics Toolkit for R' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-base64enc + r-bh + r-biocgenerics + r-dbi + r-digest + r-dt + r-ggplot2 + r-gridextra + r-jsonlite + r-png + r-rcpp + r-rcurl + r-rjson + r-rsvg + r-stringi +) +optdepends=( + r-biocmanager + r-biocstyle + r-chemminedrugs + r-chemmineob + r-fmcsr + r-gplots + r-knitcitations + r-knitr + r-knitrbootstrap + r-png + r-rmarkdown + r-rpostgresql + r-rsqlite + r-scatterplot3d + r-snow +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chemminer/lilac.py b/prepare/r-chemminer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chemminer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chemminer/lilac.yaml b/prepare/r-chemminer/lilac.yaml new file mode 100644 index 0000000000..afa4d467bd --- /dev/null +++ b/prepare/r-chemminer/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-bh +- r-biocgenerics +- r-dbi +- r-digest +- r-dt +- r-ggplot2 +- r-gridextra +- r-jsonlite +- r-png +- r-rcpp +- r-rcurl +- r-rjson +- r-rsvg +- r-stringi +update_on: +- regex: ChemmineR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChemmineR diff --git a/prepare/r-chemometrics/PKGBUILD b/prepare/r-chemometrics/PKGBUILD new file mode 100644 index 0000000000..ef918d071f --- /dev/null +++ b/prepare/r-chemometrics/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=chemometrics +_pkgver=1.4.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multivariate Statistical Analysis in Chemometrics' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-e1071 + r-lars + r-mclust + r-pcapp + r-pls + r-robustbase + r-som +) +optdepends=( + r-gclus +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chemometrics/lilac.py b/prepare/r-chemometrics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chemometrics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chemometrics/lilac.yaml b/prepare/r-chemometrics/lilac.yaml new file mode 100644 index 0000000000..78cc050274 --- /dev/null +++ b/prepare/r-chemometrics/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-e1071 +- r-lars +- r-mclust +- r-pcapp +- r-pls +- r-robustbase +- r-som +update_on: +- regex: chemometrics_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=chemometrics diff --git a/prepare/r-chetah/PKGBUILD b/prepare/r-chetah/PKGBUILD new file mode 100644 index 0000000000..5ef503b839 --- /dev/null +++ b/prepare/r-chetah/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CHETAH +_pkgver=1.9.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast and accurate scRNA-seq cell type identification' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-biodist + r-corrplot + r-cowplot + r-dendextend + r-ggplot2 + r-gplots + r-pheatmap + r-plotly + r-reshape2 + r-s4vectors + r-shiny + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-knitr + r-matrix + r-rmarkdown + r-testthat + r-vdiffr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chetah/lilac.py b/prepare/r-chetah/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chetah/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chetah/lilac.yaml b/prepare/r-chetah/lilac.yaml new file mode 100644 index 0000000000..185b581ff2 --- /dev/null +++ b/prepare/r-chetah/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biodist +- r-corrplot +- r-cowplot +- r-dendextend +- r-ggplot2 +- r-gplots +- r-pheatmap +- r-plotly +- r-reshape2 +- r-s4vectors +- r-shiny +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: CHETAH_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CHETAH diff --git a/prepare/r-chic.data/PKGBUILD b/prepare/r-chic.data/PKGBUILD new file mode 100644 index 0000000000..27420280b7 --- /dev/null +++ b/prepare/r-chic.data/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ChIC.data +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ChIC package data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-caret + r-genomeintervals + r-randomforest +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chic.data/lilac.py b/prepare/r-chic.data/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chic.data/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chic.data/lilac.yaml b/prepare/r-chic.data/lilac.yaml new file mode 100644 index 0000000000..48c20910d6 --- /dev/null +++ b/prepare/r-chic.data/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-caret +- r-genomeintervals +- r-randomforest +update_on: +- regex: ChIC.data_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChIC.data diff --git a/prepare/r-chic/PKGBUILD b/prepare/r-chic/PKGBUILD new file mode 100644 index 0000000000..9ede541f27 --- /dev/null +++ b/prepare/r-chic/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ChIC +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quality Control Pipeline for ChIP-Seq Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-caret + r-catools + r-chic.data + r-genomeintervals + r-genomicranges + r-iranges + r-progress + r-randomforest + r-rsamtools + r-s4vectors + r-spp +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chic/lilac.py b/prepare/r-chic/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chic/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chic/lilac.yaml b/prepare/r-chic/lilac.yaml new file mode 100644 index 0000000000..5c41f06f2d --- /dev/null +++ b/prepare/r-chic/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-caret +- r-catools +- r-chic.data +- r-genomeintervals +- r-genomicranges +- r-iranges +- r-progress +- r-randomforest +- r-rsamtools +- r-s4vectors +- r-spp +update_on: +- regex: ChIC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChIC diff --git a/prepare/r-chicago/PKGBUILD b/prepare/r-chicago/PKGBUILD new file mode 100644 index 0000000000..4441505a9a --- /dev/null +++ b/prepare/r-chicago/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Chicago +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CHiCAGO: Capture Hi-C Analysis of Genomic Organization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-data.table + r-delaporte + r-hmisc + r-matrixstats +) +optdepends=( + r-annotationhub + r-argparser + r-biocstyle + r-genomicinteractions + r-genomicranges + r-iranges + r-knitr + r-pchicdata + r-rmarkdown + r-rsamtools + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chicago/lilac.py b/prepare/r-chicago/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chicago/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chicago/lilac.yaml b/prepare/r-chicago/lilac.yaml new file mode 100644 index 0000000000..f8d4940afc --- /dev/null +++ b/prepare/r-chicago/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-delaporte +- r-hmisc +- r-matrixstats +update_on: +- regex: Chicago_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Chicago diff --git a/prepare/r-chimeraviz/PKGBUILD b/prepare/r-chimeraviz/PKGBUILD new file mode 100644 index 0000000000..6333aa15be --- /dev/null +++ b/prepare/r-chimeraviz/PKGBUILD @@ -0,0 +1,60 @@ +# system requirements: bowtie, samtools, and egrep are required for somefunctionalities +# Maintainer: Guoyi Zhang + +_pkgname=chimeraviz +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization tools for gene fusions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-annotationfilter + r-biocstyle + r-biostrings + r-checkmate + r-data.table + r-dplyr + r-dt + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-graph + r-gtools + r-gviz + r-iranges + r-magick + r-org.hs.eg.db + r-org.mm.eg.db + r-plyr + r-rcircos + r-rcolorbrewer + r-rgraphviz + r-rmarkdown + r-rsamtools + r-s4vectors +) +optdepends=( + r-devtools + r-knitr + r-lintr + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chimeraviz/lilac.py b/prepare/r-chimeraviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chimeraviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chimeraviz/lilac.yaml b/prepare/r-chimeraviz/lilac.yaml new file mode 100644 index 0000000000..6d6d65a68d --- /dev/null +++ b/prepare/r-chimeraviz/lilac.yaml @@ -0,0 +1,35 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationfilter +- r-biocstyle +- r-biostrings +- r-checkmate +- r-data.table +- r-dplyr +- r-dt +- r-ensembldb +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-graph +- r-gtools +- r-gviz +- r-iranges +- r-magick +- r-org.hs.eg.db +- r-org.mm.eg.db +- r-plyr +- r-rcircos +- r-rcolorbrewer +- r-rgraphviz +- r-rmarkdown +- r-rsamtools +- r-s4vectors +update_on: +- regex: chimeraviz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/chimeraviz diff --git a/prepare/r-chipanalyser/PKGBUILD b/prepare/r-chipanalyser/PKGBUILD new file mode 100644 index 0000000000..ba2d3185f3 --- /dev/null +++ b/prepare/r-chipanalyser/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ChIPanalyser +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ChIPanalyser: Predicting Transcription Factor Binding Sites' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocmanager + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-iranges + r-rcpproll + r-rocr + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocgenerics + r-bsgenome.dmelanogaster.ucsc.dm3 + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chipanalyser/lilac.py b/prepare/r-chipanalyser/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chipanalyser/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chipanalyser/lilac.yaml b/prepare/r-chipanalyser/lilac.yaml new file mode 100644 index 0000000000..157d1a1049 --- /dev/null +++ b/prepare/r-chipanalyser/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocmanager +- r-biostrings +- r-bsgenome +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rcpproll +- r-rocr +- r-rtracklayer +- r-s4vectors +update_on: +- regex: ChIPanalyser_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChIPanalyser diff --git a/prepare/r-chipcomp/PKGBUILD b/prepare/r-chipcomp/PKGBUILD new file mode 100644 index 0000000000..439ed879d6 --- /dev/null +++ b/prepare/r-chipcomp/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ChIPComp +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quantitative comparison of multiple ChIP-seq datasets' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.mmusculus.ucsc.mm9 + r-genomeinfodb + r-genomicranges + r-iranges + r-limma + r-rsamtools + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocstyle + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chipcomp/lilac.py b/prepare/r-chipcomp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chipcomp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chipcomp/lilac.yaml b/prepare/r-chipcomp/lilac.yaml new file mode 100644 index 0000000000..99a23f18ee --- /dev/null +++ b/prepare/r-chipcomp/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-bsgenome.hsapiens.ucsc.hg19 +- r-bsgenome.mmusculus.ucsc.mm9 +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-limma +- r-rsamtools +- r-rtracklayer +- r-s4vectors +update_on: +- regex: ChIPComp_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChIPComp diff --git a/prepare/r-chipenrich.data/PKGBUILD b/prepare/r-chipenrich.data/PKGBUILD new file mode 100644 index 0000000000..aae32d7f4f --- /dev/null +++ b/prepare/r-chipenrich.data/PKGBUILD @@ -0,0 +1,58 @@ +# Maintainer: Guoyi Zhang + +_pkgname=chipenrich.data +_pkgver=2.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Companion package to chipenrich' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocgenerics + r-genomeinfodb + r-genomicranges + r-iranges + r-readr + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocstyle + r-devtools + r-go.db + r-knitr + r-org.dm.eg.db + r-org.dr.eg.db + r-org.hs.eg.db + r-org.mm.eg.db + r-org.rn.eg.db + r-rmarkdown + r-roxygen2 + r-testthat + r-txdb.dmelanogaster.ucsc.dm3.ensgene + r-txdb.dmelanogaster.ucsc.dm6.ensgene + r-txdb.drerio.ucsc.danrer10.refgene + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.hsapiens.ucsc.hg38.knowngene + r-txdb.mmusculus.ucsc.mm10.knowngene + r-txdb.mmusculus.ucsc.mm9.knowngene + r-txdb.rnorvegicus.ucsc.rn4.ensgene + r-txdb.rnorvegicus.ucsc.rn5.refgene + r-txdb.rnorvegicus.ucsc.rn6.refgene +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chipenrich.data/lilac.py b/prepare/r-chipenrich.data/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chipenrich.data/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chipenrich.data/lilac.yaml b/prepare/r-chipenrich.data/lilac.yaml new file mode 100644 index 0000000000..6b628b25d8 --- /dev/null +++ b/prepare/r-chipenrich.data/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-readr +- r-rtracklayer +- r-s4vectors +update_on: +- regex: chipenrich.data_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/chipenrich.data diff --git a/prepare/r-chipenrich/PKGBUILD b/prepare/r-chipenrich/PKGBUILD new file mode 100644 index 0000000000..c3435a79a7 --- /dev/null +++ b/prepare/r-chipenrich/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=chipenrich +_pkgver=2.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Set Enrichment For ChIP-seq Peak Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocgenerics + r-chipenrich.data + r-genomeinfodb + r-genomicranges + r-iranges + r-latticeextra + r-org.dm.eg.db + r-org.dr.eg.db + r-org.hs.eg.db + r-org.mm.eg.db + r-org.rn.eg.db + r-plyr + r-rms + r-rtracklayer + r-s4vectors + r-stringr +) +optdepends=( + r-biocstyle + r-devtools + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chipenrich/lilac.py b/prepare/r-chipenrich/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chipenrich/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chipenrich/lilac.yaml b/prepare/r-chipenrich/lilac.yaml new file mode 100644 index 0000000000..576471976e --- /dev/null +++ b/prepare/r-chipenrich/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-chipenrich.data +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-latticeextra +- r-org.dm.eg.db +- r-org.dr.eg.db +- r-org.hs.eg.db +- r-org.mm.eg.db +- r-org.rn.eg.db +- r-plyr +- r-rms +- r-rtracklayer +- r-s4vectors +- r-stringr +update_on: +- regex: chipenrich_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/chipenrich diff --git a/prepare/r-chipexoqual/PKGBUILD b/prepare/r-chipexoqual/PKGBUILD new file mode 100644 index 0000000000..03700b23f9 --- /dev/null +++ b/prepare/r-chipexoqual/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ChIPexoQual +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ChIPexoQual' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-biovizbase + r-broom + r-data.table + r-dplyr + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-hexbin + r-iranges + r-rcolorbrewer + r-rmarkdown + r-rsamtools + r-s4vectors + r-scales + r-viridis +) +optdepends=( + r-biocstyle + r-chipexoqualexample + r-gridextra + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chipexoqual/lilac.py b/prepare/r-chipexoqual/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chipexoqual/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chipexoqual/lilac.yaml b/prepare/r-chipexoqual/lilac.yaml new file mode 100644 index 0000000000..9333ca106f --- /dev/null +++ b/prepare/r-chipexoqual/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-biovizbase +- r-broom +- r-data.table +- r-dplyr +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-hexbin +- r-iranges +- r-rcolorbrewer +- r-rmarkdown +- r-rsamtools +- r-s4vectors +- r-scales +- r-viridis +update_on: +- regex: ChIPexoQual_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChIPexoQual diff --git a/prepare/r-chippeakanno/PKGBUILD b/prepare/r-chippeakanno/PKGBUILD new file mode 100644 index 0000000000..bc2e0ca9fb --- /dev/null +++ b/prepare/r-chippeakanno/PKGBUILD @@ -0,0 +1,82 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ChIPpeakAnno +_pkgver=3.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocgenerics + r-biomart + r-biostrings + r-dbi + r-dplyr + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-graph + r-interactionset + r-iranges + r-keggrest + r-matrixstats + r-multtest + r-rbgl + r-regioner + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-venndiagram +) +optdepends=( + r-annotationhub + r-biocmanager + r-biocstyle + r-bsgenome + r-bsgenome.celegans.ucsc.ce10 + r-bsgenome.drerio.ucsc.danrer7 + r-bsgenome.ecoli.ncbi.20080805 + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.hsapiens.ucsc.hg38 + r-delayedarray + r-ensdb.hsapiens.v75 + r-ensdb.hsapiens.v79 + r-go.db + r-gplots + r-idr + r-knitr + r-limma + r-motifstack + r-org.ce.eg.db + r-org.hs.eg.db + r-organismdbi + r-reactome.db + r-rmarkdown + r-seqinr + r-testthat + r-trackviewer + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.hsapiens.ucsc.hg38.knowngene + r-upsetr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chippeakanno/lilac.py b/prepare/r-chippeakanno/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chippeakanno/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chippeakanno/lilac.yaml b/prepare/r-chippeakanno/lilac.yaml new file mode 100644 index 0000000000..47362978ae --- /dev/null +++ b/prepare/r-chippeakanno/lilac.yaml @@ -0,0 +1,34 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-biomart +- r-biostrings +- r-dbi +- r-dplyr +- r-ensembldb +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-graph +- r-interactionset +- r-iranges +- r-keggrest +- r-matrixstats +- r-multtest +- r-rbgl +- r-regioner +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +- r-venndiagram +update_on: +- regex: ChIPpeakAnno_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChIPpeakAnno diff --git a/prepare/r-chipqc/PKGBUILD b/prepare/r-chipqc/PKGBUILD new file mode 100644 index 0000000000..05d13edaf5 --- /dev/null +++ b/prepare/r-chipqc/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ChIPQC +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quality metrics for ChIPseq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-chipseq + r-diffbind + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-gtools + r-iranges + r-nozzle.r1 + r-reshape2 + r-rsamtools + r-s4vectors + r-txdb.celegans.ucsc.ce6.ensgene + r-txdb.dmelanogaster.ucsc.dm3.ensgene + r-txdb.hsapiens.ucsc.hg18.knowngene + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.mmusculus.ucsc.mm10.knowngene + r-txdb.mmusculus.ucsc.mm9.knowngene + r-txdb.rnorvegicus.ucsc.rn4.ensgene +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chipqc/lilac.py b/prepare/r-chipqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chipqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chipqc/lilac.yaml b/prepare/r-chipqc/lilac.yaml new file mode 100644 index 0000000000..ed5ee6bc41 --- /dev/null +++ b/prepare/r-chipqc/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-chipseq +- r-diffbind +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-gtools +- r-iranges +- r-nozzle.r1 +- r-reshape2 +- r-rsamtools +- r-s4vectors +- r-txdb.celegans.ucsc.ce6.ensgene +- r-txdb.dmelanogaster.ucsc.dm3.ensgene +- r-txdb.hsapiens.ucsc.hg18.knowngene +- r-txdb.hsapiens.ucsc.hg19.knowngene +- r-txdb.mmusculus.ucsc.mm10.knowngene +- r-txdb.mmusculus.ucsc.mm9.knowngene +- r-txdb.rnorvegicus.ucsc.rn4.ensgene +update_on: +- regex: ChIPQC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChIPQC diff --git a/prepare/r-chipseeker/PKGBUILD b/prepare/r-chipseeker/PKGBUILD new file mode 100644 index 0000000000..49f5ea4ee5 --- /dev/null +++ b/prepare/r-chipseeker/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ChIPseeker +_pkgver=1.30.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ChIPseeker for ChIP peak Annotation, Comparison, and Visualization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biocgenerics + r-dplyr + r-enrichplot + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-gplots + r-gtools + r-iranges + r-magrittr + r-plotrix + r-rcolorbrewer + r-rtracklayer + r-s4vectors + r-txdb.hsapiens.ucsc.hg19.knowngene +) +optdepends=( + r-clusterprofiler + r-ggimage + r-ggplotify + r-ggupset + r-knitr + r-org.hs.eg.db + r-reactomepa + r-rmarkdown + r-testthat + r-tibble +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chipseeker/lilac.py b/prepare/r-chipseeker/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chipseeker/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chipseeker/lilac.yaml b/prepare/r-chipseeker/lilac.yaml new file mode 100644 index 0000000000..d537cc63cd --- /dev/null +++ b/prepare/r-chipseeker/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-dplyr +- r-enrichplot +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-gplots +- r-gtools +- r-iranges +- r-magrittr +- r-plotrix +- r-rcolorbrewer +- r-rtracklayer +- r-s4vectors +- r-txdb.hsapiens.ucsc.hg19.knowngene +update_on: +- regex: ChIPseeker_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChIPseeker diff --git a/prepare/r-chipseq/PKGBUILD b/prepare/r-chipseq/PKGBUILD new file mode 100644 index 0000000000..7a9ec4bbc3 --- /dev/null +++ b/prepare/r-chipseq/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=chipseq +_pkgver=1.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='chipseq: A package for analyzing chipseq data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-genomicranges + r-iranges + r-s4vectors + r-shortread +) +optdepends=( + r-bsgenome + r-genomicfeatures + r-txdb.mmusculus.ucsc.mm9.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chipseq/lilac.py b/prepare/r-chipseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chipseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chipseq/lilac.yaml b/prepare/r-chipseq/lilac.yaml new file mode 100644 index 0000000000..26cd98ab05 --- /dev/null +++ b/prepare/r-chipseq/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomicranges +- r-iranges +- r-s4vectors +- r-shortread +update_on: +- regex: chipseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/chipseq diff --git a/prepare/r-chipseqr/PKGBUILD b/prepare/r-chipseqr/PKGBUILD new file mode 100644 index 0000000000..537227f095 --- /dev/null +++ b/prepare/r-chipseqr/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ChIPseqR +_pkgver=1.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identifying Protein Binding Sites in High-Throughput Sequencing Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-fbasics + r-genomicranges + r-hilbertvis + r-iranges + r-s4vectors + r-shortread + r-timsac +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chipseqr/lilac.py b/prepare/r-chipseqr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chipseqr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chipseqr/lilac.yaml b/prepare/r-chipseqr/lilac.yaml new file mode 100644 index 0000000000..1989d8e919 --- /dev/null +++ b/prepare/r-chipseqr/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-fbasics +- r-genomicranges +- r-hilbertvis +- r-iranges +- r-s4vectors +- r-shortread +- r-timsac +update_on: +- regex: ChIPseqR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChIPseqR diff --git a/prepare/r-chipsim/PKGBUILD b/prepare/r-chipsim/PKGBUILD new file mode 100644 index 0000000000..09ead30459 --- /dev/null +++ b/prepare/r-chipsim/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ChIPsim +_pkgver=1.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Simulation of ChIP-seq experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-iranges + r-shortread + r-xvector +) +optdepends=( + r-actuar + r-zoo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chipsim/lilac.py b/prepare/r-chipsim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chipsim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chipsim/lilac.yaml b/prepare/r-chipsim/lilac.yaml new file mode 100644 index 0000000000..0240376b22 --- /dev/null +++ b/prepare/r-chipsim/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-iranges +- r-shortread +- r-xvector +update_on: +- regex: ChIPsim_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChIPsim diff --git a/prepare/r-chipxpress/PKGBUILD b/prepare/r-chipxpress/PKGBUILD new file mode 100644 index 0000000000..6832c23f49 --- /dev/null +++ b/prepare/r-chipxpress/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ChIPXpress +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-biganalytics + r-bigmemory + r-biobase + r-chipxpressdata + r-frma + r-geoquery +) +optdepends=( + r-biocgenerics + r-mouse4302.db + r-mouse4302cdf + r-mouse4302frmavecs + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chipxpress/lilac.py b/prepare/r-chipxpress/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chipxpress/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chipxpress/lilac.yaml b/prepare/r-chipxpress/lilac.yaml new file mode 100644 index 0000000000..8052b2c26b --- /dev/null +++ b/prepare/r-chipxpress/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biganalytics +- r-bigmemory +- r-biobase +- r-chipxpressdata +- r-frma +- r-geoquery +update_on: +- regex: ChIPXpress_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChIPXpress diff --git a/prepare/r-chipxpressdata/PKGBUILD b/prepare/r-chipxpressdata/PKGBUILD new file mode 100644 index 0000000000..ee5347be1d --- /dev/null +++ b/prepare/r-chipxpressdata/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ChIPXpressData +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ChIPXpress Pre-built Databases' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bigmemory +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chipxpressdata/lilac.py b/prepare/r-chipxpressdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chipxpressdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chipxpressdata/lilac.yaml b/prepare/r-chipxpressdata/lilac.yaml new file mode 100644 index 0000000000..0ecdf69183 --- /dev/null +++ b/prepare/r-chipxpressdata/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bigmemory +update_on: +- regex: ChIPXpressData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChIPXpressData diff --git a/prepare/r-chk/PKGBUILD b/prepare/r-chk/PKGBUILD new file mode 100644 index 0000000000..26a6e0d958 --- /dev/null +++ b/prepare/r-chk/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=chk +_pkgver=0.7.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Check User-Supplied Function Arguments' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-lifecycle + r-rlang +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-testthat + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chk/lilac.py b/prepare/r-chk/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chk/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chk/lilac.yaml b/prepare/r-chk/lilac.yaml new file mode 100644 index 0000000000..b96ebb1f63 --- /dev/null +++ b/prepare/r-chk/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lifecycle +- r-rlang +update_on: +- regex: chk_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=chk diff --git a/prepare/r-chopsticks/PKGBUILD b/prepare/r-chopsticks/PKGBUILD new file mode 100644 index 0000000000..e966876c3a --- /dev/null +++ b/prepare/r-chopsticks/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=chopsticks +_pkgver=1.60.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="The 'snp.matrix' and 'X.snp.matrix' Classes" +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-hexbin +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chopsticks/lilac.py b/prepare/r-chopsticks/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chopsticks/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chopsticks/lilac.yaml b/prepare/r-chopsticks/lilac.yaml new file mode 100644 index 0000000000..0296cda16e --- /dev/null +++ b/prepare/r-chopsticks/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: chopsticks_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/chopsticks diff --git a/prepare/r-chromdraw/PKGBUILD b/prepare/r-chromdraw/PKGBUILD new file mode 100644 index 0000000000..736af4dfce --- /dev/null +++ b/prepare/r-chromdraw/PKGBUILD @@ -0,0 +1,29 @@ +# system requirements: Rtools (>= 3.1) +# Maintainer: Guoyi Zhang + +_pkgname=chromDraw +_pkgver=2.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicranges + r-rcpp +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chromdraw/lilac.py b/prepare/r-chromdraw/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chromdraw/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chromdraw/lilac.yaml b/prepare/r-chromdraw/lilac.yaml new file mode 100644 index 0000000000..bd5486fa65 --- /dev/null +++ b/prepare/r-chromdraw/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-rcpp +update_on: +- regex: chromDraw_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/chromDraw diff --git a/prepare/r-chromheatmap/PKGBUILD b/prepare/r-chromheatmap/PKGBUILD new file mode 100644 index 0000000000..854cd6d06e --- /dev/null +++ b/prepare/r-chromheatmap/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ChromHeatMap +_pkgver=1.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Heat map plotting by genome coordinate' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-genomicranges + r-iranges + r-rtracklayer +) +optdepends=( + r-all + r-hgu95av2.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chromheatmap/lilac.py b/prepare/r-chromheatmap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chromheatmap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chromheatmap/lilac.yaml b/prepare/r-chromheatmap/lilac.yaml new file mode 100644 index 0000000000..a7bc69f1f4 --- /dev/null +++ b/prepare/r-chromheatmap/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-genomicranges +- r-iranges +- r-rtracklayer +update_on: +- regex: ChromHeatMap_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChromHeatMap diff --git a/prepare/r-chromhmmdata/PKGBUILD b/prepare/r-chromhmmdata/PKGBUILD new file mode 100644 index 0000000000..29ea240363 --- /dev/null +++ b/prepare/r-chromhmmdata/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=chromhmmData +_pkgver=0.99.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Chromosome Size, Coordinates and Anchor Files' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chromhmmdata/lilac.py b/prepare/r-chromhmmdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chromhmmdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chromhmmdata/lilac.yaml b/prepare/r-chromhmmdata/lilac.yaml new file mode 100644 index 0000000000..db1d0f9586 --- /dev/null +++ b/prepare/r-chromhmmdata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: chromhmmData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/chromhmmData diff --git a/prepare/r-chromplot/PKGBUILD b/prepare/r-chromplot/PKGBUILD new file mode 100644 index 0000000000..877db04c11 --- /dev/null +++ b/prepare/r-chromplot/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=chromPlot +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Global visualization tool of genomic data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-genomicranges +) +optdepends=( + r-genomicfeatures + r-qtl + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chromplot/lilac.py b/prepare/r-chromplot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chromplot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chromplot/lilac.yaml b/prepare/r-chromplot/lilac.yaml new file mode 100644 index 0000000000..3d90050aa2 --- /dev/null +++ b/prepare/r-chromplot/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-genomicranges +update_on: +- regex: chromPlot_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/chromPlot diff --git a/prepare/r-chromscape/PKGBUILD b/prepare/r-chromscape/PKGBUILD new file mode 100644 index 0000000000..8658676455 --- /dev/null +++ b/prepare/r-chromscape/PKGBUILD @@ -0,0 +1,82 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ChromSCape +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of single-cell epigenomics datasets with a Shiny App' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-batchelor + r-biocparallel + r-colorramps + r-colourpicker + r-consensusclusterplus + r-coop + r-delayedarray + r-dplyr + r-dt + r-edger + r-forcats + r-fs + r-genomicranges + r-ggplot2 + r-iranges + r-irlba + r-jsonlite + r-kableextra + r-matrixtests + r-msigdbr + r-plotly + r-qs + r-qualv + r-rcpp + r-rlist + r-rsamtools + r-rtracklayer + r-rtsne + r-s4vectors + r-scater + r-scran + r-shiny + r-shinycssloaders + r-shinydashboard + r-shinydashboardplus + r-shinyfiles + r-shinyhelper + r-shinyjs + r-shinywidgets + r-singlecellexperiment + r-stringdist + r-summarizedexperiment + r-sushi + r-tibble + r-tidyr + r-umap + r-viridis +) +optdepends=( + r-biocstyle + r-future + r-knitr + r-markdown + r-rmarkdown + r-signac + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chromscape/lilac.py b/prepare/r-chromscape/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chromscape/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chromscape/lilac.yaml b/prepare/r-chromscape/lilac.yaml new file mode 100644 index 0000000000..bae18b0862 --- /dev/null +++ b/prepare/r-chromscape/lilac.yaml @@ -0,0 +1,56 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-batchelor +- r-biocparallel +- r-colorramps +- r-colourpicker +- r-consensusclusterplus +- r-coop +- r-delayedarray +- r-dplyr +- r-dt +- r-edger +- r-forcats +- r-fs +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-irlba +- r-jsonlite +- r-kableextra +- r-matrixtests +- r-msigdbr +- r-plotly +- r-qs +- r-qualv +- r-rcpp +- r-rlist +- r-rsamtools +- r-rtracklayer +- r-rtsne +- r-s4vectors +- r-scater +- r-scran +- r-shiny +- r-shinycssloaders +- r-shinydashboard +- r-shinydashboardplus +- r-shinyfiles +- r-shinyhelper +- r-shinyjs +- r-shinywidgets +- r-singlecellexperiment +- r-stringdist +- r-summarizedexperiment +- r-sushi +- r-tibble +- r-tidyr +- r-umap +- r-viridis +update_on: +- regex: ChromSCape_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ChromSCape diff --git a/prepare/r-chromstar/PKGBUILD b/prepare/r-chromstar/PKGBUILD new file mode 100644 index 0000000000..53ff68b12b --- /dev/null +++ b/prepare/r-chromstar/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=chromstaR +_pkgver=1.20.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bamsignals + r-biocgenerics + r-chromstardata + r-doparallel + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-mvtnorm + r-reshape2 + r-rsamtools + r-s4vectors +) +optdepends=( + r-biocstyle + r-biomart + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chromstar/lilac.py b/prepare/r-chromstar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chromstar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chromstar/lilac.yaml b/prepare/r-chromstar/lilac.yaml new file mode 100644 index 0000000000..45504ddd3f --- /dev/null +++ b/prepare/r-chromstar/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bamsignals +- r-biocgenerics +- r-chromstardata +- r-doparallel +- r-foreach +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-mvtnorm +- r-reshape2 +- r-rsamtools +- r-s4vectors +update_on: +- regex: chromstaR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/chromstaR diff --git a/prepare/r-chromstardata/PKGBUILD b/prepare/r-chromstardata/PKGBUILD new file mode 100644 index 0000000000..aa2c956100 --- /dev/null +++ b/prepare/r-chromstardata/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=chromstaRData +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ChIP-seq data for Demonstration Purposes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chromstardata/lilac.py b/prepare/r-chromstardata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chromstardata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chromstardata/lilac.yaml b/prepare/r-chromstardata/lilac.yaml new file mode 100644 index 0000000000..a7e120de98 --- /dev/null +++ b/prepare/r-chromstardata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: chromstaRData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/chromstaRData diff --git a/prepare/r-chromswitch/PKGBUILD b/prepare/r-chromswitch/PKGBUILD new file mode 100644 index 0000000000..93200d30f9 --- /dev/null +++ b/prepare/r-chromswitch/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=chromswitch +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package to detect chromatin state switches from epigenomic data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-biocparallel + r-dplyr + r-genomicranges + r-gplots + r-iranges + r-lazyeval + r-magrittr + r-matrixstats + r-nmf + r-rtracklayer + r-s4vectors + r-tidyr +) +optdepends=( + r-biocstyle + r-desctools + r-devtools + r-genomeinfodb + r-knitr + r-mclust + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chromswitch/lilac.py b/prepare/r-chromswitch/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chromswitch/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chromswitch/lilac.yaml b/prepare/r-chromswitch/lilac.yaml new file mode 100644 index 0000000000..3326c56757 --- /dev/null +++ b/prepare/r-chromswitch/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocparallel +- r-dplyr +- r-genomicranges +- r-gplots +- r-iranges +- r-lazyeval +- r-magrittr +- r-matrixstats +- r-nmf +- r-rtracklayer +- r-s4vectors +- r-tidyr +update_on: +- regex: chromswitch_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/chromswitch diff --git a/prepare/r-chromvar/PKGBUILD b/prepare/r-chromvar/PKGBUILD new file mode 100644 index 0000000000..cdd78d9eb7 --- /dev/null +++ b/prepare/r-chromvar/PKGBUILD @@ -0,0 +1,59 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=chromVAR +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Chromatin Variation Across Regions' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-dt + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-miniui + r-nabor + r-plotly + r-rcolorbrewer + r-rcpp + r-rcpparmadillo + r-rsamtools + r-rtsne + r-s4vectors + r-shiny + r-summarizedexperiment + r-tfbstools +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg19 + r-jaspar2016 + r-knitr + r-motifmatchr + r-pheatmap + r-readr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chromvar/lilac.py b/prepare/r-chromvar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chromvar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chromvar/lilac.yaml b/prepare/r-chromvar/lilac.yaml new file mode 100644 index 0000000000..d12b65afb1 --- /dev/null +++ b/prepare/r-chromvar/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-dt +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-miniui +- r-nabor +- r-plotly +- r-rcolorbrewer +- r-rcpp +- r-rcpparmadillo +- r-rsamtools +- r-rtsne +- r-s4vectors +- r-shiny +- r-summarizedexperiment +- r-tfbstools +update_on: +- regex: chromVAR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/chromVAR diff --git a/prepare/r-chron/PKGBUILD b/prepare/r-chron/PKGBUILD new file mode 100644 index 0000000000..c635af7edc --- /dev/null +++ b/prepare/r-chron/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=chron +_pkgver=2.3-56 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Chronological Objects which can Handle Dates and Times' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-ggplot2 + r-scales + r-zoo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chron/lilac.py b/prepare/r-chron/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chron/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chron/lilac.yaml b/prepare/r-chron/lilac.yaml new file mode 100644 index 0000000000..c88e0368c0 --- /dev/null +++ b/prepare/r-chron/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: chron_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=chron diff --git a/prepare/r-chronos/PKGBUILD b/prepare/r-chronos/PKGBUILD new file mode 100644 index 0000000000..92c83a2c8a --- /dev/null +++ b/prepare/r-chronos/PKGBUILD @@ -0,0 +1,44 @@ +# system requirements: Java version >= 1.7, Pandoc +# Maintainer: Guoyi Zhang + +_pkgname=CHRONOS +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-circlize + r-doparallel + r-foreach + r-graph + r-igraph + r-openxlsx + r-rbgl + r-rcurl + r-rjava + r-xml +) +optdepends=( + r-biocgenerics + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-chronos/lilac.py b/prepare/r-chronos/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-chronos/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-chronos/lilac.yaml b/prepare/r-chronos/lilac.yaml new file mode 100644 index 0000000000..db469b0f89 --- /dev/null +++ b/prepare/r-chronos/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-circlize +- r-doparallel +- r-foreach +- r-graph +- r-igraph +- r-openxlsx +- r-rbgl +- r-rcurl +- r-rjava +- r-xml +update_on: +- regex: CHRONOS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CHRONOS diff --git a/prepare/r-cicero/PKGBUILD b/prepare/r-cicero/PKGBUILD new file mode 100644 index 0000000000..4900c6d9b8 --- /dev/null +++ b/prepare/r-cicero/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cicero +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Precict cis-co-accessibility from single-cell chromatin accessibility data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-assertthat + r-biobase + r-biocgenerics + r-data.table + r-dplyr + r-fnn + r-genomicranges + r-ggplot2 + r-glasso + r-gviz + r-igraph + r-iranges + r-monocle + r-plyr + r-reshape2 + r-s4vectors + r-stringi + r-stringr + r-tibble + r-tidyr + r-vgam +) +optdepends=( + r-annotationdbi + r-covr + r-knitr + r-rmarkdown + r-rtracklayer + r-testthat + r-vdiffr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cicero/lilac.py b/prepare/r-cicero/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cicero/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cicero/lilac.yaml b/prepare/r-cicero/lilac.yaml new file mode 100644 index 0000000000..321b737ddf --- /dev/null +++ b/prepare/r-cicero/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biobase +- r-biocgenerics +- r-data.table +- r-dplyr +- r-fnn +- r-genomicranges +- r-ggplot2 +- r-glasso +- r-gviz +- r-igraph +- r-iranges +- r-monocle +- r-plyr +- r-reshape2 +- r-s4vectors +- r-stringi +- r-stringr +- r-tibble +- r-tidyr +- r-vgam +update_on: +- regex: cicero_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cicero diff --git a/prepare/r-cimice/PKGBUILD b/prepare/r-cimice/PKGBUILD new file mode 100644 index 0000000000..094eee5f20 --- /dev/null +++ b/prepare/r-cimice/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CIMICE +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-assertthat + r-dplyr + r-ggcorrplot + r-ggplot2 + r-ggraph + r-glue + r-igraph + r-maftools + r-networkd3 + r-purrr + r-relations + r-tidyr + r-visnetwork +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat + r-webshot +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cimice/lilac.py b/prepare/r-cimice/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cimice/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cimice/lilac.yaml b/prepare/r-cimice/lilac.yaml new file mode 100644 index 0000000000..2aef988d3b --- /dev/null +++ b/prepare/r-cimice/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-dplyr +- r-ggcorrplot +- r-ggplot2 +- r-ggraph +- r-glue +- r-igraph +- r-maftools +- r-networkd3 +- r-purrr +- r-relations +- r-tidyr +- r-visnetwork +update_on: +- regex: CIMICE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CIMICE diff --git a/prepare/r-cindex/PKGBUILD b/prepare/r-cindex/PKGBUILD new file mode 100644 index 0000000000..7f0ef9af37 --- /dev/null +++ b/prepare/r-cindex/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CINdex +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Chromosome Instability Index' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bitops + r-dplyr + r-genomeinfodb + r-genomicranges + r-gplots + r-gridextra + r-iranges + r-png + r-s4vectors + r-som + r-stringr +) +optdepends=( + r-annotationhub + r-biocgenerics + r-biostrings + r-biovizbase + r-homo.sapiens + r-knitr + r-methods + r-org.hs.eg.db + r-pd.genomewidesnp.6 + r-r.utils + r-reactomepa + r-rtracklayer + r-runit + r-testthat + r-txdb.hsapiens.ucsc.hg18.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cindex/lilac.py b/prepare/r-cindex/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cindex/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cindex/lilac.yaml b/prepare/r-cindex/lilac.yaml new file mode 100644 index 0000000000..30343ccf8c --- /dev/null +++ b/prepare/r-cindex/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bitops +- r-dplyr +- r-genomeinfodb +- r-genomicranges +- r-gplots +- r-gridextra +- r-iranges +- r-png +- r-s4vectors +- r-som +- r-stringr +update_on: +- regex: CINdex_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CINdex diff --git a/prepare/r-circlize/PKGBUILD b/prepare/r-circlize/PKGBUILD new file mode 100644 index 0000000000..00938fe42f --- /dev/null +++ b/prepare/r-circlize/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=circlize +_pkgver=0.4.13 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Circular Visualization' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-colorspace + r-globaloptions + r-shape +) +optdepends=( + r-bezier + r-complexheatmap + r-dendextend + r-gridbase + r-knitr + r-markdown + r-png +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-circlize/lilac.py b/prepare/r-circlize/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-circlize/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-circlize/lilac.yaml b/prepare/r-circlize/lilac.yaml new file mode 100644 index 0000000000..50df659725 --- /dev/null +++ b/prepare/r-circlize/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colorspace +- r-globaloptions +- r-shape +update_on: +- regex: circlize_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=circlize diff --git a/prepare/r-circrnaprofiler/PKGBUILD b/prepare/r-circrnaprofiler/PKGBUILD new file mode 100644 index 0000000000..fd8d0d0a63 --- /dev/null +++ b/prepare/r-circrnaprofiler/PKGBUILD @@ -0,0 +1,63 @@ +# Maintainer: Guoyi Zhang + +_pkgname=circRNAprofiler +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationhub + r-biostrings + r-bsgenome + r-bsgenome.hsapiens.ucsc.hg19 + r-deseq2 + r-dplyr + r-edger + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gwascat + r-iranges + r-magrittr + r-r.utils + r-readr + r-reshape2 + r-rlang + r-rtracklayer + r-s4vectors + r-seqinr + r-stringi + r-stringr + r-universalmotif +) +optdepends=( + r-biocmanager + r-bsgenome.hsapiens.ucsc.hg38 + r-bsgenome.mmusculus.ucsc.mm10 + r-bsgenome.mmusculus.ucsc.mm9 + r-devtools + r-ggpubr + r-gridextra + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat + r-venndiagram +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-circrnaprofiler/lilac.py b/prepare/r-circrnaprofiler/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-circrnaprofiler/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-circrnaprofiler/lilac.yaml b/prepare/r-circrnaprofiler/lilac.yaml new file mode 100644 index 0000000000..18576bc24a --- /dev/null +++ b/prepare/r-circrnaprofiler/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-biostrings +- r-bsgenome +- r-bsgenome.hsapiens.ucsc.hg19 +- r-deseq2 +- r-dplyr +- r-edger +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-gwascat +- r-iranges +- r-magrittr +- r-r.utils +- r-readr +- r-reshape2 +- r-rlang +- r-rtracklayer +- r-s4vectors +- r-seqinr +- r-stringi +- r-stringr +- r-universalmotif +update_on: +- regex: circRNAprofiler_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/circRNAprofiler diff --git a/prepare/r-circstats/PKGBUILD b/prepare/r-circstats/PKGBUILD new file mode 100644 index 0000000000..fe226abd31 --- /dev/null +++ b/prepare/r-circstats/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CircStats +_pkgver=0.2-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Circular Statistics, from "Topics in Circular Statistics" (2001)' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-circstats/lilac.py b/prepare/r-circstats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-circstats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-circstats/lilac.yaml b/prepare/r-circstats/lilac.yaml new file mode 100644 index 0000000000..dc736c9512 --- /dev/null +++ b/prepare/r-circstats/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: CircStats_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=CircStats diff --git a/prepare/r-circular/PKGBUILD b/prepare/r-circular/PKGBUILD new file mode 100644 index 0000000000..b3fbb9bb9d --- /dev/null +++ b/prepare/r-circular/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=circular +_pkgver=0.4-93 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Circular Statistics' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mvtnorm +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-circular/lilac.py b/prepare/r-circular/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-circular/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-circular/lilac.yaml b/prepare/r-circular/lilac.yaml new file mode 100644 index 0000000000..61a85347a7 --- /dev/null +++ b/prepare/r-circular/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mvtnorm +update_on: +- regex: circular_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=circular diff --git a/prepare/r-cispath/PKGBUILD b/prepare/r-cispath/PKGBUILD new file mode 100644 index 0000000000..07d468e569 --- /dev/null +++ b/prepare/r-cispath/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cisPath +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization and management of the protein-protein interaction networks.' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cispath/lilac.py b/prepare/r-cispath/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cispath/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cispath/lilac.yaml b/prepare/r-cispath/lilac.yaml new file mode 100644 index 0000000000..f41d3924fa --- /dev/null +++ b/prepare/r-cispath/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: cisPath_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cisPath diff --git a/prepare/r-citefuse/PKGBUILD b/prepare/r-citefuse/PKGBUILD new file mode 100644 index 0000000000..e13e820482 --- /dev/null +++ b/prepare/r-citefuse/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CiteFuse +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CiteFuse: multi-modal analysis of CITE-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cowplot + r-dbscan + r-ggplot2 + r-ggraph + r-ggridges + r-gridextra + r-igraph + r-mixtools + r-pheatmap + r-propr + r-randomforest + r-reshape2 + r-rhdf5 + r-rlang + r-rtsne + r-s4vectors + r-scales + r-scran + r-singlecellexperiment + r-summarizedexperiment + r-uwot +) +optdepends=( + r-biocstyle + r-dt + r-exposition + r-knitr + r-mclust + r-pkgdown + r-rmarkdown + r-scater +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-citefuse/lilac.py b/prepare/r-citefuse/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-citefuse/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-citefuse/lilac.yaml b/prepare/r-citefuse/lilac.yaml new file mode 100644 index 0000000000..739dae1c85 --- /dev/null +++ b/prepare/r-citefuse/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cowplot +- r-dbscan +- r-ggplot2 +- r-ggraph +- r-ggridges +- r-gridextra +- r-igraph +- r-mixtools +- r-pheatmap +- r-propr +- r-randomforest +- r-reshape2 +- r-rhdf5 +- r-rlang +- r-rtsne +- r-s4vectors +- r-scales +- r-scran +- r-singlecellexperiment +- r-summarizedexperiment +- r-uwot +update_on: +- regex: CiteFuse_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CiteFuse diff --git a/prepare/r-ckmeans.1d.dp/PKGBUILD b/prepare/r-ckmeans.1d.dp/PKGBUILD new file mode 100644 index 0000000000..417aea9aa1 --- /dev/null +++ b/prepare/r-ckmeans.1d.dp/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Ckmeans.1d.dp +_pkgver=4.3.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Optimal, Fast, and Reproducible Univariate Clustering' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-rcpp + r-rdpack +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ckmeans.1d.dp/lilac.py b/prepare/r-ckmeans.1d.dp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ckmeans.1d.dp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ckmeans.1d.dp/lilac.yaml b/prepare/r-ckmeans.1d.dp/lilac.yaml new file mode 100644 index 0000000000..a0e3a40936 --- /dev/null +++ b/prepare/r-ckmeans.1d.dp/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rdpack +update_on: +- regex: Ckmeans.1d.dp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Ckmeans.1d.dp diff --git a/prepare/r-classifyr/PKGBUILD b/prepare/r-classifyr/PKGBUILD new file mode 100644 index 0000000000..de8b6b7257 --- /dev/null +++ b/prepare/r-classifyr/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ClassifyR +_pkgver=2.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-locfit + r-multiassayexperiment + r-plyr + r-s4vectors +) +optdepends=( + r-biocstyle + r-car + r-class + r-cowplot + r-e1071 + r-edger + r-genefilter + r-ggplot2 + r-glmnet + r-gridextra + r-gtable + r-htmltools + r-iranges + r-knitr + r-limma + r-pamr + r-parathyroidse + r-poiclaclu + r-randomforest + r-rmarkdown + r-rmixmod + r-robustbase + r-scales +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-classifyr/lilac.py b/prepare/r-classifyr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-classifyr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-classifyr/lilac.yaml b/prepare/r-classifyr/lilac.yaml new file mode 100644 index 0000000000..9356ad3569 --- /dev/null +++ b/prepare/r-classifyr/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-locfit +- r-multiassayexperiment +- r-plyr +- r-s4vectors +update_on: +- regex: ClassifyR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ClassifyR diff --git a/prepare/r-classint/PKGBUILD b/prepare/r-classint/PKGBUILD new file mode 100644 index 0000000000..3b925029a0 --- /dev/null +++ b/prepare/r-classint/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=classInt +_pkgver=0.4-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Choose Univariate Class Intervals' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-e1071 +) +optdepends=( + r-knitr + r-rmarkdown + r-spdata + r-units +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-classint/lilac.py b/prepare/r-classint/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-classint/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-classint/lilac.yaml b/prepare/r-classint/lilac.yaml new file mode 100644 index 0000000000..8972c1d7b9 --- /dev/null +++ b/prepare/r-classint/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-e1071 +update_on: +- regex: classInt_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=classInt diff --git a/prepare/r-cleanupdtseq/PKGBUILD b/prepare/r-cleanupdtseq/PKGBUILD new file mode 100644 index 0000000000..00151dd22a --- /dev/null +++ b/prepare/r-cleanupdtseq/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cleanUpdTSeq +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-bsgenome + r-bsgenome.drerio.ucsc.danrer7 + r-e1071 + r-genomeinfodb + r-genomicranges + r-iranges + r-seqinr + r-stringr +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cleanupdtseq/lilac.py b/prepare/r-cleanupdtseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cleanupdtseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cleanupdtseq/lilac.yaml b/prepare/r-cleanupdtseq/lilac.yaml new file mode 100644 index 0000000000..411ec26c15 --- /dev/null +++ b/prepare/r-cleanupdtseq/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome +- r-bsgenome.drerio.ucsc.danrer7 +- r-e1071 +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-seqinr +- r-stringr +update_on: +- regex: cleanUpdTSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cleanUpdTSeq diff --git a/prepare/r-cleaver/PKGBUILD b/prepare/r-cleaver/PKGBUILD new file mode 100644 index 0000000000..fa0ec249dd --- /dev/null +++ b/prepare/r-cleaver/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cleaver +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cleavage of Polypeptide Sequences' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-iranges + r-s4vectors +) +optdepends=( + r-biocstyle + r-brain + r-knitr + r-rmarkdown + r-testthat + r-uniprot.ws +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cleaver/lilac.py b/prepare/r-cleaver/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cleaver/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cleaver/lilac.yaml b/prepare/r-cleaver/lilac.yaml new file mode 100644 index 0000000000..b5c3f0fcbd --- /dev/null +++ b/prepare/r-cleaver/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-iranges +- r-s4vectors +update_on: +- regex: cleaver_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cleaver diff --git a/prepare/r-clinfun/PKGBUILD b/prepare/r-clinfun/PKGBUILD new file mode 100644 index 0000000000..b4fec69150 --- /dev/null +++ b/prepare/r-clinfun/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clinfun +_pkgver=1.0.15 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clinical Trial Design and Data Analysis Functions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mvtnorm +) +optdepends=( + r-survival +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clinfun/lilac.py b/prepare/r-clinfun/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clinfun/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clinfun/lilac.yaml b/prepare/r-clinfun/lilac.yaml new file mode 100644 index 0000000000..fb76a241bf --- /dev/null +++ b/prepare/r-clinfun/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mvtnorm +update_on: +- regex: clinfun_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=clinfun diff --git a/prepare/r-clippda/PKGBUILD b/prepare/r-clippda/PKGBUILD new file mode 100644 index 0000000000..6d500e5fdf --- /dev/null +++ b/prepare/r-clippda/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clippda +_pkgver=1.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A package for the clinical proteomic profiling data analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-limma + r-rgl + r-scatterplot3d + r-statmod +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clippda/lilac.py b/prepare/r-clippda/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clippda/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clippda/lilac.yaml b/prepare/r-clippda/lilac.yaml new file mode 100644 index 0000000000..9080191312 --- /dev/null +++ b/prepare/r-clippda/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-limma +- r-rgl +- r-scatterplot3d +- r-statmod +update_on: +- regex: clippda_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/clippda diff --git a/prepare/r-clipper/PKGBUILD b/prepare/r-clipper/PKGBUILD new file mode 100644 index 0000000000..2de297bdb9 --- /dev/null +++ b/prepare/r-clipper/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clipper +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Set Analysis Exploiting Pathway Topology' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-biobase + r-corpcor + r-graph + r-grbase + r-igraph + r-kegggraph + r-qpgraph + r-rbgl + r-rcpp +) +optdepends=( + r-all + r-biocgenerics + r-biocstyle + r-graphite + r-hgu95av2.db + r-mass + r-rcy3 + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clipper/lilac.py b/prepare/r-clipper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clipper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clipper/lilac.yaml b/prepare/r-clipper/lilac.yaml new file mode 100644 index 0000000000..40db200862 --- /dev/null +++ b/prepare/r-clipper/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-corpcor +- r-graph +- r-grbase +- r-igraph +- r-kegggraph +- r-qpgraph +- r-rbgl +- r-rcpp +update_on: +- regex: clipper_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/clipper diff --git a/prepare/r-clipr/PKGBUILD b/prepare/r-clipr/PKGBUILD new file mode 100644 index 0000000000..4bb319a620 --- /dev/null +++ b/prepare/r-clipr/PKGBUILD @@ -0,0 +1,34 @@ +# system requirements: xclip (https://github.com/astrand/xclip) or xsel(http://www.vergenet.net/~conrad/software/xsel/) for accessingthe X11 clipboard +# Maintainer: Guoyi Zhang + +_pkgname=clipr +_pkgver=0.7.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Read and Write from the System Clipboard' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-rstudioapi + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clipr/lilac.py b/prepare/r-clipr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clipr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clipr/lilac.yaml b/prepare/r-clipr/lilac.yaml new file mode 100644 index 0000000000..1d6ac998cb --- /dev/null +++ b/prepare/r-clipr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: clipr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=clipr diff --git a/prepare/r-cliprofiler/PKGBUILD b/prepare/r-cliprofiler/PKGBUILD new file mode 100644 index 0000000000..349e19e50a --- /dev/null +++ b/prepare/r-cliprofiler/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cliProfiler +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A package for the CLIP data visualization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-bsgenome + r-dplyr + r-genomicranges + r-ggplot2 + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocstyle + r-bookdown + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cliprofiler/lilac.py b/prepare/r-cliprofiler/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cliprofiler/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cliprofiler/lilac.yaml b/prepare/r-cliprofiler/lilac.yaml new file mode 100644 index 0000000000..fb263604f8 --- /dev/null +++ b/prepare/r-cliprofiler/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome +- r-dplyr +- r-genomicranges +- r-ggplot2 +- r-rtracklayer +- r-s4vectors +update_on: +- regex: cliProfiler_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cliProfiler diff --git a/prepare/r-cliquems/PKGBUILD b/prepare/r-cliquems/PKGBUILD new file mode 100644 index 0000000000..cf5b9a5a34 --- /dev/null +++ b/prepare/r-cliquems/PKGBUILD @@ -0,0 +1,41 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=cliqueMS +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bh + r-igraph + r-matrixstats + r-msnbase + r-qlcmatrix + r-rcpp + r-rcpparmadillo + r-xcms +) +optdepends=( + r-camera + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cliquems/lilac.py b/prepare/r-cliquems/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cliquems/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cliquems/lilac.yaml b/prepare/r-cliquems/lilac.yaml new file mode 100644 index 0000000000..ae68b3771d --- /dev/null +++ b/prepare/r-cliquems/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-igraph +- r-matrixstats +- r-msnbase +- r-qlcmatrix +- r-rcpp +- r-rcpparmadillo +- r-xcms +update_on: +- regex: cliqueMS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cliqueMS diff --git a/prepare/r-clisymbols/PKGBUILD b/prepare/r-clisymbols/PKGBUILD new file mode 100644 index 0000000000..cf379ba471 --- /dev/null +++ b/prepare/r-clisymbols/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clisymbols +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Unicode Symbols at the R Prompt' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clisymbols/lilac.py b/prepare/r-clisymbols/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clisymbols/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clisymbols/lilac.yaml b/prepare/r-clisymbols/lilac.yaml new file mode 100644 index 0000000000..f48a2b9772 --- /dev/null +++ b/prepare/r-clisymbols/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: clisymbols_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=clisymbols diff --git a/prepare/r-clomial/PKGBUILD b/prepare/r-clomial/PKGBUILD new file mode 100644 index 0000000000..073b6962f9 --- /dev/null +++ b/prepare/r-clomial/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Clomial +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Infers clonal composition of a tumor' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-matrixstats + r-permute +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clomial/lilac.py b/prepare/r-clomial/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clomial/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clomial/lilac.yaml b/prepare/r-clomial/lilac.yaml new file mode 100644 index 0000000000..46a1254d06 --- /dev/null +++ b/prepare/r-clomial/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-matrixstats +- r-permute +update_on: +- regex: Clomial_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Clomial diff --git a/prepare/r-clonality/PKGBUILD b/prepare/r-clonality/PKGBUILD new file mode 100644 index 0000000000..f810871214 --- /dev/null +++ b/prepare/r-clonality/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Clonality +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clonality testing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dnacopy +) +optdepends=( + r-gdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clonality/lilac.py b/prepare/r-clonality/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clonality/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clonality/lilac.yaml b/prepare/r-clonality/lilac.yaml new file mode 100644 index 0000000000..d6a5999983 --- /dev/null +++ b/prepare/r-clonality/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dnacopy +update_on: +- regex: Clonality_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Clonality diff --git a/prepare/r-clonotyper/PKGBUILD b/prepare/r-clonotyper/PKGBUILD new file mode 100644 index 0000000000..d6d2edcac7 --- /dev/null +++ b/prepare/r-clonotyper/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clonotypeR +_pkgver=1.32.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='High throughput analysis of T cell antigen receptor sequences' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r +) +optdepends=( + r-biocgenerics + r-edger + r-knitr + r-pvclust + r-rmarkdown + r-runit + r-vegan +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clonotyper/lilac.py b/prepare/r-clonotyper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clonotyper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clonotyper/lilac.yaml b/prepare/r-clonotyper/lilac.yaml new file mode 100644 index 0000000000..a46bc8c1cc --- /dev/null +++ b/prepare/r-clonotyper/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: clonotypeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/clonotypeR diff --git a/prepare/r-clst/PKGBUILD b/prepare/r-clst/PKGBUILD new file mode 100644 index 0000000000..0961101f61 --- /dev/null +++ b/prepare/r-clst/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clst +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Classification by local similarity threshold' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-roc +) +optdepends=( + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clst/lilac.py b/prepare/r-clst/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clst/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clst/lilac.yaml b/prepare/r-clst/lilac.yaml new file mode 100644 index 0000000000..0c7410bb15 --- /dev/null +++ b/prepare/r-clst/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-roc +update_on: +- regex: clst_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/clst diff --git a/prepare/r-clstutils/PKGBUILD b/prepare/r-clstutils/PKGBUILD new file mode 100644 index 0000000000..aa09be107f --- /dev/null +++ b/prepare/r-clstutils/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clstutils +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for performing taxonomic assignment' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-clst + r-rjson + r-rsqlite +) +optdepends=( + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clstutils/lilac.py b/prepare/r-clstutils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clstutils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clstutils/lilac.yaml b/prepare/r-clstutils/lilac.yaml new file mode 100644 index 0000000000..2754d8f326 --- /dev/null +++ b/prepare/r-clstutils/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-clst +- r-rjson +- r-rsqlite +update_on: +- regex: clstutils_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/clstutils diff --git a/prepare/r-clue/PKGBUILD b/prepare/r-clue/PKGBUILD new file mode 100644 index 0000000000..648a3f9629 --- /dev/null +++ b/prepare/r-clue/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clue +_pkgver=0.3-60 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cluster Ensembles' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-ape + r-cba + r-cclust + r-e1071 + r-flexclust + r-flexmix + r-kernlab + r-lpsolve + r-mclust + r-modeltools + r-movmf + r-quadprog + r-relations + r-rweka +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clue/lilac.py b/prepare/r-clue/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clue/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clue/lilac.yaml b/prepare/r-clue/lilac.yaml new file mode 100644 index 0000000000..3bce7d85d5 --- /dev/null +++ b/prepare/r-clue/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: clue_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=clue diff --git a/prepare/r-clumsid/PKGBUILD b/prepare/r-clumsid/PKGBUILD new file mode 100644 index 0000000000..fe0e3e88bd --- /dev/null +++ b/prepare/r-clumsid/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CluMSID +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clustering of MS2 Spectra for Metabolite Identification' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-ape + r-biobase + r-dbscan + r-ggally + r-ggplot2 + r-gplots + r-msnbase + r-mzr + r-network + r-plotly + r-rcolorbrewer + r-s4vectors + r-sna +) +optdepends=( + r-clumsiddata + r-dplyr + r-knitr + r-magrittr + r-metams + r-metamsdata + r-readr + r-rmarkdown + r-stringr + r-testthat + r-xcms +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clumsid/lilac.py b/prepare/r-clumsid/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clumsid/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clumsid/lilac.yaml b/prepare/r-clumsid/lilac.yaml new file mode 100644 index 0000000000..dfeffa6453 --- /dev/null +++ b/prepare/r-clumsid/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-biobase +- r-dbscan +- r-ggally +- r-ggplot2 +- r-gplots +- r-msnbase +- r-mzr +- r-network +- r-plotly +- r-rcolorbrewer +- r-s4vectors +- r-sna +update_on: +- regex: CluMSID_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CluMSID diff --git a/prepare/r-clustcomp/PKGBUILD b/prepare/r-clustcomp/PKGBUILD new file mode 100644 index 0000000000..944fac0d70 --- /dev/null +++ b/prepare/r-clustcomp/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clustComp +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clustering Comparison Package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-sm +) +optdepends=( + r-biobase + r-biocgenerics + r-colonca + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clustcomp/lilac.py b/prepare/r-clustcomp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clustcomp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clustcomp/lilac.yaml b/prepare/r-clustcomp/lilac.yaml new file mode 100644 index 0000000000..fe7a8d8d69 --- /dev/null +++ b/prepare/r-clustcomp/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-sm +update_on: +- regex: clustComp_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/clustComp diff --git a/prepare/r-clustercrit/PKGBUILD b/prepare/r-clustercrit/PKGBUILD new file mode 100644 index 0000000000..d75f571221 --- /dev/null +++ b/prepare/r-clustercrit/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clusterCrit +_pkgver=1.2.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clustering Indices' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-rbenchmark + r-runit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clustercrit/lilac.py b/prepare/r-clustercrit/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clustercrit/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clustercrit/lilac.yaml b/prepare/r-clustercrit/lilac.yaml new file mode 100644 index 0000000000..e2cb6cf005 --- /dev/null +++ b/prepare/r-clustercrit/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: clusterCrit_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=clusterCrit diff --git a/prepare/r-clusterexperiment/PKGBUILD b/prepare/r-clusterexperiment/PKGBUILD new file mode 100644 index 0000000000..dc2caad2d9 --- /dev/null +++ b/prepare/r-clusterexperiment/PKGBUILD @@ -0,0 +1,59 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clusterExperiment +_pkgver=2.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Compare Clusterings for Single-Cell Sequencing' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ape + r-biocgenerics + r-biocsingular + r-delayedarray + r-edger + r-hdf5array + r-howmany + r-kernlab + r-limma + r-locfdr + r-matrixstats + r-mbkmeans + r-nmf + r-phylobase + r-pracma + r-rcolorbrewer + r-rcpp + r-s4vectors + r-scales + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-zinbwave +) +optdepends=( + r-biocstyle + r-igraph + r-knitr + r-mast + r-rmarkdown + r-rtsne + r-scran + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clusterexperiment/lilac.py b/prepare/r-clusterexperiment/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clusterexperiment/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clusterexperiment/lilac.yaml b/prepare/r-clusterexperiment/lilac.yaml new file mode 100644 index 0000000000..4b27dd1c56 --- /dev/null +++ b/prepare/r-clusterexperiment/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-biocgenerics +- r-biocsingular +- r-delayedarray +- r-edger +- r-hdf5array +- r-howmany +- r-kernlab +- r-limma +- r-locfdr +- r-matrixstats +- r-mbkmeans +- r-nmf +- r-phylobase +- r-pracma +- r-rcolorbrewer +- r-rcpp +- r-s4vectors +- r-scales +- r-singlecellexperiment +- r-stringr +- r-summarizedexperiment +- r-zinbwave +update_on: +- regex: clusterExperiment_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/clusterExperiment diff --git a/prepare/r-clusterjudge/PKGBUILD b/prepare/r-clusterjudge/PKGBUILD new file mode 100644 index 0000000000..0b92749172 --- /dev/null +++ b/prepare/r-clusterjudge/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ClusterJudge +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Judging Quality of Clustering Methods using Mutual Information' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-httr + r-infotheo + r-jsonlite + r-latticeextra +) +optdepends=( + r-biomart + r-devtools + r-knitr + r-rmarkdown + r-testthat + r-yeastexpdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clusterjudge/lilac.py b/prepare/r-clusterjudge/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clusterjudge/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clusterjudge/lilac.yaml b/prepare/r-clusterjudge/lilac.yaml new file mode 100644 index 0000000000..c0001a8ea5 --- /dev/null +++ b/prepare/r-clusterjudge/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-httr +- r-infotheo +- r-jsonlite +- r-latticeextra +update_on: +- regex: ClusterJudge_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ClusterJudge diff --git a/prepare/r-clusterprofiler/PKGBUILD b/prepare/r-clusterprofiler/PKGBUILD new file mode 100644 index 0000000000..931b699c64 --- /dev/null +++ b/prepare/r-clusterprofiler/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clusterProfiler +_pkgver=4.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A universal enrichment tool for interpreting omics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-dose + r-downloader + r-dplyr + r-enrichplot + r-go.db + r-gosemsim + r-magrittr + r-plyr + r-qvalue + r-rlang + r-tidyr + r-yulab.utils +) +optdepends=( + r-annotationhub + r-knitr + r-org.hs.eg.db + r-prettydoc + r-reactomepa + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clusterprofiler/lilac.py b/prepare/r-clusterprofiler/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clusterprofiler/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clusterprofiler/lilac.yaml b/prepare/r-clusterprofiler/lilac.yaml new file mode 100644 index 0000000000..3627189630 --- /dev/null +++ b/prepare/r-clusterprofiler/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-dose +- r-downloader +- r-dplyr +- r-enrichplot +- r-go.db +- r-gosemsim +- r-magrittr +- r-plyr +- r-qvalue +- r-rlang +- r-tidyr +- r-yulab.utils +update_on: +- regex: clusterProfiler_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/clusterProfiler diff --git a/prepare/r-clusterr/PKGBUILD b/prepare/r-clusterr/PKGBUILD new file mode 100644 index 0000000000..60c8ffeb6f --- /dev/null +++ b/prepare/r-clusterr/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: libarmadillo: apt-get install -y libarmadillo-dev(deb), libblas: apt-get install -y libblas-dev (deb),liblapack: apt-get install -y liblapack-dev (deb),libarpack++2: apt-get install -y libarpack++2-dev (deb),gfortran: apt-get install -y gfortran (deb), libgmp3: apt-getinstall -y libgmp3-dev (deb), libfftw3: apt-get install -ylibfftw3-dev (deb), libtiff5: apt-get install -y libtiff5-dev(deb) +# Maintainer: Guoyi Zhang + +_pkgname=ClusterR +_pkgver=1.2.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids and Affinity Propagation Clustering' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-gmp + r-gtools + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-covr + r-fd + r-knitr + r-openimager + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clusterr/lilac.py b/prepare/r-clusterr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clusterr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clusterr/lilac.yaml b/prepare/r-clusterr/lilac.yaml new file mode 100644 index 0000000000..c28e82da11 --- /dev/null +++ b/prepare/r-clusterr/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gmp +- r-gtools +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: ClusterR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ClusterR diff --git a/prepare/r-clusterrepro/PKGBUILD b/prepare/r-clusterrepro/PKGBUILD new file mode 100644 index 0000000000..992f5a58a4 --- /dev/null +++ b/prepare/r-clusterrepro/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clusterRepro +_pkgver=0.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Reproducibility of Gene Expression Clusters' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clusterrepro/lilac.py b/prepare/r-clusterrepro/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clusterrepro/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clusterrepro/lilac.yaml b/prepare/r-clusterrepro/lilac.yaml new file mode 100644 index 0000000000..11fc24eb03 --- /dev/null +++ b/prepare/r-clusterrepro/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: clusterRepro_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=clusterRepro diff --git a/prepare/r-clusterseq/PKGBUILD b/prepare/r-clusterseq/PKGBUILD new file mode 100644 index 0000000000..c087b5acdc --- /dev/null +++ b/prepare/r-clusterseq/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clusterSeq +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clustering of high-throughput sequencing data by identifying co-expression patterns' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bayseq + r-biocgenerics + r-biocparallel +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clusterseq/lilac.py b/prepare/r-clusterseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clusterseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clusterseq/lilac.yaml b/prepare/r-clusterseq/lilac.yaml new file mode 100644 index 0000000000..529af410ad --- /dev/null +++ b/prepare/r-clusterseq/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bayseq +- r-biocgenerics +- r-biocparallel +update_on: +- regex: clusterSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/clusterSeq diff --git a/prepare/r-clustersignificance/PKGBUILD b/prepare/r-clustersignificance/PKGBUILD new file mode 100644 index 0000000000..c3522c89a5 --- /dev/null +++ b/prepare/r-clustersignificance/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ClusterSignificance +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-pracma + r-princurve + r-rcolorbrewer + r-scatterplot3d +) +optdepends=( + r-biocstyle + r-covr + r-ggplot2 + r-knitr + r-plsgenomics + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clustersignificance/lilac.py b/prepare/r-clustersignificance/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clustersignificance/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clustersignificance/lilac.yaml b/prepare/r-clustersignificance/lilac.yaml new file mode 100644 index 0000000000..215ffda4f4 --- /dev/null +++ b/prepare/r-clustersignificance/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-pracma +- r-princurve +- r-rcolorbrewer +- r-scatterplot3d +update_on: +- regex: ClusterSignificance_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ClusterSignificance diff --git a/prepare/r-clustersim/PKGBUILD b/prepare/r-clustersim/PKGBUILD new file mode 100644 index 0000000000..c258a53ff8 --- /dev/null +++ b/prepare/r-clustersim/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clusterSim +_pkgver=0.49-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Searching for Optimal Clustering Procedure for a Data Set' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ade4 + r-e1071 + r-r2html + r-rgl +) +optdepends=( + r-mlbench + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clustersim/lilac.py b/prepare/r-clustersim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clustersim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clustersim/lilac.yaml b/prepare/r-clustersim/lilac.yaml new file mode 100644 index 0000000000..7e72e9115c --- /dev/null +++ b/prepare/r-clustersim/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ade4 +- r-e1071 +- r-r2html +- r-rgl +update_on: +- regex: clusterSim_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=clusterSim diff --git a/prepare/r-clusterstab/PKGBUILD b/prepare/r-clusterstab/PKGBUILD new file mode 100644 index 0000000000..d77e9882c0 --- /dev/null +++ b/prepare/r-clusterstab/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clusterStab +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Compute cluster stability scores for microarray data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase +) +optdepends=( + r-fibroeset + r-genefilter +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clusterstab/lilac.py b/prepare/r-clusterstab/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clusterstab/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clusterstab/lilac.yaml b/prepare/r-clusterstab/lilac.yaml new file mode 100644 index 0000000000..f06dff33dc --- /dev/null +++ b/prepare/r-clusterstab/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: clusterStab_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/clusterStab diff --git a/prepare/r-clustifyr/PKGBUILD b/prepare/r-clustifyr/PKGBUILD new file mode 100644 index 0000000000..1ac3008d0b --- /dev/null +++ b/prepare/r-clustifyr/PKGBUILD @@ -0,0 +1,58 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clustifyr +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Classifier for Single-cell RNA-seq Using Cell Clusters' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-cowplot + r-dplyr + r-entropy + r-fgsea + r-ggplot2 + r-httr + r-matrixstats + r-proxy + r-readr + r-rlang + r-s4vectors + r-scales + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-tibble + r-tidyr +) +optdepends=( + r-biocmanager + r-biocstyle + r-complexheatmap + r-covr + r-ggrepel + r-gprofiler2 + r-knitr + r-purrr + r-remotes + r-rmarkdown + r-shiny + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clustifyr/lilac.py b/prepare/r-clustifyr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clustifyr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clustifyr/lilac.yaml b/prepare/r-clustifyr/lilac.yaml new file mode 100644 index 0000000000..2387e699f2 --- /dev/null +++ b/prepare/r-clustifyr/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cowplot +- r-dplyr +- r-entropy +- r-fgsea +- r-ggplot2 +- r-httr +- r-matrixstats +- r-proxy +- r-readr +- r-rlang +- r-s4vectors +- r-scales +- r-singlecellexperiment +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-tidyr +update_on: +- regex: clustifyr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/clustifyr diff --git a/prepare/r-clustree/PKGBUILD b/prepare/r-clustree/PKGBUILD new file mode 100644 index 0000000000..fc30a5f092 --- /dev/null +++ b/prepare/r-clustree/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clustree +_pkgver=0.4.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualise Clusterings at Different Resolutions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-checkmate + r-dplyr + r-ggplot2 + r-ggraph + r-ggrepel + r-igraph + r-rlang + r-tidygraph + r-viridis +) +optdepends=( + r-covr + r-knitr + r-pkgdown + r-rmarkdown + r-seurat + r-singlecellexperiment + r-spelling + r-summarizedexperiment + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clustree/lilac.py b/prepare/r-clustree/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clustree/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clustree/lilac.yaml b/prepare/r-clustree/lilac.yaml new file mode 100644 index 0000000000..653d116003 --- /dev/null +++ b/prepare/r-clustree/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-checkmate +- r-dplyr +- r-ggplot2 +- r-ggraph +- r-ggrepel +- r-igraph +- r-rlang +- r-tidygraph +- r-viridis +update_on: +- regex: clustree_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=clustree diff --git a/prepare/r-clustvarsel/PKGBUILD b/prepare/r-clustvarsel/PKGBUILD new file mode 100644 index 0000000000..144dbecd6e --- /dev/null +++ b/prepare/r-clustvarsel/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clustvarsel +_pkgver=2.3.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Variable Selection for Gaussian Model-Based Clustering' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bma + r-foreach + r-iterators + r-mclust +) +optdepends=( + r-doparallel + r-knitr + r-mass + r-parallel + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clustvarsel/lilac.py b/prepare/r-clustvarsel/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clustvarsel/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clustvarsel/lilac.yaml b/prepare/r-clustvarsel/lilac.yaml new file mode 100644 index 0000000000..5bc16a80d3 --- /dev/null +++ b/prepare/r-clustvarsel/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bma +- r-foreach +- r-iterators +- r-mclust +update_on: +- regex: clustvarsel_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=clustvarsel diff --git a/prepare/r-clv/PKGBUILD b/prepare/r-clv/PKGBUILD new file mode 100644 index 0000000000..e159eb9331 --- /dev/null +++ b/prepare/r-clv/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clv +_pkgver=0.3-2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cluster Validation Techniques' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clv/lilac.py b/prepare/r-clv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clv/lilac.yaml b/prepare/r-clv/lilac.yaml new file mode 100644 index 0000000000..0670de07ee --- /dev/null +++ b/prepare/r-clv/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: clv_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=clv diff --git a/prepare/r-clvalid/PKGBUILD b/prepare/r-clvalid/PKGBUILD new file mode 100644 index 0000000000..70eade7c0a --- /dev/null +++ b/prepare/r-clvalid/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=clValid +_pkgver=0.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Validation of Clustering Results' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +optdepends=( + r-annotate + r-biobase + r-go.db + r-kohonen + r-mclust + r-moe430a.db + r-rankaggreg +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-clvalid/lilac.py b/prepare/r-clvalid/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-clvalid/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-clvalid/lilac.yaml b/prepare/r-clvalid/lilac.yaml new file mode 100644 index 0000000000..632c76c1e1 --- /dev/null +++ b/prepare/r-clvalid/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: clValid_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=clValid diff --git a/prepare/r-cma/PKGBUILD b/prepare/r-cma/PKGBUILD new file mode 100644 index 0000000000..fa205e5b65 --- /dev/null +++ b/prepare/r-cma/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CMA +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Synthesis of microarray-based classification' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +optdepends=( + r-class + r-corpcor + r-e1071 + r-gbm + r-glmnet + r-limma + r-mass + r-mgcv + r-mvtnorm + r-nnet + r-plsgenomics + r-randomforest + r-st +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cma/lilac.py b/prepare/r-cma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cma/lilac.yaml b/prepare/r-cma/lilac.yaml new file mode 100644 index 0000000000..39ac8347c7 --- /dev/null +++ b/prepare/r-cma/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: CMA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CMA diff --git a/prepare/r-cmap2data/PKGBUILD b/prepare/r-cmap2data/PKGBUILD new file mode 100644 index 0000000000..2a89e5dc32 --- /dev/null +++ b/prepare/r-cmap2data/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cMap2data +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Connectivity Map (version 2) Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cmap2data/lilac.py b/prepare/r-cmap2data/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cmap2data/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cmap2data/lilac.yaml b/prepare/r-cmap2data/lilac.yaml new file mode 100644 index 0000000000..5da6e9f14f --- /dev/null +++ b/prepare/r-cmap2data/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: cMap2data_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cMap2data diff --git a/prepare/r-cmapr/PKGBUILD b/prepare/r-cmapr/PKGBUILD new file mode 100644 index 0000000000..3f554e227d --- /dev/null +++ b/prepare/r-cmapr/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cmapR +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CMap Tools in R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-data.table + r-flowcore + r-matrixstats + r-rhdf5 + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cmapr/lilac.py b/prepare/r-cmapr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cmapr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cmapr/lilac.yaml b/prepare/r-cmapr/lilac.yaml new file mode 100644 index 0000000000..6d59a2f645 --- /dev/null +++ b/prepare/r-cmapr/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-flowcore +- r-matrixstats +- r-rhdf5 +- r-summarizedexperiment +update_on: +- regex: cmapR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cmapR diff --git a/prepare/r-cmdfun/PKGBUILD b/prepare/r-cmdfun/PKGBUILD new file mode 100644 index 0000000000..ab0df4789b --- /dev/null +++ b/prepare/r-cmdfun/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cmdfun +_pkgver=1.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Framework for Building Interfaces to Shell Commands' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-magrittr + r-purrr + r-r.utils + r-rlang + r-testthat + r-usethis +) +optdepends=( + r-cli + r-covr + r-knitr + r-processx + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cmdfun/lilac.py b/prepare/r-cmdfun/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cmdfun/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cmdfun/lilac.yaml b/prepare/r-cmdfun/lilac.yaml new file mode 100644 index 0000000000..8c14708e95 --- /dev/null +++ b/prepare/r-cmdfun/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-magrittr +- r-purrr +- r-r.utils +- r-rlang +- r-testthat +- r-usethis +update_on: +- regex: cmdfun_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=cmdfun diff --git a/prepare/r-cmplot/PKGBUILD b/prepare/r-cmplot/PKGBUILD new file mode 100644 index 0000000000..1c73d3266d --- /dev/null +++ b/prepare/r-cmplot/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CMplot +_pkgver=3.7.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Circle Manhattan Plot' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cmplot/lilac.py b/prepare/r-cmplot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cmplot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cmplot/lilac.yaml b/prepare/r-cmplot/lilac.yaml new file mode 100644 index 0000000000..7c90943ee3 --- /dev/null +++ b/prepare/r-cmplot/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: CMplot_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=CMplot diff --git a/prepare/r-cn.farms/PKGBUILD b/prepare/r-cn.farms/PKGBUILD new file mode 100644 index 0000000000..0b648af2f6 --- /dev/null +++ b/prepare/r-cn.farms/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cn.farms +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='cn.FARMS - factor analysis for copy number estimation' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-affxparser + r-biobase + r-dbi + r-dnacopy + r-ff + r-oligo + r-oligoclasses + r-preprocesscore + r-snow +) +optdepends=( + r-pd.genomewidesnp.5 + r-pd.genomewidesnp.6 + r-pd.mapping250k.nsp + r-pd.mapping250k.sty +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cn.farms/lilac.py b/prepare/r-cn.farms/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cn.farms/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cn.farms/lilac.yaml b/prepare/r-cn.farms/lilac.yaml new file mode 100644 index 0000000000..b1e6f97d0d --- /dev/null +++ b/prepare/r-cn.farms/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affxparser +- r-biobase +- r-dbi +- r-dnacopy +- r-ff +- r-oligo +- r-oligoclasses +- r-preprocesscore +- r-snow +update_on: +- regex: cn.farms_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cn.farms diff --git a/prepare/r-cn.mops/PKGBUILD b/prepare/r-cn.mops/PKGBUILD new file mode 100644 index 0000000000..aacf5bf1b6 --- /dev/null +++ b/prepare/r-cn.mops/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cn.mops +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='cn.mops - Mixture of Poissons for CNV detection in NGS data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-biocgenerics + r-exomecopy + r-genomeinfodb + r-genomicranges + r-iranges + r-rsamtools + r-s4vectors +) +optdepends=( + r-dnacopy +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cn.mops/lilac.py b/prepare/r-cn.mops/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cn.mops/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cn.mops/lilac.yaml b/prepare/r-cn.mops/lilac.yaml new file mode 100644 index 0000000000..00b040364a --- /dev/null +++ b/prepare/r-cn.mops/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-exomecopy +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rsamtools +- r-s4vectors +update_on: +- regex: cn.mops_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cn.mops diff --git a/prepare/r-cnanorm/PKGBUILD b/prepare/r-cnanorm/PKGBUILD new file mode 100644 index 0000000000..14096b0064 --- /dev/null +++ b/prepare/r-cnanorm/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CNAnorm +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A normalization method for Copy Number Aberration in cancer samples' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dnacopy +) +makedepends=( + gcc-fortran +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cnanorm/lilac.py b/prepare/r-cnanorm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cnanorm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cnanorm/lilac.yaml b/prepare/r-cnanorm/lilac.yaml new file mode 100644 index 0000000000..13ea73b411 --- /dev/null +++ b/prepare/r-cnanorm/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dnacopy +update_on: +- regex: CNAnorm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CNAnorm diff --git a/prepare/r-cner/PKGBUILD b/prepare/r-cner/PKGBUILD new file mode 100644 index 0000000000..890b14cf4c --- /dev/null +++ b/prepare/r-cner/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CNEr +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CNE Detection and Visualization' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotate + r-biocgenerics + r-biostrings + r-dbi + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-go.db + r-iranges + r-keggrest + r-powerlaw + r-r.utils + r-readr + r-reshape2 + r-rsqlite + r-rtracklayer + r-s4vectors + r-xvector +) +optdepends=( + r-biocstyle + r-bsgenome.drerio.ucsc.danrer10 + r-bsgenome.ggallus.ucsc.galgal3 + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.hsapiens.ucsc.hg38 + r-gviz + r-knitr + r-rmarkdown + r-testthat + r-txdb.drerio.ucsc.danrer10.refgene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cner/lilac.py b/prepare/r-cner/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cner/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cner/lilac.yaml b/prepare/r-cner/lilac.yaml new file mode 100644 index 0000000000..3cd09cb2f4 --- /dev/null +++ b/prepare/r-cner/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-biocgenerics +- r-biostrings +- r-dbi +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-go.db +- r-iranges +- r-keggrest +- r-powerlaw +- r-r.utils +- r-readr +- r-reshape2 +- r-rsqlite +- r-rtracklayer +- r-s4vectors +- r-xvector +update_on: +- regex: CNEr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CNEr diff --git a/prepare/r-cnordt/PKGBUILD b/prepare/r-cnordt/PKGBUILD new file mode 100644 index 0000000000..1723a61349 --- /dev/null +++ b/prepare/r-cnordt/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CNORdt +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Add-on to CellNOptR: Discretized time treatments' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-cellnoptr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cnordt/lilac.py b/prepare/r-cnordt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cnordt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cnordt/lilac.yaml b/prepare/r-cnordt/lilac.yaml new file mode 100644 index 0000000000..28dfe39829 --- /dev/null +++ b/prepare/r-cnordt/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-cellnoptr +update_on: +- regex: CNORdt_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CNORdt diff --git a/prepare/r-cnorfeeder/PKGBUILD b/prepare/r-cnorfeeder/PKGBUILD new file mode 100644 index 0000000000..c400eb1f96 --- /dev/null +++ b/prepare/r-cnorfeeder/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CNORfeeder +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integration of CellNOptR to add missing links' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cellnoptr + r-graph +) +optdepends=( + r-biocgenerics + r-catnet + r-igraph + r-meigor + r-minet + r-rgraphviz + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cnorfeeder/lilac.py b/prepare/r-cnorfeeder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cnorfeeder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cnorfeeder/lilac.yaml b/prepare/r-cnorfeeder/lilac.yaml new file mode 100644 index 0000000000..68f5f52620 --- /dev/null +++ b/prepare/r-cnorfeeder/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cellnoptr +- r-graph +update_on: +- regex: CNORfeeder_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CNORfeeder diff --git a/prepare/r-cnorfuzzy/PKGBUILD b/prepare/r-cnorfuzzy/PKGBUILD new file mode 100644 index 0000000000..a18e963d31 --- /dev/null +++ b/prepare/r-cnorfuzzy/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CNORfuzzy +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Addon to CellNOptR: Fuzzy Logic' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cellnoptr + r-nloptr +) +optdepends=( + r-biocgenerics + r-rgraphviz + r-runit + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cnorfuzzy/lilac.py b/prepare/r-cnorfuzzy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cnorfuzzy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cnorfuzzy/lilac.yaml b/prepare/r-cnorfuzzy/lilac.yaml new file mode 100644 index 0000000000..bfc76e84bf --- /dev/null +++ b/prepare/r-cnorfuzzy/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cellnoptr +- r-nloptr +update_on: +- regex: CNORfuzzy_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CNORfuzzy diff --git a/prepare/r-cnorode/PKGBUILD b/prepare/r-cnorode/PKGBUILD new file mode 100644 index 0000000000..3d71b96302 --- /dev/null +++ b/prepare/r-cnorode/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CNORode +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ODE add-on to CellNOptR' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cellnoptr + r-genalg +) +optdepends=( + r-doparallel + r-foreach + r-meigor +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cnorode/lilac.py b/prepare/r-cnorode/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cnorode/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cnorode/lilac.yaml b/prepare/r-cnorode/lilac.yaml new file mode 100644 index 0000000000..d4458fa654 --- /dev/null +++ b/prepare/r-cnorode/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cellnoptr +- r-genalg +update_on: +- regex: CNORode_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CNORode diff --git a/prepare/r-cntools/PKGBUILD b/prepare/r-cntools/PKGBUILD new file mode 100644 index 0000000000..4df363f4ad --- /dev/null +++ b/prepare/r-cntools/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CNTools +_pkgver=1.50.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Convert segment data into a region by sample matrix to allow for other high level computational analyses.' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-genefilter +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cntools/lilac.py b/prepare/r-cntools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cntools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cntools/lilac.yaml b/prepare/r-cntools/lilac.yaml new file mode 100644 index 0000000000..944d7c286f --- /dev/null +++ b/prepare/r-cntools/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genefilter +update_on: +- regex: CNTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CNTools diff --git a/prepare/r-cnvfilter/PKGBUILD b/prepare/r-cnvfilter/PKGBUILD new file mode 100644 index 0000000000..16eeb40429 --- /dev/null +++ b/prepare/r-cnvfilter/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CNVfilteR +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identifies false positives of CNV calling tools by using SNV calls' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-assertthat + r-biostrings + r-copynumberplots + r-genomeinfodb + r-genomicranges + r-iranges + r-karyoploter + r-pracma + r-regioner + r-rsamtools + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.hsapiens.ucsc.hg19.masked + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cnvfilter/lilac.py b/prepare/r-cnvfilter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cnvfilter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cnvfilter/lilac.yaml b/prepare/r-cnvfilter/lilac.yaml new file mode 100644 index 0000000000..6cc159ff80 --- /dev/null +++ b/prepare/r-cnvfilter/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biostrings +- r-copynumberplots +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-karyoploter +- r-pracma +- r-regioner +- r-rsamtools +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: CNVfilteR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CNVfilteR diff --git a/prepare/r-cnvgears/PKGBUILD b/prepare/r-cnvgears/PKGBUILD new file mode 100644 index 0000000000..37a6e97a85 --- /dev/null +++ b/prepare/r-cnvgears/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CNVgears +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Framework of Functions to Combine, Analize and Interpret CNVs Calling Results' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-ggplot2 +) +optdepends=( + r-biomart + r-cn.mops + r-cowplot + r-delayedarray + r-devtools + r-evobir + r-genomicranges + r-knitr + r-r.utils + r-rmarkdown + r-scales + r-testthat + r-usethis + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cnvgears/lilac.py b/prepare/r-cnvgears/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cnvgears/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cnvgears/lilac.yaml b/prepare/r-cnvgears/lilac.yaml new file mode 100644 index 0000000000..506e2ff08f --- /dev/null +++ b/prepare/r-cnvgears/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-ggplot2 +update_on: +- regex: CNVgears_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CNVgears diff --git a/prepare/r-cnvgsa/PKGBUILD b/prepare/r-cnvgsa/PKGBUILD new file mode 100644 index 0000000000..2353111044 --- /dev/null +++ b/prepare/r-cnvgsa/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cnvGSA +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Set Analysis of (Rare) Copy Number Variants' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-brglm + r-doparallel + r-foreach + r-genomicranges + r-splitstackshape +) +optdepends=( + r-cnvgsadata + r-org.hs.eg.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cnvgsa/lilac.py b/prepare/r-cnvgsa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cnvgsa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cnvgsa/lilac.yaml b/prepare/r-cnvgsa/lilac.yaml new file mode 100644 index 0000000000..b76e7e992f --- /dev/null +++ b/prepare/r-cnvgsa/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-brglm +- r-doparallel +- r-foreach +- r-genomicranges +- r-splitstackshape +update_on: +- regex: cnvGSA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cnvGSA diff --git a/prepare/r-cnviz/PKGBUILD b/prepare/r-cnviz/PKGBUILD new file mode 100644 index 0000000000..a092044fab --- /dev/null +++ b/prepare/r-cnviz/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CNViz +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Copy Number Visualization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-copynumberplots + r-dplyr + r-dt + r-genomicranges + r-karyoploter + r-magrittr + r-plotly + r-scales + r-shiny +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cnviz/lilac.py b/prepare/r-cnviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cnviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cnviz/lilac.yaml b/prepare/r-cnviz/lilac.yaml new file mode 100644 index 0000000000..f46e117404 --- /dev/null +++ b/prepare/r-cnviz/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-copynumberplots +- r-dplyr +- r-dt +- r-genomicranges +- r-karyoploter +- r-magrittr +- r-plotly +- r-scales +- r-shiny +update_on: +- regex: CNViz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CNViz diff --git a/prepare/r-cnvpanelizer/PKGBUILD b/prepare/r-cnvpanelizer/PKGBUILD new file mode 100644 index 0000000000..24685ac6dc --- /dev/null +++ b/prepare/r-cnvpanelizer/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CNVPanelizer +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Reliable CNV detection in targeted sequencing applications' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-exomecopy + r-foreach + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gplots + r-iranges + r-noiseq + r-openxlsx + r-plyr + r-reshape2 + r-rsamtools + r-s4vectors + r-shiny + r-shinyfiles + r-shinyjs + r-stringr + r-testthat +) +optdepends=( + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cnvpanelizer/lilac.py b/prepare/r-cnvpanelizer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cnvpanelizer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cnvpanelizer/lilac.yaml b/prepare/r-cnvpanelizer/lilac.yaml new file mode 100644 index 0000000000..a55f698906 --- /dev/null +++ b/prepare/r-cnvpanelizer/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-exomecopy +- r-foreach +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-gplots +- r-iranges +- r-noiseq +- r-openxlsx +- r-plyr +- r-reshape2 +- r-rsamtools +- r-s4vectors +- r-shiny +- r-shinyfiles +- r-shinyjs +- r-stringr +- r-testthat +update_on: +- regex: CNVPanelizer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CNVPanelizer diff --git a/prepare/r-cnvranger/PKGBUILD b/prepare/r-cnvranger/PKGBUILD new file mode 100644 index 0000000000..f080512634 --- /dev/null +++ b/prepare/r-cnvranger/PKGBUILD @@ -0,0 +1,59 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CNVRanger +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Summarization and expression/phenotype association of CNV ranges' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biocparallel + r-data.table + r-edger + r-gdsarray + r-gdsfmt + r-genomeinfodb + r-genomicranges + r-iranges + r-limma + r-plyr + r-qqman + r-raggedexperiment + r-rappdirs + r-reshape2 + r-s4vectors + r-snprelate + r-summarizedexperiment +) +optdepends=( + r-annotationhub + r-biocstyle + r-bsgenome.btaurus.ucsc.bostau6.masked + r-complexheatmap + r-curatedtcgadata + r-ensembldb + r-grid + r-gviz + r-knitr + r-multiassayexperiment + r-regioner + r-rmarkdown + r-tcgautils +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cnvranger/lilac.py b/prepare/r-cnvranger/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cnvranger/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cnvranger/lilac.yaml b/prepare/r-cnvranger/lilac.yaml new file mode 100644 index 0000000000..0ff89c60b5 --- /dev/null +++ b/prepare/r-cnvranger/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-data.table +- r-edger +- r-gdsarray +- r-gdsfmt +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-limma +- r-plyr +- r-qqman +- r-raggedexperiment +- r-rappdirs +- r-reshape2 +- r-s4vectors +- r-snprelate +- r-summarizedexperiment +update_on: +- regex: CNVRanger_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CNVRanger diff --git a/prepare/r-cnvrd2/PKGBUILD b/prepare/r-cnvrd2/PKGBUILD new file mode 100644 index 0000000000..4b70c74fa5 --- /dev/null +++ b/prepare/r-cnvrd2/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CNVrd2 +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dnacopy + r-ggplot2 + r-gridextra + r-iranges + r-rjags + r-rsamtools + r-variantannotation +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cnvrd2/lilac.py b/prepare/r-cnvrd2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cnvrd2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cnvrd2/lilac.yaml b/prepare/r-cnvrd2/lilac.yaml new file mode 100644 index 0000000000..dc2956c7f0 --- /dev/null +++ b/prepare/r-cnvrd2/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dnacopy +- r-ggplot2 +- r-gridextra +- r-iranges +- r-rjags +- r-rsamtools +- r-variantannotation +update_on: +- regex: CNVrd2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CNVrd2 diff --git a/prepare/r-cobs/PKGBUILD b/prepare/r-cobs/PKGBUILD new file mode 100644 index 0000000000..b442629642 --- /dev/null +++ b/prepare/r-cobs/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cobs +_pkgver=1.3-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Constrained B-Splines (Sparse Matrix Based)' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-quantreg + r-sparsem +) +optdepends=( + r-matrix +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cobs/lilac.py b/prepare/r-cobs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cobs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cobs/lilac.yaml b/prepare/r-cobs/lilac.yaml new file mode 100644 index 0000000000..7d3636622d --- /dev/null +++ b/prepare/r-cobs/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-quantreg +- r-sparsem +update_on: +- regex: cobs_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=cobs diff --git a/prepare/r-cocitestats/PKGBUILD b/prepare/r-cocitestats/PKGBUILD new file mode 100644 index 0000000000..5062c2b5a3 --- /dev/null +++ b/prepare/r-cocitestats/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CoCiteStats +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Different test statistics based on co-citation.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CPL') +depends=( + r + r-annotationdbi + r-org.hs.eg.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cocitestats/lilac.py b/prepare/r-cocitestats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cocitestats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cocitestats/lilac.yaml b/prepare/r-cocitestats/lilac.yaml new file mode 100644 index 0000000000..a311d4245d --- /dev/null +++ b/prepare/r-cocitestats/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-org.hs.eg.db +update_on: +- regex: CoCiteStats_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CoCiteStats diff --git a/prepare/r-cocoa/PKGBUILD b/prepare/r-cocoa/PKGBUILD new file mode 100644 index 0000000000..293dac3ee3 --- /dev/null +++ b/prepare/r-cocoa/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=COCOA +_pkgver=2.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Coordinate Covariation Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-complexheatmap + r-data.table + r-fitdistrplus + r-genomicranges + r-ggplot2 + r-iranges + r-mira + r-s4vectors + r-simplecache + r-tidyr +) +optdepends=( + r-annotationhub + r-biocstyle + r-knitr + r-lola + r-parallel + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cocoa/lilac.py b/prepare/r-cocoa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cocoa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cocoa/lilac.yaml b/prepare/r-cocoa/lilac.yaml new file mode 100644 index 0000000000..8cd5c96f8c --- /dev/null +++ b/prepare/r-cocoa/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-complexheatmap +- r-data.table +- r-fitdistrplus +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-mira +- r-s4vectors +- r-simplecache +- r-tidyr +update_on: +- regex: COCOA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/COCOA diff --git a/prepare/r-coda/PKGBUILD b/prepare/r-coda/PKGBUILD new file mode 100644 index 0000000000..f4d5b81bf2 --- /dev/null +++ b/prepare/r-coda/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=coda +_pkgver=0.19-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Output Analysis and Diagnostics for MCMC' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-coda/lilac.py b/prepare/r-coda/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-coda/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-coda/lilac.yaml b/prepare/r-coda/lilac.yaml new file mode 100644 index 0000000000..529e730503 --- /dev/null +++ b/prepare/r-coda/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: coda_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=coda diff --git a/prepare/r-codedepends/PKGBUILD b/prepare/r-codedepends/PKGBUILD new file mode 100644 index 0000000000..6e3708a328 --- /dev/null +++ b/prepare/r-codedepends/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CodeDepends +_pkgver=0.6.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of R Code for Reproducible Research and Code Comprehension' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-graph + r-xml +) +optdepends=( + r-highlight + r-knitr + r-rcpp + r-rcurl + r-rgraphviz + r-rjsonio + r-runit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-codedepends/lilac.py b/prepare/r-codedepends/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-codedepends/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-codedepends/lilac.yaml b/prepare/r-codedepends/lilac.yaml new file mode 100644 index 0000000000..ae6d619ea6 --- /dev/null +++ b/prepare/r-codedepends/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +- r-xml +update_on: +- regex: CodeDepends_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=CodeDepends diff --git a/prepare/r-codelink/PKGBUILD b/prepare/r-codelink/PKGBUILD new file mode 100644 index 0000000000..92bf5b78c1 --- /dev/null +++ b/prepare/r-codelink/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=codelink +_pkgver=1.62.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Manipulation of Codelink microarray data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotate + r-biobase + r-biocgenerics + r-limma +) +optdepends=( + r-genefilter + r-knitr + r-parallel +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-codelink/lilac.py b/prepare/r-codelink/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-codelink/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-codelink/lilac.yaml b/prepare/r-codelink/lilac.yaml new file mode 100644 index 0000000000..a285394b63 --- /dev/null +++ b/prepare/r-codelink/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-biobase +- r-biocgenerics +- r-limma +update_on: +- regex: codelink_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/codelink diff --git a/prepare/r-codex/PKGBUILD b/prepare/r-codex/PKGBUILD new file mode 100644 index 0000000000..f5027fbb03 --- /dev/null +++ b/prepare/r-codex/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CODEX +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-bsgenome.hsapiens.ucsc.hg19 + r-genomeinfodb + r-iranges + r-rsamtools + r-s4vectors +) +optdepends=( + r-wes.1kg.wugsc +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-codex/lilac.py b/prepare/r-codex/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-codex/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-codex/lilac.yaml b/prepare/r-codex/lilac.yaml new file mode 100644 index 0000000000..2fdaa19aac --- /dev/null +++ b/prepare/r-codex/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome.hsapiens.ucsc.hg19 +- r-genomeinfodb +- r-iranges +- r-rsamtools +- r-s4vectors +update_on: +- regex: CODEX_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CODEX diff --git a/prepare/r-coexnet/PKGBUILD b/prepare/r-coexnet/PKGBUILD new file mode 100644 index 0000000000..a1fa9223d8 --- /dev/null +++ b/prepare/r-coexnet/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=coexnet +_pkgver=1.15.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='coexnet: An R package to build CO-EXpression NETworks from Microarray Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-acde + r-affy + r-biobase + r-geoquery + r-igraph + r-limma + r-minet + r-rmarkdown + r-siggenes + r-stringdb + r-summarizedexperiment + r-vsn +) +optdepends=( + r-biocgenerics + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-coexnet/lilac.py b/prepare/r-coexnet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-coexnet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-coexnet/lilac.yaml b/prepare/r-coexnet/lilac.yaml new file mode 100644 index 0000000000..bd324df1e9 --- /dev/null +++ b/prepare/r-coexnet/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-acde +- r-affy +- r-biobase +- r-geoquery +- r-igraph +- r-limma +- r-minet +- r-rmarkdown +- r-siggenes +- r-stringdb +- r-summarizedexperiment +- r-vsn +update_on: +- regex: coexnet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/coexnet diff --git a/prepare/r-cogaps/PKGBUILD b/prepare/r-cogaps/PKGBUILD new file mode 100644 index 0000000000..c983db2619 --- /dev/null +++ b/prepare/r-cogaps/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CoGAPS +_pkgver=3.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Coordinated Gene Activity in Pattern Sets' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-bh + r-biocparallel + r-gplots + r-rcolorbrewer + r-rcpp + r-rhdf5 + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cogaps/lilac.py b/prepare/r-cogaps/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cogaps/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cogaps/lilac.yaml b/prepare/r-cogaps/lilac.yaml new file mode 100644 index 0000000000..902b845feb --- /dev/null +++ b/prepare/r-cogaps/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-biocparallel +- r-gplots +- r-rcolorbrewer +- r-rcpp +- r-rhdf5 +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: CoGAPS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CoGAPS diff --git a/prepare/r-cogena/PKGBUILD b/prepare/r-cogena/PKGBUILD new file mode 100644 index 0000000000..93c2b90aa1 --- /dev/null +++ b/prepare/r-cogena/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cogena +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='co-expressed gene-set enrichment analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-amap + r-apcluster + r-biobase + r-biwt + r-corrplot + r-devtools + r-doparallel + r-dplyr + r-fastcluster + r-foreach + r-ggplot2 + r-gplots + r-kohonen + r-mclust + r-reshape2 + r-stringr + r-tibble + r-tidyr +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cogena/lilac.py b/prepare/r-cogena/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cogena/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cogena/lilac.yaml b/prepare/r-cogena/lilac.yaml new file mode 100644 index 0000000000..34872a2611 --- /dev/null +++ b/prepare/r-cogena/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-amap +- r-apcluster +- r-biobase +- r-biwt +- r-corrplot +- r-devtools +- r-doparallel +- r-dplyr +- r-fastcluster +- r-foreach +- r-ggplot2 +- r-gplots +- r-kohonen +- r-mclust +- r-reshape2 +- r-stringr +- r-tibble +- r-tidyr +update_on: +- regex: cogena_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cogena diff --git a/prepare/r-cogito/PKGBUILD b/prepare/r-cogito/PKGBUILD new file mode 100644 index 0000000000..a6c6954fb4 --- /dev/null +++ b/prepare/r-cogito/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Cogito +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-annotationdbi + r-biocmanager + r-entropy + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-jsonlite + r-magrittr + r-rmarkdown + r-s4vectors + r-txdb.mmusculus.ucsc.mm9.knowngene +) +optdepends=( + r-biocstyle + r-knitr + r-markdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cogito/lilac.py b/prepare/r-cogito/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cogito/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cogito/lilac.yaml b/prepare/r-cogito/lilac.yaml new file mode 100644 index 0000000000..3a19c6835b --- /dev/null +++ b/prepare/r-cogito/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocmanager +- r-entropy +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-jsonlite +- r-magrittr +- r-rmarkdown +- r-s4vectors +- r-txdb.mmusculus.ucsc.mm9.knowngene +update_on: +- regex: Cogito_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Cogito diff --git a/prepare/r-cogps/PKGBUILD b/prepare/r-cogps/PKGBUILD new file mode 100644 index 0000000000..6b51ee6119 --- /dev/null +++ b/prepare/r-cogps/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=coGPS +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='cancer outlier Gene Profile Sets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-limma +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cogps/lilac.py b/prepare/r-cogps/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cogps/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cogps/lilac.yaml b/prepare/r-cogps/lilac.yaml new file mode 100644 index 0000000000..e63d7fceaf --- /dev/null +++ b/prepare/r-cogps/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: coGPS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/coGPS diff --git a/prepare/r-cohcap/PKGBUILD b/prepare/r-cohcap/PKGBUILD new file mode 100644 index 0000000000..e6220da3fa --- /dev/null +++ b/prepare/r-cohcap/PKGBUILD @@ -0,0 +1,34 @@ +# system requirements: Perl +# Maintainer: Guoyi Zhang + +_pkgname=COHCAP +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bh + r-cohcapanno + r-gplots + r-rcolorbrewer + r-rcpp + r-rcpparmadillo + r-writexls +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cohcap/lilac.py b/prepare/r-cohcap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cohcap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cohcap/lilac.yaml b/prepare/r-cohcap/lilac.yaml new file mode 100644 index 0000000000..6e42389bbb --- /dev/null +++ b/prepare/r-cohcap/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-cohcapanno +- r-gplots +- r-rcolorbrewer +- r-rcpp +- r-rcpparmadillo +- r-writexls +update_on: +- regex: COHCAP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/COHCAP diff --git a/prepare/r-cohcapanno/PKGBUILD b/prepare/r-cohcapanno/PKGBUILD new file mode 100644 index 0000000000..c486970952 --- /dev/null +++ b/prepare/r-cohcapanno/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=COHCAPanno +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotations for City of Hope CpG Island Analysis Pipeline' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cohcapanno/lilac.py b/prepare/r-cohcapanno/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cohcapanno/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cohcapanno/lilac.yaml b/prepare/r-cohcapanno/lilac.yaml new file mode 100644 index 0000000000..79ba6a1c1c --- /dev/null +++ b/prepare/r-cohcapanno/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: COHCAPanno_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/COHCAPanno diff --git a/prepare/r-coin/PKGBUILD b/prepare/r-coin/PKGBUILD new file mode 100644 index 0000000000..905276acde --- /dev/null +++ b/prepare/r-coin/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=coin +_pkgver=1.4-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Conditional Inference Procedures in a Permutation Test Framework' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-libcoin + r-matrixstats + r-modeltools + r-multcomp + r-mvtnorm +) +optdepends=( + r-e1071 + r-th.data + r-vcd + r-xtable +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-coin/lilac.py b/prepare/r-coin/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-coin/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-coin/lilac.yaml b/prepare/r-coin/lilac.yaml new file mode 100644 index 0000000000..6173d4bf27 --- /dev/null +++ b/prepare/r-coin/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-libcoin +- r-matrixstats +- r-modeltools +- r-multcomp +- r-mvtnorm +update_on: +- regex: coin_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=coin diff --git a/prepare/r-cola/PKGBUILD b/prepare/r-cola/PKGBUILD new file mode 100644 index 0000000000..66050c49b8 --- /dev/null +++ b/prepare/r-cola/PKGBUILD @@ -0,0 +1,78 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cola +_pkgver=2.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Framework for Consensus Partitioning' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-brew + r-circlize + r-clue + r-complexheatmap + r-crayon + r-digest + r-doparallel + r-eulerr + r-foreach + r-getoptlong + r-globaloptions + r-httr + r-impute + r-irlba + r-knitr + r-markdown + r-matrixstats + r-mclust + r-microbenchmark + r-png + r-rcolorbrewer + r-rcpp + r-skmeans + r-xml2 +) +optdepends=( + r-annotationdbi + r-biocmanager + r-clusterprofiler + r-cowplot + r-data.tree + r-dendextend + r-dose + r-flexclust + r-genefilter + r-gplots + r-hu6800.db + r-kohonen + r-mvtnorm + r-nmf + r-pamr + r-polychrome + r-reactomepa + r-rmarkdown + r-rtsne + r-samr + r-simplifyenrichment + r-testthat + r-umap + r-wgcna +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cola/lilac.py b/prepare/r-cola/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cola/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cola/lilac.yaml b/prepare/r-cola/lilac.yaml new file mode 100644 index 0000000000..7ade113944 --- /dev/null +++ b/prepare/r-cola/lilac.yaml @@ -0,0 +1,34 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-brew +- r-circlize +- r-clue +- r-complexheatmap +- r-crayon +- r-digest +- r-doparallel +- r-eulerr +- r-foreach +- r-getoptlong +- r-globaloptions +- r-httr +- r-impute +- r-irlba +- r-knitr +- r-markdown +- r-matrixstats +- r-mclust +- r-microbenchmark +- r-png +- r-rcolorbrewer +- r-rcpp +- r-skmeans +- r-xml2 +update_on: +- regex: cola_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cola diff --git a/prepare/r-colorramps/PKGBUILD b/prepare/r-colorramps/PKGBUILD new file mode 100644 index 0000000000..2e0bdf30c3 --- /dev/null +++ b/prepare/r-colorramps/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=colorRamps +_pkgver=2.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Builds color tables' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-colorramps/lilac.py b/prepare/r-colorramps/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-colorramps/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-colorramps/lilac.yaml b/prepare/r-colorramps/lilac.yaml new file mode 100644 index 0000000000..c70e02ed8a --- /dev/null +++ b/prepare/r-colorramps/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: colorRamps_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=colorRamps diff --git a/prepare/r-colorspace/PKGBUILD b/prepare/r-colorspace/PKGBUILD new file mode 100644 index 0000000000..e27b1ac0c1 --- /dev/null +++ b/prepare/r-colorspace/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=colorspace +_pkgver=2.0-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Toolbox for Manipulating and Assessing Colors and Palettes' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +optdepends=( + r-datasets + r-dplyr + r-ggplot2 + r-grid + r-jpeg + r-kernlab + r-kernsmooth + r-knitr + r-mass + r-mvtnorm + r-png + r-rcartocolor + r-rcolorbrewer + r-rmarkdown + r-scales + r-scico + r-shiny + r-shinyjs + r-tcltk + r-utils + r-vcd + r-viridis + r-wesanderson +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-colorspace/lilac.py b/prepare/r-colorspace/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-colorspace/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-colorspace/lilac.yaml b/prepare/r-colorspace/lilac.yaml new file mode 100644 index 0000000000..0d4cd1d4c1 --- /dev/null +++ b/prepare/r-colorspace/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: colorspace_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=colorspace diff --git a/prepare/r-colortools/PKGBUILD b/prepare/r-colortools/PKGBUILD new file mode 100644 index 0000000000..85b3a11bf8 --- /dev/null +++ b/prepare/r-colortools/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=colortools +_pkgver=0.1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for colors in a Hue-Saturation-Value (HSV) color model' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-colortools/lilac.py b/prepare/r-colortools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-colortools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-colortools/lilac.yaml b/prepare/r-colortools/lilac.yaml new file mode 100644 index 0000000000..01a4369d75 --- /dev/null +++ b/prepare/r-colortools/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: colortools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=colortools diff --git a/prepare/r-colourpicker/PKGBUILD b/prepare/r-colourpicker/PKGBUILD new file mode 100644 index 0000000000..faccf40f18 --- /dev/null +++ b/prepare/r-colourpicker/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=colourpicker +_pkgver=1.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Colour Picker Tool for Shiny and for Selecting Colours in Plots' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-ggplot2 + r-htmltools + r-htmlwidgets + r-jsonlite + r-miniui + r-shiny + r-shinyjs +) +optdepends=( + r-knitr + r-rmarkdown + r-rstudioapi + r-shinydisconnect +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-colourpicker/lilac.py b/prepare/r-colourpicker/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-colourpicker/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-colourpicker/lilac.yaml b/prepare/r-colourpicker/lilac.yaml new file mode 100644 index 0000000000..322446f698 --- /dev/null +++ b/prepare/r-colourpicker/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-htmltools +- r-htmlwidgets +- r-jsonlite +- r-miniui +- r-shiny +- r-shinyjs +update_on: +- regex: colourpicker_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=colourpicker diff --git a/prepare/r-combi/PKGBUILD b/prepare/r-combi/PKGBUILD new file mode 100644 index 0000000000..9ba3fd281e --- /dev/null +++ b/prepare/r-combi/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=combi +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Compositional omics model based visual integration' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-alabama + r-bb + r-biobase + r-cobs + r-ggplot2 + r-limma + r-nleqslv + r-phyloseq + r-reshape2 + r-summarizedexperiment + r-tensor + r-vegan +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-combi/lilac.py b/prepare/r-combi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-combi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-combi/lilac.yaml b/prepare/r-combi/lilac.yaml new file mode 100644 index 0000000000..4cd3b70b28 --- /dev/null +++ b/prepare/r-combi/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-alabama +- r-bb +- r-biobase +- r-cobs +- r-ggplot2 +- r-limma +- r-nleqslv +- r-phyloseq +- r-reshape2 +- r-summarizedexperiment +- r-tensor +- r-vegan +update_on: +- regex: combi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/combi diff --git a/prepare/r-combinat/PKGBUILD b/prepare/r-combinat/PKGBUILD new file mode 100644 index 0000000000..8e750d8cbe --- /dev/null +++ b/prepare/r-combinat/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=combinat +_pkgver=0.0-8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='combinatorics utilities' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-combinat/lilac.py b/prepare/r-combinat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-combinat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-combinat/lilac.yaml b/prepare/r-combinat/lilac.yaml new file mode 100644 index 0000000000..06a5a7689f --- /dev/null +++ b/prepare/r-combinat/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: combinat_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=combinat diff --git a/prepare/r-combinepvalue/PKGBUILD b/prepare/r-combinepvalue/PKGBUILD new file mode 100644 index 0000000000..b2521c0a50 --- /dev/null +++ b/prepare/r-combinepvalue/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CombinePValue +_pkgver=1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Combine a Vector of Correlated p-values' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-combinepvalue/lilac.py b/prepare/r-combinepvalue/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-combinepvalue/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-combinepvalue/lilac.yaml b/prepare/r-combinepvalue/lilac.yaml new file mode 100644 index 0000000000..779defc384 --- /dev/null +++ b/prepare/r-combinepvalue/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: CombinePValue_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=CombinePValue diff --git a/prepare/r-comet/PKGBUILD b/prepare/r-comet/PKGBUILD new file mode 100644 index 0000000000..2c79bab2bd --- /dev/null +++ b/prepare/r-comet/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=coMET +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-colortools + r-corrplot + r-genomicranges + r-gridextra + r-gviz + r-hash + r-iranges + r-psych + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-comet/lilac.py b/prepare/r-comet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-comet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-comet/lilac.yaml b/prepare/r-comet/lilac.yaml new file mode 100644 index 0000000000..28965a1042 --- /dev/null +++ b/prepare/r-comet/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-colortools +- r-corrplot +- r-genomicranges +- r-gridextra +- r-gviz +- r-hash +- r-iranges +- r-psych +- r-rtracklayer +- r-s4vectors +update_on: +- regex: coMET_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/coMET diff --git a/prepare/r-commonmark/PKGBUILD b/prepare/r-commonmark/PKGBUILD new file mode 100644 index 0000000000..9e91f02671 --- /dev/null +++ b/prepare/r-commonmark/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=commonmark +_pkgver=1.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='High Performance CommonMark and Github Markdown Rendering in R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +optdepends=( + r-curl + r-testthat + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-commonmark/lilac.py b/prepare/r-commonmark/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-commonmark/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-commonmark/lilac.yaml b/prepare/r-commonmark/lilac.yaml new file mode 100644 index 0000000000..e3db1574fa --- /dev/null +++ b/prepare/r-commonmark/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: commonmark_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=commonmark diff --git a/prepare/r-compartmap/PKGBUILD b/prepare/r-compartmap/PKGBUILD new file mode 100644 index 0000000000..7c024dca17 --- /dev/null +++ b/prepare/r-compartmap/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=compartmap +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Higher-order chromatin domain inference in single cells from scRNA-seq and scATAC-seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocsingular + r-delayedarray + r-delayedmatrixstats + r-genomicranges + r-ggplot2 + r-hdf5array + r-raggedexperiment + r-reshape2 + r-rmtstat + r-rtracklayer + r-scales + r-summarizedexperiment +) +optdepends=( + r-covr + r-knitr + r-markdown + r-rcpp + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-compartmap/lilac.py b/prepare/r-compartmap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-compartmap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-compartmap/lilac.yaml b/prepare/r-compartmap/lilac.yaml new file mode 100644 index 0000000000..decda81b1d --- /dev/null +++ b/prepare/r-compartmap/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocsingular +- r-delayedarray +- r-delayedmatrixstats +- r-genomicranges +- r-ggplot2 +- r-hdf5array +- r-raggedexperiment +- r-reshape2 +- r-rmtstat +- r-rtracklayer +- r-scales +- r-summarizedexperiment +update_on: +- regex: compartmap_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/compartmap diff --git a/prepare/r-compass/PKGBUILD b/prepare/r-compass/PKGBUILD new file mode 100644 index 0000000000..1cc2584eb7 --- /dev/null +++ b/prepare/r-compass/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=COMPASS +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Combinatorial Polyfunctionality Analysis of Single Cells' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-abind + r-biocstyle + r-clue + r-coda + r-data.table + r-dplyr + r-foreach + r-knitr + r-magrittr + r-pdist + r-plyr + r-rcolorbrewer + r-rcpp + r-reshape2 + r-rlang + r-rmarkdown + r-scales + r-tidyr +) +optdepends=( + r-devtools + r-flowcore + r-flowworkspace + r-flowworkspacedata + r-ggplot2 + r-ncdfflow + r-progress + r-shiny + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-compass/lilac.py b/prepare/r-compass/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-compass/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-compass/lilac.yaml b/prepare/r-compass/lilac.yaml new file mode 100644 index 0000000000..2a49deb0be --- /dev/null +++ b/prepare/r-compass/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-biocstyle +- r-clue +- r-coda +- r-data.table +- r-dplyr +- r-foreach +- r-knitr +- r-magrittr +- r-pdist +- r-plyr +- r-rcolorbrewer +- r-rcpp +- r-reshape2 +- r-rlang +- r-rmarkdown +- r-scales +- r-tidyr +update_on: +- regex: COMPASS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/COMPASS diff --git a/prepare/r-compcoder/PKGBUILD b/prepare/r-compcoder/PKGBUILD new file mode 100644 index 0000000000..6e6045e9de --- /dev/null +++ b/prepare/r-compcoder/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=compcodeR +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-catools + r-edger + r-ggplot2 + r-gplots + r-gtools + r-knitr + r-limma + r-markdown + r-modeest + r-rocr + r-sm + r-stringr + r-vioplot +) +optdepends=( + r-bayseq + r-biocstyle + r-deseq2 + r-dss + r-ebseq + r-genefilter + r-nbpseq + r-noiseq + r-rmarkdown + r-rpanel + r-tcc + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-compcoder/lilac.py b/prepare/r-compcoder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-compcoder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-compcoder/lilac.yaml b/prepare/r-compcoder/lilac.yaml new file mode 100644 index 0000000000..8c26bff411 --- /dev/null +++ b/prepare/r-compcoder/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-catools +- r-edger +- r-ggplot2 +- r-gplots +- r-gtools +- r-knitr +- r-limma +- r-markdown +- r-modeest +- r-rocr +- r-sm +- r-stringr +- r-vioplot +update_on: +- regex: compcodeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/compcodeR diff --git a/prepare/r-compepitools/PKGBUILD b/prepare/r-compepitools/PKGBUILD new file mode 100644 index 0000000000..8ddd8c0663 --- /dev/null +++ b/prepare/r-compepitools/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=compEpiTools +_pkgver=1.27.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for computational epigenomics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocgenerics + r-biostrings + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-go.db + r-gplots + r-iranges + r-methylpipe + r-rsamtools + r-s4vectors + r-topgo + r-xvector +) +optdepends=( + r-bsgenome.mmusculus.ucsc.mm9 + r-knitr + r-org.mm.eg.db + r-rtracklayer + r-txdb.mmusculus.ucsc.mm9.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-compepitools/lilac.py b/prepare/r-compepitools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-compepitools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-compepitools/lilac.yaml b/prepare/r-compepitools/lilac.yaml new file mode 100644 index 0000000000..238c1f5e49 --- /dev/null +++ b/prepare/r-compepitools/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-biostrings +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-go.db +- r-gplots +- r-iranges +- r-methylpipe +- r-rsamtools +- r-s4vectors +- r-topgo +- r-xvector +update_on: +- regex: compEpiTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/compEpiTools diff --git a/prepare/r-complexheatmap/PKGBUILD b/prepare/r-complexheatmap/PKGBUILD new file mode 100644 index 0000000000..04e137ed9b --- /dev/null +++ b/prepare/r-complexheatmap/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ComplexHeatmap +_pkgver=2.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Make Complex Heatmaps' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-circlize + r-clue + r-colorspace + r-digest + r-doparallel + r-foreach + r-getoptlong + r-globaloptions + r-iranges + r-matrixstats + r-png + r-rcolorbrewer +) +optdepends=( + r-cairo + r-dendextend + r-dendsort + r-enrichedheatmap + r-fastcluster + r-genomicranges + r-glue + r-gplots + r-gridgraphics + r-gridtext + r-grimport + r-grimport2 + r-jpeg + r-knitr + r-markdown + r-pheatmap + r-rmarkdown + r-testthat + r-tiff +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-complexheatmap/lilac.py b/prepare/r-complexheatmap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-complexheatmap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-complexheatmap/lilac.yaml b/prepare/r-complexheatmap/lilac.yaml new file mode 100644 index 0000000000..15627379e1 --- /dev/null +++ b/prepare/r-complexheatmap/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circlize +- r-clue +- r-colorspace +- r-digest +- r-doparallel +- r-foreach +- r-getoptlong +- r-globaloptions +- r-iranges +- r-matrixstats +- r-png +- r-rcolorbrewer +update_on: +- regex: ComplexHeatmap_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ComplexHeatmap diff --git a/prepare/r-compositions/PKGBUILD b/prepare/r-compositions/PKGBUILD new file mode 100644 index 0000000000..02dae0c41c --- /dev/null +++ b/prepare/r-compositions/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=compositions +_pkgver=2.0-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Compositional Data Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bayesm + r-robustbase + r-tensora +) +optdepends=( + r-combinat + r-energy + r-knitr + r-rgl + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-compositions/lilac.py b/prepare/r-compositions/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-compositions/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-compositions/lilac.yaml b/prepare/r-compositions/lilac.yaml new file mode 100644 index 0000000000..f29f00b588 --- /dev/null +++ b/prepare/r-compositions/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bayesm +- r-robustbase +- r-tensora +update_on: +- regex: compositions_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=compositions diff --git a/prepare/r-compquadform/PKGBUILD b/prepare/r-compquadform/PKGBUILD new file mode 100644 index 0000000000..1435619e68 --- /dev/null +++ b/prepare/r-compquadform/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CompQuadForm +_pkgver=1.4.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Distribution Function of Quadratic Forms in Normal Variables' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-compquadform/lilac.py b/prepare/r-compquadform/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-compquadform/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-compquadform/lilac.yaml b/prepare/r-compquadform/lilac.yaml new file mode 100644 index 0000000000..dabc6bc15f --- /dev/null +++ b/prepare/r-compquadform/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: CompQuadForm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=CompQuadForm diff --git a/prepare/r-compran/PKGBUILD b/prepare/r-compran/PKGBUILD new file mode 100644 index 0000000000..e5483611c1 --- /dev/null +++ b/prepare/r-compran/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ComPrAn +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Complexome Profiling Analysis package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-data.table + r-dplyr + r-dt + r-forcats + r-ggplot2 + r-magrittr + r-purrr + r-rcolorbrewer + r-rio + r-rlang + r-scales + r-shiny + r-shinydashboard + r-shinyjs + r-stringr + r-tibble + r-tidyr + r-venndiagram +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-compran/lilac.py b/prepare/r-compran/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-compran/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-compran/lilac.yaml b/prepare/r-compran/lilac.yaml new file mode 100644 index 0000000000..63abc9e619 --- /dev/null +++ b/prepare/r-compran/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-dplyr +- r-dt +- r-forcats +- r-ggplot2 +- r-magrittr +- r-purrr +- r-rcolorbrewer +- r-rio +- r-rlang +- r-scales +- r-shiny +- r-shinydashboard +- r-shinyjs +- r-stringr +- r-tibble +- r-tidyr +- r-venndiagram +update_on: +- regex: ComPrAn_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ComPrAn diff --git a/prepare/r-concaveman/PKGBUILD b/prepare/r-concaveman/PKGBUILD new file mode 100644 index 0000000000..5a97fb96fa --- /dev/null +++ b/prepare/r-concaveman/PKGBUILD @@ -0,0 +1,35 @@ +# system requirements: GDAL (>= 2.0.0), GEOS (>= 3.3.0), PROJ.4 (>= 4.8.0) +# Maintainer: Guoyi Zhang + +_pkgname=concaveman +_pkgver=1.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Very Fast 2D Concave Hull Algorithm' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-jsonlite + r-magrittr + r-sf + r-v8 +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-concaveman/lilac.py b/prepare/r-concaveman/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-concaveman/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-concaveman/lilac.yaml b/prepare/r-concaveman/lilac.yaml new file mode 100644 index 0000000000..22eba1bd52 --- /dev/null +++ b/prepare/r-concaveman/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-jsonlite +- r-magrittr +- r-sf +- r-v8 +update_on: +- regex: concaveman_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=concaveman diff --git a/prepare/r-conclus/PKGBUILD b/prepare/r-conclus/PKGBUILD new file mode 100644 index 0000000000..771ceb789c --- /dev/null +++ b/prepare/r-conclus/PKGBUILD @@ -0,0 +1,59 @@ +# Maintainer: Guoyi Zhang + +_pkgname=conclus +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biobase + r-biocfilecache + r-biomart + r-clusterprofiler + r-dbscan + r-doparallel + r-dplyr + r-factoextra + r-foreach + r-fpc + r-geoquery + r-ggplot2 + r-gridextra + r-pheatmap + r-rtsne + r-scales + r-scater + r-scran + r-singlecellexperiment + r-stringr + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-dynamictreecut + r-knitr + r-matrixstats + r-org.hs.eg.db + r-org.mm.eg.db + r-rmarkdown + r-s4vectors + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-conclus/lilac.py b/prepare/r-conclus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-conclus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-conclus/lilac.yaml b/prepare/r-conclus/lilac.yaml new file mode 100644 index 0000000000..4c00b3bc00 --- /dev/null +++ b/prepare/r-conclus/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocfilecache +- r-biomart +- r-clusterprofiler +- r-dbscan +- r-doparallel +- r-dplyr +- r-factoextra +- r-foreach +- r-fpc +- r-geoquery +- r-ggplot2 +- r-gridextra +- r-pheatmap +- r-rtsne +- r-scales +- r-scater +- r-scran +- r-singlecellexperiment +- r-stringr +- r-summarizedexperiment +update_on: +- regex: conclus_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/conclus diff --git a/prepare/r-condformat/PKGBUILD b/prepare/r-condformat/PKGBUILD new file mode 100644 index 0000000000..621d4a7544 --- /dev/null +++ b/prepare/r-condformat/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=condformat +_pkgver=0.9.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Conditional Formatting in Data Frames' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-dplyr + r-gridextra + r-gtable + r-htmltable + r-htmltools + r-knitr + r-magrittr + r-openxlsx + r-rlang + r-rmarkdown + r-scales + r-tibble + r-tidyselect +) +optdepends=( + r-promises + r-shiny + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-condformat/lilac.py b/prepare/r-condformat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-condformat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-condformat/lilac.yaml b/prepare/r-condformat/lilac.yaml new file mode 100644 index 0000000000..a56aaac468 --- /dev/null +++ b/prepare/r-condformat/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-gridextra +- r-gtable +- r-htmltable +- r-htmltools +- r-knitr +- r-magrittr +- r-openxlsx +- r-rlang +- r-rmarkdown +- r-scales +- r-tibble +- r-tidyselect +update_on: +- regex: condformat_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=condformat diff --git a/prepare/r-condiments/PKGBUILD b/prepare/r-condiments/PKGBUILD new file mode 100644 index 0000000000..b51247efa8 --- /dev/null +++ b/prepare/r-condiments/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=condiments +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential Topology, Progression and Differentiation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocparallel + r-dplyr + r-ecume + r-igraph + r-magrittr + r-matrixstats + r-pbapply + r-rann + r-singlecellexperiment + r-slingshot + r-summarizedexperiment + r-trajectoryutils +) +optdepends=( + r-covr + r-ggplot2 + r-knitr + r-randomforest + r-rcolorbrewer + r-rmarkdown + r-testthat + r-tidyr + r-tscan + r-viridis +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-condiments/lilac.py b/prepare/r-condiments/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-condiments/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-condiments/lilac.yaml b/prepare/r-condiments/lilac.yaml new file mode 100644 index 0000000000..92ac752a8a --- /dev/null +++ b/prepare/r-condiments/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-dplyr +- r-ecume +- r-igraph +- r-magrittr +- r-matrixstats +- r-pbapply +- r-rann +- r-singlecellexperiment +- r-slingshot +- r-summarizedexperiment +- r-trajectoryutils +update_on: +- regex: condiments_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/condiments diff --git a/prepare/r-confess/PKGBUILD b/prepare/r-confess/PKGBUILD new file mode 100644 index 0000000000..817a14bcd8 --- /dev/null +++ b/prepare/r-confess/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CONFESS +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cell OrderiNg by FluorEScence Signal' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-changepoint + r-contrast + r-data.table + r-ebimage + r-ecp + r-flexmix + r-flowclust + r-flowcore + r-flowmeans + r-flowmerge + r-flowpeaks + r-foreach + r-ggplot2 + r-limma + r-moments + r-outliers + r-plotrix + r-raster + r-readbitmap + r-reshape2 + r-samspectral + r-waveslim + r-wavethresh + r-zoo +) +optdepends=( + r-biocstyle + r-confessdata + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-confess/lilac.py b/prepare/r-confess/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-confess/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-confess/lilac.yaml b/prepare/r-confess/lilac.yaml new file mode 100644 index 0000000000..822d80762f --- /dev/null +++ b/prepare/r-confess/lilac.yaml @@ -0,0 +1,33 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-changepoint +- r-contrast +- r-data.table +- r-ebimage +- r-ecp +- r-flexmix +- r-flowclust +- r-flowcore +- r-flowmeans +- r-flowmerge +- r-flowpeaks +- r-foreach +- r-ggplot2 +- r-limma +- r-moments +- r-outliers +- r-plotrix +- r-raster +- r-readbitmap +- r-reshape2 +- r-samspectral +- r-waveslim +- r-wavethresh +- r-zoo +update_on: +- regex: CONFESS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CONFESS diff --git a/prepare/r-config/PKGBUILD b/prepare/r-config/PKGBUILD new file mode 100644 index 0000000000..9f8bda6400 --- /dev/null +++ b/prepare/r-config/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=config +_pkgver=0.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Manage Environment Specific Configuration Values' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-yaml +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-spelling + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-config/lilac.py b/prepare/r-config/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-config/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-config/lilac.yaml b/prepare/r-config/lilac.yaml new file mode 100644 index 0000000000..e034d91c7d --- /dev/null +++ b/prepare/r-config/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-yaml +update_on: +- regex: config_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=config diff --git a/prepare/r-conicfit/PKGBUILD b/prepare/r-conicfit/PKGBUILD new file mode 100644 index 0000000000..09ec650f9e --- /dev/null +++ b/prepare/r-conicfit/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=conicfit +_pkgver=1.0.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Algorithms for Fitting Circles, Ellipses and Conics Based on the Work by Prof. Nikolai Chernov' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-geigen + r-pracma +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-conicfit/lilac.py b/prepare/r-conicfit/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-conicfit/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-conicfit/lilac.yaml b/prepare/r-conicfit/lilac.yaml new file mode 100644 index 0000000000..fcf0cac388 --- /dev/null +++ b/prepare/r-conicfit/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-geigen +- r-pracma +update_on: +- regex: conicfit_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=conicfit diff --git a/prepare/r-conquer/PKGBUILD b/prepare/r-conquer/PKGBUILD new file mode 100644 index 0000000000..a77e939bb4 --- /dev/null +++ b/prepare/r-conquer/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=conquer +_pkgver=1.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Convolution-Type Smoothed Quantile Regression' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-caret + r-matrixstats + r-rcpp + r-rcpparmadillo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-conquer/lilac.py b/prepare/r-conquer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-conquer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-conquer/lilac.yaml b/prepare/r-conquer/lilac.yaml new file mode 100644 index 0000000000..aa94ded52f --- /dev/null +++ b/prepare/r-conquer/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-caret +- r-matrixstats +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: conquer_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=conquer diff --git a/prepare/r-consensus/PKGBUILD b/prepare/r-consensus/PKGBUILD new file mode 100644 index 0000000000..c40e20cbbc --- /dev/null +++ b/prepare/r-consensus/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=consensus +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cross-platform consensus analysis of genomic measurements via interlaboratory testing method' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-gplots + r-matrixstats + r-rcolorbrewer +) +optdepends=( + r-biocgenerics + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-consensus/lilac.py b/prepare/r-consensus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-consensus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-consensus/lilac.yaml b/prepare/r-consensus/lilac.yaml new file mode 100644 index 0000000000..d8965ae45f --- /dev/null +++ b/prepare/r-consensus/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gplots +- r-matrixstats +- r-rcolorbrewer +update_on: +- regex: consensus_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/consensus diff --git a/prepare/r-consensusclusterplus/PKGBUILD b/prepare/r-consensusclusterplus/PKGBUILD new file mode 100644 index 0000000000..42caa8d527 --- /dev/null +++ b/prepare/r-consensusclusterplus/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ConsensusClusterPlus +_pkgver=1.58.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ConsensusClusterPlus' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-all + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-consensusclusterplus/lilac.py b/prepare/r-consensusclusterplus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-consensusclusterplus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-consensusclusterplus/lilac.yaml b/prepare/r-consensusclusterplus/lilac.yaml new file mode 100644 index 0000000000..f7880fde1c --- /dev/null +++ b/prepare/r-consensusclusterplus/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-all +- r-biobase +update_on: +- regex: ConsensusClusterPlus_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ConsensusClusterPlus diff --git a/prepare/r-consensusde/PKGBUILD b/prepare/r-consensusde/PKGBUILD new file mode 100644 index 0000000000..c4aacf4b0e --- /dev/null +++ b/prepare/r-consensusde/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=consensusDE +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RNA-seq analysis using multiple algorithms' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-airway + r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-data.table + r-dendextend + r-deseq2 + r-edaseq + r-edger + r-ensdb.hsapiens.v86 + r-ensembldb + r-genomicalignments + r-genomicfeatures + r-limma + r-org.hs.eg.db + r-pcamethods + r-rcolorbrewer + r-rsamtools + r-ruvseq + r-s4vectors + r-summarizedexperiment + r-txdb.dmelanogaster.ucsc.dm3.ensgene +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-consensusde/lilac.py b/prepare/r-consensusde/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-consensusde/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-consensusde/lilac.yaml b/prepare/r-consensusde/lilac.yaml new file mode 100644 index 0000000000..312adcace6 --- /dev/null +++ b/prepare/r-consensusde/lilac.yaml @@ -0,0 +1,33 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-airway +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-data.table +- r-dendextend +- r-deseq2 +- r-edaseq +- r-edger +- r-ensdb.hsapiens.v86 +- r-ensembldb +- r-genomicalignments +- r-genomicfeatures +- r-limma +- r-org.hs.eg.db +- r-pcamethods +- r-rcolorbrewer +- r-rsamtools +- r-ruvseq +- r-s4vectors +- r-summarizedexperiment +- r-txdb.dmelanogaster.ucsc.dm3.ensgene +update_on: +- regex: consensusDE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/consensusDE diff --git a/prepare/r-consensusov/PKGBUILD b/prepare/r-consensusov/PKGBUILD new file mode 100644 index 0000000000..8c849a341e --- /dev/null +++ b/prepare/r-consensusov/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=consensusOV +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene expression-based subtype classification for high-grade serous ovarian cancer' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-gdata + r-genefu + r-gsva + r-limma + r-matrixstats + r-randomforest +) +optdepends=( + r-biocstyle + r-ggplot2 + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-consensusov/lilac.py b/prepare/r-consensusov/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-consensusov/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-consensusov/lilac.yaml b/prepare/r-consensusov/lilac.yaml new file mode 100644 index 0000000000..aa01d72395 --- /dev/null +++ b/prepare/r-consensusov/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-gdata +- r-genefu +- r-gsva +- r-limma +- r-matrixstats +- r-randomforest +update_on: +- regex: consensusOV_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/consensusOV diff --git a/prepare/r-consensusseeker/PKGBUILD b/prepare/r-consensusseeker/PKGBUILD new file mode 100644 index 0000000000..8271bca272 --- /dev/null +++ b/prepare/r-consensusseeker/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=consensusSeekeR +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicranges + r-iranges + r-rtracklayer + r-s4vectors + r-stringr +) +optdepends=( + r-biocstyle + r-ggplot2 + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-consensusseeker/lilac.py b/prepare/r-consensusseeker/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-consensusseeker/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-consensusseeker/lilac.yaml b/prepare/r-consensusseeker/lilac.yaml new file mode 100644 index 0000000000..e5b084523e --- /dev/null +++ b/prepare/r-consensusseeker/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rtracklayer +- r-s4vectors +- r-stringr +update_on: +- regex: consensusSeekeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/consensusSeekeR diff --git a/prepare/r-constand/PKGBUILD b/prepare/r-constand/PKGBUILD new file mode 100644 index 0000000000..bae8602a22 --- /dev/null +++ b/prepare/r-constand/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CONSTANd +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data normalization by matrix raking' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r +) +optdepends=( + r-biocstyle + r-cairo + r-ggplot2 + r-gridextra + r-knitr + r-limma + r-magick + r-rmarkdown + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-constand/lilac.py b/prepare/r-constand/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-constand/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-constand/lilac.yaml b/prepare/r-constand/lilac.yaml new file mode 100644 index 0000000000..aca02736d0 --- /dev/null +++ b/prepare/r-constand/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: CONSTANd_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CONSTANd diff --git a/prepare/r-contibait/PKGBUILD b/prepare/r-contibait/PKGBUILD new file mode 100644 index 0000000000..a9c490df1f --- /dev/null +++ b/prepare/r-contibait/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=contiBAIT +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Improves Early Build Genome Assemblies using Strand-Seq Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-bh + r-biocgenerics + r-biocparallel + r-clue + r-colorspace + r-data.table + r-diagram + r-dnacopy + r-exomecopy + r-genomicalignments + r-genomicfiles + r-genomicranges + r-ggplot2 + r-gplots + r-gtools + r-iranges + r-rcpp + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors + r-tsp +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-contibait/lilac.py b/prepare/r-contibait/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-contibait/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-contibait/lilac.yaml b/prepare/r-contibait/lilac.yaml new file mode 100644 index 0000000000..13b7402116 --- /dev/null +++ b/prepare/r-contibait/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-biocgenerics +- r-biocparallel +- r-clue +- r-colorspace +- r-data.table +- r-diagram +- r-dnacopy +- r-exomecopy +- r-genomicalignments +- r-genomicfiles +- r-genomicranges +- r-ggplot2 +- r-gplots +- r-gtools +- r-iranges +- r-rcpp +- r-reshape2 +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-tsp +update_on: +- regex: contiBAIT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/contiBAIT diff --git a/prepare/r-contrast/PKGBUILD b/prepare/r-contrast/PKGBUILD new file mode 100644 index 0000000000..8553ef11dd --- /dev/null +++ b/prepare/r-contrast/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=contrast +_pkgver=0.24.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Collection of Contrast Methods' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rms + r-sandwich +) +optdepends=( + r-covr + r-dplyr + r-geepack + r-ggplot2 + r-kableextra + r-knitr + r-rmarkdown + r-splines + r-testthat + r-tidyr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-contrast/lilac.py b/prepare/r-contrast/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-contrast/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-contrast/lilac.yaml b/prepare/r-contrast/lilac.yaml new file mode 100644 index 0000000000..ac35fd29ca --- /dev/null +++ b/prepare/r-contrast/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rms +- r-sandwich +update_on: +- regex: contrast_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=contrast diff --git a/prepare/r-conumee/PKGBUILD b/prepare/r-conumee/PKGBUILD new file mode 100644 index 0000000000..34f19438a8 --- /dev/null +++ b/prepare/r-conumee/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=conumee +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Enhanced copy-number variation analysis using Illumina DNA methylation arrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dnacopy + r-genomeinfodb + r-genomicranges + r-illuminahumanmethylation450kanno.ilmn12.hg19 + r-illuminahumanmethylation450kmanifest + r-illuminahumanmethylationepicanno.ilm10b2.hg19 + r-illuminahumanmethylationepicmanifest + r-iranges + r-minfi + r-rtracklayer +) +optdepends=( + r-biocstyle + r-knitr + r-minfidata + r-rcurl + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-conumee/lilac.py b/prepare/r-conumee/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-conumee/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-conumee/lilac.yaml b/prepare/r-conumee/lilac.yaml new file mode 100644 index 0000000000..7a5996e212 --- /dev/null +++ b/prepare/r-conumee/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dnacopy +- r-genomeinfodb +- r-genomicranges +- r-illuminahumanmethylation450kanno.ilmn12.hg19 +- r-illuminahumanmethylation450kmanifest +- r-illuminahumanmethylationepicanno.ilm10b2.hg19 +- r-illuminahumanmethylationepicmanifest +- r-iranges +- r-minfi +- r-rtracklayer +update_on: +- regex: conumee_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/conumee diff --git a/prepare/r-convert/PKGBUILD b/prepare/r-convert/PKGBUILD new file mode 100644 index 0000000000..656e50a944 --- /dev/null +++ b/prepare/r-convert/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=convert +_pkgver=1.70.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Convert Microarray Data Objects' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-limma + r-marray +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-convert/lilac.py b/prepare/r-convert/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-convert/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-convert/lilac.yaml b/prepare/r-convert/lilac.yaml new file mode 100644 index 0000000000..cea3cf63ec --- /dev/null +++ b/prepare/r-convert/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-limma +- r-marray +update_on: +- regex: convert_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/convert diff --git a/prepare/r-coop/PKGBUILD b/prepare/r-coop/PKGBUILD new file mode 100644 index 0000000000..b08c563c74 --- /dev/null +++ b/prepare/r-coop/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=coop +_pkgver=0.6-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Co-Operation: Fast Covariance, Correlation, and Cosine Similarity Operations' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +optdepends=( + r-matrix + r-memuse + r-slam +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-coop/lilac.py b/prepare/r-coop/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-coop/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-coop/lilac.yaml b/prepare/r-coop/lilac.yaml new file mode 100644 index 0000000000..4492b5baf0 --- /dev/null +++ b/prepare/r-coop/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: coop_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=coop diff --git a/prepare/r-copa/PKGBUILD b/prepare/r-copa/PKGBUILD new file mode 100644 index 0000000000..d749a1e7b8 --- /dev/null +++ b/prepare/r-copa/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=copa +_pkgver=1.62.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions to perform cancer outlier profile analysis.' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase +) +optdepends=( + r-colonca +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-copa/lilac.py b/prepare/r-copa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-copa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-copa/lilac.yaml b/prepare/r-copa/lilac.yaml new file mode 100644 index 0000000000..6b15aa92e9 --- /dev/null +++ b/prepare/r-copa/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: copa_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/copa diff --git a/prepare/r-copula/PKGBUILD b/prepare/r-copula/PKGBUILD new file mode 100644 index 0000000000..acf327b607 --- /dev/null +++ b/prepare/r-copula/PKGBUILD @@ -0,0 +1,67 @@ +# system requirements: pdfcrop (part of TexLive) is required to rebuildthe vignettes. +# Maintainer: Guoyi Zhang + +_pkgname=copula +_pkgver=1.0-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multivariate Dependence with Copulas' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-adgoftest + r-colorspace + r-gsl + r-mvtnorm + r-numderiv + r-pcapp + r-pspline + r-stabledist +) +optdepends=( + r-abind + r-bbmle + r-copuladata + r-crop + r-gridextra + r-kernsmooth + r-knitr + r-lcopula + r-mass + r-mev + r-mvnormtest + r-nor1mix + r-parallel + r-partitions + r-polynom + r-qrng + r-randtoolbox + r-rmarkdown + r-rmpfr + r-rugarch + r-runuran + r-scatterplot3d + r-sfsmisc + r-tseries + r-vgam + r-vinecopula + r-zoo +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-copula/lilac.py b/prepare/r-copula/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-copula/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-copula/lilac.yaml b/prepare/r-copula/lilac.yaml new file mode 100644 index 0000000000..18bce87733 --- /dev/null +++ b/prepare/r-copula/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-adgoftest +- r-colorspace +- r-gsl +- r-mvtnorm +- r-numderiv +- r-pcapp +- r-pspline +- r-stabledist +update_on: +- regex: copula_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=copula diff --git a/prepare/r-copyhelper/PKGBUILD b/prepare/r-copyhelper/PKGBUILD new file mode 100644 index 0000000000..3c6f381f6f --- /dev/null +++ b/prepare/r-copyhelper/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CopyhelpeR +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Helper files for CopywriteR' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-copyhelper/lilac.py b/prepare/r-copyhelper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-copyhelper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-copyhelper/lilac.yaml b/prepare/r-copyhelper/lilac.yaml new file mode 100644 index 0000000000..03f5135693 --- /dev/null +++ b/prepare/r-copyhelper/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: CopyhelpeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CopyhelpeR diff --git a/prepare/r-copynumber/PKGBUILD b/prepare/r-copynumber/PKGBUILD new file mode 100644 index 0000000000..8231a83eac --- /dev/null +++ b/prepare/r-copynumber/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=copynumber +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Segmentation of single- and multi-track copy number data by penalized least squares regression.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-genomicranges + r-iranges + r-s4vectors +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-copynumber/lilac.py b/prepare/r-copynumber/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-copynumber/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-copynumber/lilac.yaml b/prepare/r-copynumber/lilac.yaml new file mode 100644 index 0000000000..a3fa11833b --- /dev/null +++ b/prepare/r-copynumber/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomicranges +- r-iranges +- r-s4vectors +update_on: +- regex: copynumber_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/copynumber diff --git a/prepare/r-copynumberplots/PKGBUILD b/prepare/r-copynumberplots/PKGBUILD new file mode 100644 index 0000000000..262596fcd2 --- /dev/null +++ b/prepare/r-copynumberplots/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CopyNumberPlots +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Create Copy-Number Plots using karyoploteR functionality' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-cn.mops + r-genomeinfodb + r-genomicranges + r-iranges + r-karyoploter + r-regioner + r-rhdf5 + r-rsamtools + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19.masked + r-dnacopy + r-knitr + r-panelcn.mops + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-copynumberplots/lilac.py b/prepare/r-copynumberplots/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-copynumberplots/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-copynumberplots/lilac.yaml b/prepare/r-copynumberplots/lilac.yaml new file mode 100644 index 0000000000..997c41a824 --- /dev/null +++ b/prepare/r-copynumberplots/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cn.mops +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-karyoploter +- r-regioner +- r-rhdf5 +- r-rsamtools +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: CopyNumberPlots_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CopyNumberPlots diff --git a/prepare/r-copywriter/PKGBUILD b/prepare/r-copywriter/PKGBUILD new file mode 100644 index 0000000000..0c91b678a5 --- /dev/null +++ b/prepare/r-copywriter/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CopywriteR +_pkgver=2.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Copy number information from targeted sequencing using off-target reads' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-chipseq + r-copyhelper + r-data.table + r-dnacopy + r-futile.logger + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-gtools + r-iranges + r-matrixstats + r-rsamtools + r-s4vectors +) +optdepends=( + r-biocstyle + r-sclcbam + r-snow +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-copywriter/lilac.py b/prepare/r-copywriter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-copywriter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-copywriter/lilac.yaml b/prepare/r-copywriter/lilac.yaml new file mode 100644 index 0000000000..89d775b490 --- /dev/null +++ b/prepare/r-copywriter/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-chipseq +- r-copyhelper +- r-data.table +- r-dnacopy +- r-futile.logger +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-gtools +- r-iranges +- r-matrixstats +- r-rsamtools +- r-s4vectors +update_on: +- regex: CopywriteR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CopywriteR diff --git a/prepare/r-cordon/PKGBUILD b/prepare/r-cordon/PKGBUILD new file mode 100644 index 0000000000..5e3b8eb8d4 --- /dev/null +++ b/prepare/r-cordon/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=coRdon +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Codon Usage Analysis and Prediction of Gene Expressivity' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biostrings + r-data.table + r-dplyr + r-ggplot2 + r-purrr + r-stringr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cordon/lilac.py b/prepare/r-cordon/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cordon/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cordon/lilac.yaml b/prepare/r-cordon/lilac.yaml new file mode 100644 index 0000000000..f0e32b2aea --- /dev/null +++ b/prepare/r-cordon/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biostrings +- r-data.table +- r-dplyr +- r-ggplot2 +- r-purrr +- r-stringr +update_on: +- regex: coRdon_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/coRdon diff --git a/prepare/r-coregnet/PKGBUILD b/prepare/r-coregnet/PKGBUILD new file mode 100644 index 0000000000..15563b7f4e --- /dev/null +++ b/prepare/r-coregnet/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CoRegNet +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CoRegNet : reconstruction and integrated analysis of co-regulatory networks' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-arules + r-igraph + r-shiny +) +optdepends=( + r-biocstyle + r-gplots + r-knitr + r-rcolorbrewer + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-coregnet/lilac.py b/prepare/r-coregnet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-coregnet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-coregnet/lilac.yaml b/prepare/r-coregnet/lilac.yaml new file mode 100644 index 0000000000..6b02e0635f --- /dev/null +++ b/prepare/r-coregnet/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-arules +- r-igraph +- r-shiny +update_on: +- regex: CoRegNet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CoRegNet diff --git a/prepare/r-coregx/PKGBUILD b/prepare/r-coregx/PKGBUILD new file mode 100644 index 0000000000..5248910291 --- /dev/null +++ b/prepare/r-coregx/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CoreGx +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Classes and Functions to Serve as the Basis for Other 'Gx' Packages" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-bumpymatrix + r-checkmate + r-crayon + r-data.table + r-glue + r-lsa + r-matrixgenerics + r-multiassayexperiment + r-piano + r-rlang + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-formatr + r-knitr + r-markdown + r-pander + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-coregx/lilac.py b/prepare/r-coregx/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-coregx/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-coregx/lilac.yaml b/prepare/r-coregx/lilac.yaml new file mode 100644 index 0000000000..ff7517e3cd --- /dev/null +++ b/prepare/r-coregx/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-bumpymatrix +- r-checkmate +- r-crayon +- r-data.table +- r-glue +- r-lsa +- r-matrixgenerics +- r-multiassayexperiment +- r-piano +- r-rlang +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: CoreGx_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CoreGx diff --git a/prepare/r-cormotif/PKGBUILD b/prepare/r-cormotif/PKGBUILD new file mode 100644 index 0000000000..11284d590c --- /dev/null +++ b/prepare/r-cormotif/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Cormotif +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Correlation Motif Fit' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-limma +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cormotif/lilac.py b/prepare/r-cormotif/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cormotif/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cormotif/lilac.yaml b/prepare/r-cormotif/lilac.yaml new file mode 100644 index 0000000000..89c961474c --- /dev/null +++ b/prepare/r-cormotif/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-limma +update_on: +- regex: Cormotif_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Cormotif diff --git a/prepare/r-corncob/PKGBUILD b/prepare/r-corncob/PKGBUILD new file mode 100644 index 0000000000..b5f05a6435 --- /dev/null +++ b/prepare/r-corncob/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=corncob +_pkgver=0.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Count Regression for Correlated Observations with the Beta-Binomial' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-detectseparation + r-dplyr + r-ggplot2 + r-magrittr + r-numderiv + r-optimr + r-phyloseq + r-rmutil + r-scales + r-trust + r-vgam +) +optdepends=( + r-covr + r-knitr + r-limma + r-r.rsp + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-corncob/lilac.py b/prepare/r-corncob/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-corncob/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-corncob/lilac.yaml b/prepare/r-corncob/lilac.yaml new file mode 100644 index 0000000000..6ea5d89221 --- /dev/null +++ b/prepare/r-corncob/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-detectseparation +- r-dplyr +- r-ggplot2 +- r-magrittr +- r-numderiv +- r-optimr +- r-phyloseq +- r-rmutil +- r-scales +- r-trust +- r-vgam +update_on: +- regex: corncob_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=corncob diff --git a/prepare/r-corpcor/PKGBUILD b/prepare/r-corpcor/PKGBUILD new file mode 100644 index 0000000000..9dbbc44c41 --- /dev/null +++ b/prepare/r-corpcor/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=corpcor +_pkgver=1.6.10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Efficient Estimation of Covariance and (Partial) Correlation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-corpcor/lilac.py b/prepare/r-corpcor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-corpcor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-corpcor/lilac.yaml b/prepare/r-corpcor/lilac.yaml new file mode 100644 index 0000000000..aca44f7298 --- /dev/null +++ b/prepare/r-corpcor/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: corpcor_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=corpcor diff --git a/prepare/r-corral/PKGBUILD b/prepare/r-corral/PKGBUILD new file mode 100644 index 0000000000..2b1826499b --- /dev/null +++ b/prepare/r-corral/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=corral +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Correspondence Analysis for Single Cell Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-ggthemes + r-gridextra + r-irlba + r-multiassayexperiment + r-pals + r-singlecellexperiment + r-summarizedexperiment + r-transport +) +optdepends=( + r-ade4 + r-biocstyle + r-cellbench + r-duoclustering2018 + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-corral/lilac.py b/prepare/r-corral/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-corral/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-corral/lilac.yaml b/prepare/r-corral/lilac.yaml new file mode 100644 index 0000000000..792ef6fdd9 --- /dev/null +++ b/prepare/r-corral/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-ggthemes +- r-gridextra +- r-irlba +- r-multiassayexperiment +- r-pals +- r-singlecellexperiment +- r-summarizedexperiment +- r-transport +update_on: +- regex: corral_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/corral diff --git a/prepare/r-correp/PKGBUILD b/prepare/r-correp/PKGBUILD new file mode 100644 index 0000000000..069e94497a --- /dev/null +++ b/prepare/r-correp/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CORREP +_pkgver=1.60.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multivariate Correlation Estimator and Statistical Inference Procedures.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-e1071 +) +optdepends=( + r-cluster + r-mass +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-correp/lilac.py b/prepare/r-correp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-correp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-correp/lilac.yaml b/prepare/r-correp/lilac.yaml new file mode 100644 index 0000000000..d813e946b7 --- /dev/null +++ b/prepare/r-correp/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-e1071 +update_on: +- regex: CORREP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CORREP diff --git a/prepare/r-corrgram/PKGBUILD b/prepare/r-corrgram/PKGBUILD new file mode 100644 index 0000000000..a360e153f6 --- /dev/null +++ b/prepare/r-corrgram/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=corrgram +_pkgver=1.14 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Plot a Correlogram' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-gridbase + r-knitr + r-matrix + r-psych + r-rmarkdown + r-seriation + r-sfsmisc + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-corrgram/lilac.py b/prepare/r-corrgram/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-corrgram/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-corrgram/lilac.yaml b/prepare/r-corrgram/lilac.yaml new file mode 100644 index 0000000000..0fd8f2a2bf --- /dev/null +++ b/prepare/r-corrgram/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: corrgram_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=corrgram diff --git a/prepare/r-corrplot/PKGBUILD b/prepare/r-corrplot/PKGBUILD new file mode 100644 index 0000000000..0d00e6232b --- /dev/null +++ b/prepare/r-corrplot/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=corrplot +_pkgver=0.92 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization of a Correlation Matrix' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-knitr + r-magrittr + r-prettydoc + r-rcolorbrewer + r-rmarkdown + r-seriation + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-corrplot/lilac.py b/prepare/r-corrplot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-corrplot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-corrplot/lilac.yaml b/prepare/r-corrplot/lilac.yaml new file mode 100644 index 0000000000..785ab4b782 --- /dev/null +++ b/prepare/r-corrplot/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: corrplot_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=corrplot diff --git a/prepare/r-coseq/PKGBUILD b/prepare/r-coseq/PKGBUILD new file mode 100644 index 0000000000..dea4195a88 --- /dev/null +++ b/prepare/r-coseq/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=coseq +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Co-Expression Analysis of Sequencing Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-capushe + r-compositions + r-corrplot + r-deseq2 + r-e1071 + r-edger + r-ggplot2 + r-htscluster + r-htsfilter + r-mvtnorm + r-rmixmod + r-s4vectors + r-scales + r-summarizedexperiment +) +optdepends=( + r-biobase + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-coseq/lilac.py b/prepare/r-coseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-coseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-coseq/lilac.yaml b/prepare/r-coseq/lilac.yaml new file mode 100644 index 0000000000..67ce1015ba --- /dev/null +++ b/prepare/r-coseq/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-capushe +- r-compositions +- r-corrplot +- r-deseq2 +- r-e1071 +- r-edger +- r-ggplot2 +- r-htscluster +- r-htsfilter +- r-mvtnorm +- r-rmixmod +- r-s4vectors +- r-scales +- r-summarizedexperiment +update_on: +- regex: coseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/coseq diff --git a/prepare/r-cosmic.67/PKGBUILD b/prepare/r-cosmic.67/PKGBUILD new file mode 100644 index 0000000000..79c13579f1 --- /dev/null +++ b/prepare/r-cosmic.67/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=COSMIC.67 +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='COSMIC.67' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicranges + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cosmic.67/lilac.py b/prepare/r-cosmic.67/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cosmic.67/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cosmic.67/lilac.yaml b/prepare/r-cosmic.67/lilac.yaml new file mode 100644 index 0000000000..e32930084d --- /dev/null +++ b/prepare/r-cosmic.67/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: COSMIC.67_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/COSMIC.67 diff --git a/prepare/r-cosmiq/PKGBUILD b/prepare/r-cosmiq/PKGBUILD new file mode 100644 index 0000000000..dec167c8ee --- /dev/null +++ b/prepare/r-cosmiq/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cosmiq +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='cosmiq - COmbining Single Masses Into Quantities' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-faahko + r-massspecwavelet + r-pracma + r-rcpp + r-xcms +) +optdepends=( + r-biocgenerics + r-biocstyle + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cosmiq/lilac.py b/prepare/r-cosmiq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cosmiq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cosmiq/lilac.yaml b/prepare/r-cosmiq/lilac.yaml new file mode 100644 index 0000000000..4973bd3d0b --- /dev/null +++ b/prepare/r-cosmiq/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-faahko +- r-massspecwavelet +- r-pracma +- r-rcpp +- r-xcms +update_on: +- regex: cosmiq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cosmiq diff --git a/prepare/r-cosmosr/PKGBUILD b/prepare/r-cosmosr/PKGBUILD new file mode 100644 index 0000000000..b6603a1fa3 --- /dev/null +++ b/prepare/r-cosmosr/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cosmosR +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='COSMOS (Causal Oriented Search of Multi-Omic Space)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biomart + r-carnival + r-dorothea + r-dplyr + r-ggplot2 + r-gseabase + r-igraph + r-magrittr + r-org.hs.eg.db + r-plyr + r-purrr + r-readr + r-rlang + r-scales + r-stringr + r-tibble + r-visnetwork +) +optdepends=( + r-knitr + r-piano + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cosmosr/lilac.py b/prepare/r-cosmosr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cosmosr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cosmosr/lilac.yaml b/prepare/r-cosmosr/lilac.yaml new file mode 100644 index 0000000000..104dc07c71 --- /dev/null +++ b/prepare/r-cosmosr/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biomart +- r-carnival +- r-dorothea +- r-dplyr +- r-ggplot2 +- r-gseabase +- r-igraph +- r-magrittr +- r-org.hs.eg.db +- r-plyr +- r-purrr +- r-readr +- r-rlang +- r-scales +- r-stringr +- r-tibble +- r-visnetwork +update_on: +- regex: cosmosR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cosmosR diff --git a/prepare/r-cosnet/PKGBUILD b/prepare/r-cosnet/PKGBUILD new file mode 100644 index 0000000000..a5e7fcc0b1 --- /dev/null +++ b/prepare/r-cosnet/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=COSNet +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biocgenerics + r-bionetdata + r-perfmeas + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cosnet/lilac.py b/prepare/r-cosnet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cosnet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cosnet/lilac.yaml b/prepare/r-cosnet/lilac.yaml new file mode 100644 index 0000000000..7a56444b85 --- /dev/null +++ b/prepare/r-cosnet/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: COSNet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/COSNet diff --git a/prepare/r-countclust/PKGBUILD b/prepare/r-countclust/PKGBUILD new file mode 100644 index 0000000000..a3a144691a --- /dev/null +++ b/prepare/r-countclust/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CountClust +_pkgver=1.21.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cowplot + r-flexmix + r-ggplot2 + r-gtools + r-limma + r-maptpx + r-picante + r-plyr + r-reshape2 + r-slam + r-squarem +) +optdepends=( + r-biobase + r-biocstyle + r-devtools + r-kableextra + r-knitr + r-rcolorbrewer + r-roxygen2 + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-countclust/lilac.py b/prepare/r-countclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-countclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-countclust/lilac.yaml b/prepare/r-countclust/lilac.yaml new file mode 100644 index 0000000000..20624e9f26 --- /dev/null +++ b/prepare/r-countclust/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cowplot +- r-flexmix +- r-ggplot2 +- r-gtools +- r-limma +- r-maptpx +- r-picante +- r-plyr +- r-reshape2 +- r-slam +- r-squarem +update_on: +- regex: CountClust_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CountClust diff --git a/prepare/r-countrycode/PKGBUILD b/prepare/r-countrycode/PKGBUILD new file mode 100644 index 0000000000..b38bbd8003 --- /dev/null +++ b/prepare/r-countrycode/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=countrycode +_pkgver=1.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Convert Country Names and Country Codes' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-testthat + r-tibble + r-utf8 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-countrycode/lilac.py b/prepare/r-countrycode/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-countrycode/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-countrycode/lilac.yaml b/prepare/r-countrycode/lilac.yaml new file mode 100644 index 0000000000..07c3e77976 --- /dev/null +++ b/prepare/r-countrycode/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: countrycode_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=countrycode diff --git a/prepare/r-countsimqc/PKGBUILD b/prepare/r-countsimqc/PKGBUILD new file mode 100644 index 0000000000..59ab8a9f2f --- /dev/null +++ b/prepare/r-countsimqc/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=countsimQC +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Compare Characteristic Features of Count Data Sets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-catools + r-deseq2 + r-dplyr + r-dt + r-edger + r-genefilter + r-genomeinfodbdata + r-ggplot2 + r-randtests + r-rmarkdown + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-countsimqc/lilac.py b/prepare/r-countsimqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-countsimqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-countsimqc/lilac.yaml b/prepare/r-countsimqc/lilac.yaml new file mode 100644 index 0000000000..09bfa92419 --- /dev/null +++ b/prepare/r-countsimqc/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-catools +- r-deseq2 +- r-dplyr +- r-dt +- r-edger +- r-genefilter +- r-genomeinfodbdata +- r-ggplot2 +- r-randtests +- r-rmarkdown +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: countsimQC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/countsimQC diff --git a/prepare/r-coveb/PKGBUILD b/prepare/r-coveb/PKGBUILD new file mode 100644 index 0000000000..ef47509afd --- /dev/null +++ b/prepare/r-coveb/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=covEB +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Empirical Bayes estimate of block diagonal covariance matrices' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-gsl + r-igraph + r-laplacesdemon + r-mvtnorm +) +optdepends=( + r-curatedbladderdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-coveb/lilac.py b/prepare/r-coveb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-coveb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-coveb/lilac.yaml b/prepare/r-coveb/lilac.yaml new file mode 100644 index 0000000000..6b2451265d --- /dev/null +++ b/prepare/r-coveb/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-gsl +- r-igraph +- r-laplacesdemon +- r-mvtnorm +update_on: +- regex: covEB_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/covEB diff --git a/prepare/r-coverageview/PKGBUILD b/prepare/r-coverageview/PKGBUILD new file mode 100644 index 0000000000..ae9a298793 --- /dev/null +++ b/prepare/r-coverageview/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CoverageView +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Coverage visualization package for R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-genomicalignments + r-genomicranges + r-iranges + r-rsamtools + r-rtracklayer + r-s4vectors +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-coverageview/lilac.py b/prepare/r-coverageview/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-coverageview/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-coverageview/lilac.yaml b/prepare/r-coverageview/lilac.yaml new file mode 100644 index 0000000000..c8657723ed --- /dev/null +++ b/prepare/r-coverageview/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-rsamtools +- r-rtracklayer +- r-s4vectors +update_on: +- regex: CoverageView_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CoverageView diff --git a/prepare/r-covr/PKGBUILD b/prepare/r-covr/PKGBUILD new file mode 100644 index 0000000000..50556b2f14 --- /dev/null +++ b/prepare/r-covr/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=covr +_pkgver=3.5.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Test Coverage for Packages' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-crayon + r-digest + r-httr + r-jsonlite + r-rex + r-withr + r-yaml +) +optdepends=( + r-curl + r-dt + r-htmltools + r-knitr + r-memoise + r-mockery + r-parallel + r-r6 + r-rlang + r-rmarkdown + r-rstudioapi + r-testthat + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-covr/lilac.py b/prepare/r-covr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-covr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-covr/lilac.yaml b/prepare/r-covr/lilac.yaml new file mode 100644 index 0000000000..d08e59c45e --- /dev/null +++ b/prepare/r-covr/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-crayon +- r-digest +- r-httr +- r-jsonlite +- r-rex +- r-withr +- r-yaml +update_on: +- regex: covr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=covr diff --git a/prepare/r-covrna/PKGBUILD b/prepare/r-covrna/PKGBUILD new file mode 100644 index 0000000000..ead22a507e --- /dev/null +++ b/prepare/r-covrna/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=covRNA +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multivariate Analysis of Transcriptomic Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ade4 + r-biobase + r-genefilter +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-covrna/lilac.py b/prepare/r-covrna/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-covrna/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-covrna/lilac.yaml b/prepare/r-covrna/lilac.yaml new file mode 100644 index 0000000000..b88884492b --- /dev/null +++ b/prepare/r-covrna/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ade4 +- r-biobase +- r-genefilter +update_on: +- regex: covRNA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/covRNA diff --git a/prepare/r-cowplot/PKGBUILD b/prepare/r-cowplot/PKGBUILD new file mode 100644 index 0000000000..3d9258b1f7 --- /dev/null +++ b/prepare/r-cowplot/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cowplot +_pkgver=1.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Streamlined Plot Theme and Plot Annotations for 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-gtable + r-rlang + r-scales +) +optdepends=( + r-cairo + r-covr + r-dplyr + r-forcats + r-gridgraphics + r-knitr + r-lattice + r-magick + r-maps + r-paswr + r-patchwork + r-ragg + r-rmarkdown + r-testthat + r-tidyr + r-vdiffr + r-venndiagram +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cowplot/lilac.py b/prepare/r-cowplot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cowplot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cowplot/lilac.yaml b/prepare/r-cowplot/lilac.yaml new file mode 100644 index 0000000000..dacda408f0 --- /dev/null +++ b/prepare/r-cowplot/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gtable +- r-rlang +- r-scales +update_on: +- regex: cowplot_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=cowplot diff --git a/prepare/r-cp4p/PKGBUILD b/prepare/r-cp4p/PKGBUILD new file mode 100644 index 0000000000..adac6ed592 --- /dev/null +++ b/prepare/r-cp4p/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cp4p +_pkgver=0.3.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Calibration Plot for Proteomics' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-limma + r-mess + r-multtest + r-qvalue +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cp4p/lilac.py b/prepare/r-cp4p/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cp4p/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cp4p/lilac.yaml b/prepare/r-cp4p/lilac.yaml new file mode 100644 index 0000000000..95fb9c43ed --- /dev/null +++ b/prepare/r-cp4p/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-limma +- r-mess +- r-multtest +- r-qvalue +update_on: +- regex: cp4p_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=cp4p diff --git a/prepare/r-cpgassoc/PKGBUILD b/prepare/r-cpgassoc/PKGBUILD new file mode 100644 index 0000000000..ab66e4d975 --- /dev/null +++ b/prepare/r-cpgassoc/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CpGassoc +_pkgver=2.60 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Association Between Methylation and a Phenotype of Interest' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-qvalue +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cpgassoc/lilac.py b/prepare/r-cpgassoc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cpgassoc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cpgassoc/lilac.yaml b/prepare/r-cpgassoc/lilac.yaml new file mode 100644 index 0000000000..d157d21b24 --- /dev/null +++ b/prepare/r-cpgassoc/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: CpGassoc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=CpGassoc diff --git a/prepare/r-cplm/PKGBUILD b/prepare/r-cplm/PKGBUILD new file mode 100644 index 0000000000..b66a5b5218 --- /dev/null +++ b/prepare/r-cplm/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cplm +_pkgver=0.7-9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Compound Poisson Linear Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-biglm + r-coda + r-ggplot2 + r-minqa + r-reshape2 + r-statmod + r-tweedie +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cplm/lilac.py b/prepare/r-cplm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cplm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cplm/lilac.yaml b/prepare/r-cplm/lilac.yaml new file mode 100644 index 0000000000..edf6483349 --- /dev/null +++ b/prepare/r-cplm/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biglm +- r-coda +- r-ggplot2 +- r-minqa +- r-reshape2 +- r-statmod +- r-tweedie +update_on: +- regex: cplm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=cplm diff --git a/prepare/r-cpp11/PKGBUILD b/prepare/r-cpp11/PKGBUILD new file mode 100644 index 0000000000..fc75bd9e7e --- /dev/null +++ b/prepare/r-cpp11/PKGBUILD @@ -0,0 +1,51 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=cpp11 +_pkgver=0.4.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="A C++11 Interface for R's C Interface" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-bench + r-brio + r-callr + r-cli + r-covr + r-decor + r-desc + r-ggplot2 + r-glue + r-knitr + r-lobstr + r-mockery + r-progress + r-rcpp + r-rmarkdown + r-scales + r-testthat + r-tibble + r-utils + r-vctrs + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cpp11/lilac.py b/prepare/r-cpp11/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cpp11/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cpp11/lilac.yaml b/prepare/r-cpp11/lilac.yaml new file mode 100644 index 0000000000..cd7ea856c0 --- /dev/null +++ b/prepare/r-cpp11/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: cpp11_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=cpp11 diff --git a/prepare/r-cpvsnp/PKGBUILD b/prepare/r-cpvsnp/PKGBUILD new file mode 100644 index 0000000000..e91ba942a5 --- /dev/null +++ b/prepare/r-cpvsnp/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cpvSNP +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene set analysis methods for SNP association p-values that lie in genes in given gene sets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-corpcor + r-genomicfeatures + r-ggplot2 + r-gseabase + r-plyr +) +optdepends=( + r-biocgenerics + r-biocstyle + r-reportingtools + r-runit + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cpvsnp/lilac.py b/prepare/r-cpvsnp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cpvsnp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cpvsnp/lilac.yaml b/prepare/r-cpvsnp/lilac.yaml new file mode 100644 index 0000000000..43978d67e0 --- /dev/null +++ b/prepare/r-cpvsnp/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-corpcor +- r-genomicfeatures +- r-ggplot2 +- r-gseabase +- r-plyr +update_on: +- regex: cpvSNP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cpvSNP diff --git a/prepare/r-cqn/PKGBUILD b/prepare/r-cqn/PKGBUILD new file mode 100644 index 0000000000..4f4817dc99 --- /dev/null +++ b/prepare/r-cqn/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cqn +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Conditional quantile normalization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-mclust + r-nor1mix + r-preprocesscore + r-quantreg +) +optdepends=( + r-edger + r-scales +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cqn/lilac.py b/prepare/r-cqn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cqn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cqn/lilac.yaml b/prepare/r-cqn/lilac.yaml new file mode 100644 index 0000000000..15990b1aa5 --- /dev/null +++ b/prepare/r-cqn/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mclust +- r-nor1mix +- r-preprocesscore +- r-quantreg +update_on: +- regex: cqn_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cqn diff --git a/prepare/r-credentials/PKGBUILD b/prepare/r-credentials/PKGBUILD new file mode 100644 index 0000000000..fe835020fc --- /dev/null +++ b/prepare/r-credentials/PKGBUILD @@ -0,0 +1,38 @@ +# system requirements: git (optional) +# Maintainer: Guoyi Zhang + +_pkgname=credentials +_pkgver=1.3.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Managing SSH and Git Credentials' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-askpass + r-curl + r-jsonlite + r-openssl + r-sys +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-credentials/lilac.py b/prepare/r-credentials/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-credentials/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-credentials/lilac.yaml b/prepare/r-credentials/lilac.yaml new file mode 100644 index 0000000000..001027bdfc --- /dev/null +++ b/prepare/r-credentials/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-askpass +- r-curl +- r-jsonlite +- r-openssl +- r-sys +update_on: +- regex: credentials_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=credentials diff --git a/prepare/r-crimage/PKGBUILD b/prepare/r-crimage/PKGBUILD new file mode 100644 index 0000000000..4350ad7f7a --- /dev/null +++ b/prepare/r-crimage/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CRImage +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CRImage a package to classify cells and calculate tumour cellularity' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-acgh + r-dnacopy + r-e1071 + r-ebimage + r-foreach + r-sgeostat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-crimage/lilac.py b/prepare/r-crimage/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-crimage/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-crimage/lilac.yaml b/prepare/r-crimage/lilac.yaml new file mode 100644 index 0000000000..fcc0018614 --- /dev/null +++ b/prepare/r-crimage/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-acgh +- r-dnacopy +- r-e1071 +- r-ebimage +- r-foreach +- r-sgeostat +update_on: +- regex: CRImage_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CRImage diff --git a/prepare/r-crisprseek/PKGBUILD b/prepare/r-crisprseek/PKGBUILD new file mode 100644 index 0000000000..34ce08ba8a --- /dev/null +++ b/prepare/r-crisprseek/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CRISPRseek +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-bsgenome + r-data.table + r-delayedarray + r-dplyr + r-genomeinfodb + r-genomicranges + r-hash + r-iranges + r-keras + r-mltools + r-reticulate + r-rhdf5 + r-s4vectors + r-seqinr + r-xvector +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-org.hs.eg.db + r-runit + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-crisprseek/lilac.py b/prepare/r-crisprseek/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-crisprseek/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-crisprseek/lilac.yaml b/prepare/r-crisprseek/lilac.yaml new file mode 100644 index 0000000000..8db0b6cd6c --- /dev/null +++ b/prepare/r-crisprseek/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-data.table +- r-delayedarray +- r-dplyr +- r-genomeinfodb +- r-genomicranges +- r-hash +- r-iranges +- r-keras +- r-mltools +- r-reticulate +- r-rhdf5 +- r-s4vectors +- r-seqinr +- r-xvector +update_on: +- regex: CRISPRseek_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CRISPRseek diff --git a/prepare/r-crisprseekplus/PKGBUILD b/prepare/r-crisprseekplus/PKGBUILD new file mode 100644 index 0000000000..f8ac5d661c --- /dev/null +++ b/prepare/r-crisprseekplus/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=crisprseekplus +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='crisprseekplus' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocmanager + r-bsgenome + r-crisprseek + r-dt + r-genomicfeatures + r-genomicranges + r-guideseq + r-hash + r-shiny + r-shinyjs +) +optdepends=( + r-knitr + r-r.rsp + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-crisprseekplus/lilac.py b/prepare/r-crisprseekplus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-crisprseekplus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-crisprseekplus/lilac.yaml b/prepare/r-crisprseekplus/lilac.yaml new file mode 100644 index 0000000000..9910319d6a --- /dev/null +++ b/prepare/r-crisprseekplus/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocmanager +- r-bsgenome +- r-crisprseek +- r-dt +- r-genomicfeatures +- r-genomicranges +- r-guideseq +- r-hash +- r-shiny +- r-shinyjs +update_on: +- regex: crisprseekplus_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/crisprseekplus diff --git a/prepare/r-crisprvariants/PKGBUILD b/prepare/r-crisprvariants/PKGBUILD new file mode 100644 index 0000000000..12ca6dde5f --- /dev/null +++ b/prepare/r-crisprvariants/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CrispRVariants +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for counting and visualising mutations in a target location' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocparallel + r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-gridextra + r-iranges + r-reshape2 + r-rsamtools + r-s4vectors +) +optdepends=( + r-biocstyle + r-gdata + r-genomicfeatures + r-knitr + r-rmarkdown + r-rtracklayer + r-sangerseqr + r-testthat + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-crisprvariants/lilac.py b/prepare/r-crisprvariants/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-crisprvariants/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-crisprvariants/lilac.yaml b/prepare/r-crisprvariants/lilac.yaml new file mode 100644 index 0000000000..9ed92c3a25 --- /dev/null +++ b/prepare/r-crisprvariants/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocparallel +- r-biostrings +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-gridextra +- r-iranges +- r-reshape2 +- r-rsamtools +- r-s4vectors +update_on: +- regex: CrispRVariants_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CrispRVariants diff --git a/prepare/r-crlmm/PKGBUILD b/prepare/r-crlmm/PKGBUILD new file mode 100644 index 0000000000..7a7465bbea --- /dev/null +++ b/prepare/r-crlmm/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=crlmm +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-affyio + r-beanplot + r-biobase + r-biocgenerics + r-ellipse + r-ff + r-foreach + r-illuminaio + r-limma + r-matrixstats + r-mvtnorm + r-oligoclasses + r-preprocesscore + r-rcppeigen + r-vgam +) +optdepends=( + r-genomewidesnp6crlmm + r-hapmapsnp6 + r-runit + r-snpstats +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-crlmm/lilac.py b/prepare/r-crlmm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-crlmm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-crlmm/lilac.yaml b/prepare/r-crlmm/lilac.yaml new file mode 100644 index 0000000000..476369bf92 --- /dev/null +++ b/prepare/r-crlmm/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affyio +- r-beanplot +- r-biobase +- r-biocgenerics +- r-ellipse +- r-ff +- r-foreach +- r-illuminaio +- r-limma +- r-matrixstats +- r-mvtnorm +- r-oligoclasses +- r-preprocesscore +- r-rcppeigen +- r-vgam +update_on: +- regex: crlmm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/crlmm diff --git a/prepare/r-crmn/PKGBUILD b/prepare/r-crmn/PKGBUILD new file mode 100644 index 0000000000..cf19191f90 --- /dev/null +++ b/prepare/r-crmn/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=crmn +_pkgver=0.0.21 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CCMN and Other Normalization Methods for Metabolomics Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-pcamethods +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-crmn/lilac.py b/prepare/r-crmn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-crmn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-crmn/lilac.yaml b/prepare/r-crmn/lilac.yaml new file mode 100644 index 0000000000..69fde303ff --- /dev/null +++ b/prepare/r-crmn/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-pcamethods +update_on: +- regex: crmn_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=crmn diff --git a/prepare/r-crossmeta/PKGBUILD b/prepare/r-crossmeta/PKGBUILD new file mode 100644 index 0000000000..f34cfcfa79 --- /dev/null +++ b/prepare/r-crossmeta/PKGBUILD @@ -0,0 +1,70 @@ +# system requirements: libxml2: libxml2-dev (deb), libxml2-devel (rpm)libcurl: libcurl4-openssl-dev (deb), libcurl-devel (rpm)openssl: libssl-dev (deb), openssl-devel (rpm), libssl_dev(csw), openssl@1.1 (brew) +# Maintainer: Guoyi Zhang + +_pkgname=crossmeta +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cross Platform Meta-Analysis of Microarray Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-affxparser + r-affy + r-annotationdbi + r-biobase + r-biocgenerics + r-biocmanager + r-data.table + r-dbi + r-deseq2 + r-dt + r-edger + r-fdrtool + r-geoquery + r-limma + r-matrixstats + r-metama + r-miniui + r-oligo + r-rcolorbrewer + r-rcurl + r-reader + r-readxl + r-rsqlite + r-shiny + r-shinybs + r-shinyjs + r-shinypanel + r-shinywidgets + r-statmod + r-stringr + r-summarizedexperiment + r-sva + r-tibble + r-xml +) +optdepends=( + r-knitr + r-lydata + r-org.hs.eg.db + r-rmarkdown + r-testthat + r-tximportdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-crossmeta/lilac.py b/prepare/r-crossmeta/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-crossmeta/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-crossmeta/lilac.yaml b/prepare/r-crossmeta/lilac.yaml new file mode 100644 index 0000000000..bc5b696e22 --- /dev/null +++ b/prepare/r-crossmeta/lilac.yaml @@ -0,0 +1,43 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affxparser +- r-affy +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-biocmanager +- r-data.table +- r-dbi +- r-deseq2 +- r-dt +- r-edger +- r-fdrtool +- r-geoquery +- r-limma +- r-matrixstats +- r-metama +- r-miniui +- r-oligo +- r-rcolorbrewer +- r-rcurl +- r-reader +- r-readxl +- r-rsqlite +- r-shiny +- r-shinybs +- r-shinyjs +- r-shinypanel +- r-shinywidgets +- r-statmod +- r-stringr +- r-summarizedexperiment +- r-sva +- r-tibble +- r-xml +update_on: +- regex: crossmeta_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/crossmeta diff --git a/prepare/r-crosstalk/PKGBUILD b/prepare/r-crosstalk/PKGBUILD new file mode 100644 index 0000000000..0f36228018 --- /dev/null +++ b/prepare/r-crosstalk/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=crosstalk +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Inter-Widget Interactivity for HTML Widgets' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmltools + r-jsonlite + r-lazyeval + r-r6 +) +optdepends=( + r-bslib + r-ggplot2 + r-sass + r-shiny + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-crosstalk/lilac.py b/prepare/r-crosstalk/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-crosstalk/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-crosstalk/lilac.yaml b/prepare/r-crosstalk/lilac.yaml new file mode 100644 index 0000000000..4dd66bde6e --- /dev/null +++ b/prepare/r-crosstalk/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-jsonlite +- r-lazyeval +- r-r6 +update_on: +- regex: crosstalk_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=crosstalk diff --git a/prepare/r-crul/PKGBUILD b/prepare/r-crul/PKGBUILD new file mode 100644 index 0000000000..2cd5d1ece8 --- /dev/null +++ b/prepare/r-crul/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=crul +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='HTTP Client' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-curl + r-httpcode + r-jsonlite + r-mime + r-r6 + r-urltools +) +optdepends=( + r-fauxpas + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat + r-webmockr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-crul/lilac.py b/prepare/r-crul/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-crul/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-crul/lilac.yaml b/prepare/r-crul/lilac.yaml new file mode 100644 index 0000000000..2a56373821 --- /dev/null +++ b/prepare/r-crul/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-httpcode +- r-jsonlite +- r-mime +- r-r6 +- r-urltools +update_on: +- regex: crul_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=crul diff --git a/prepare/r-csar/PKGBUILD b/prepare/r-csar/PKGBUILD new file mode 100644 index 0000000000..3180c65146 --- /dev/null +++ b/prepare/r-csar/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CSAR +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical tools for the analysis of ChIP-seq data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-genomeinfodb + r-genomicranges + r-iranges + r-s4vectors +) +optdepends=( + r-biostrings + r-shortread +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-csar/lilac.py b/prepare/r-csar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-csar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-csar/lilac.yaml b/prepare/r-csar/lilac.yaml new file mode 100644 index 0000000000..0ce5f84509 --- /dev/null +++ b/prepare/r-csar/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-s4vectors +update_on: +- regex: CSAR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CSAR diff --git a/prepare/r-csaw/PKGBUILD b/prepare/r-csaw/PKGBUILD new file mode 100644 index 0000000000..078e83a695 --- /dev/null +++ b/prepare/r-csaw/PKGBUILD @@ -0,0 +1,53 @@ +# system requirements: C++11, GNU make +# Maintainer: Guoyi Zhang + +_pkgname=csaw +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ChIP-Seq Analysis with Windows' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-edger + r-genomeinfodb + r-genomicranges + r-iranges + r-limma + r-metapod + r-rcpp + r-rhtslib + r-rsamtools + r-s4vectors + r-summarizedexperiment + r-zlibbioc +) +optdepends=( + r-annotationdbi + r-biocmanager + r-biocstyle + r-genomicalignments + r-genomicfeatures + r-knitr + r-org.mm.eg.db + r-rmarkdown + r-testthat + r-txdb.mmusculus.ucsc.mm10.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-csaw/lilac.py b/prepare/r-csaw/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-csaw/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-csaw/lilac.yaml b/prepare/r-csaw/lilac.yaml new file mode 100644 index 0000000000..8502ae99de --- /dev/null +++ b/prepare/r-csaw/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-edger +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-limma +- r-metapod +- r-rcpp +- r-rhtslib +- r-rsamtools +- r-s4vectors +- r-summarizedexperiment +- r-zlibbioc +update_on: +- regex: csaw_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/csaw diff --git a/prepare/r-csdr/PKGBUILD b/prepare/r-csdr/PKGBUILD new file mode 100644 index 0000000000..3547a7f791 --- /dev/null +++ b/prepare/r-csdr/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=csdR +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential gene co-expression' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-glue + r-matrixstats + r-rcpp + r-rhpcblasctl + r-wgcna +) +optdepends=( + r-biocstyle + r-dplyr + r-igraph + r-knitr + r-magrittr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-csdr/lilac.py b/prepare/r-csdr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-csdr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-csdr/lilac.yaml b/prepare/r-csdr/lilac.yaml new file mode 100644 index 0000000000..c23f163868 --- /dev/null +++ b/prepare/r-csdr/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-glue +- r-matrixstats +- r-rcpp +- r-rhpcblasctl +- r-wgcna +update_on: +- regex: csdR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/csdR diff --git a/prepare/r-cssp/PKGBUILD b/prepare/r-cssp/PKGBUILD new file mode 100644 index 0000000000..0fcc05896a --- /dev/null +++ b/prepare/r-cssp/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CSSP +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ChIP-Seq Statistical Power' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cssp/lilac.py b/prepare/r-cssp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cssp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cssp/lilac.yaml b/prepare/r-cssp/lilac.yaml new file mode 100644 index 0000000000..d627b23c30 --- /dev/null +++ b/prepare/r-cssp/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: CSSP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CSSP diff --git a/prepare/r-cssq/PKGBUILD b/prepare/r-cssq/PKGBUILD new file mode 100644 index 0000000000..9861c05eea --- /dev/null +++ b/prepare/r-cssq/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CSSQ +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Chip-seq Signal Quantifier Pipeline' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-markdown + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cssq/lilac.py b/prepare/r-cssq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cssq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cssq/lilac.yaml b/prepare/r-cssq/lilac.yaml new file mode 100644 index 0000000000..0baf19995d --- /dev/null +++ b/prepare/r-cssq/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: CSSQ_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CSSQ diff --git a/prepare/r-ctc/PKGBUILD b/prepare/r-ctc/PKGBUILD new file mode 100644 index 0000000000..f00d17df76 --- /dev/null +++ b/prepare/r-ctc/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ctc +_pkgver=1.68.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cluster and Tree Conversion.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-amap +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ctc/lilac.py b/prepare/r-ctc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ctc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ctc/lilac.yaml b/prepare/r-ctc/lilac.yaml new file mode 100644 index 0000000000..68ad42a1a1 --- /dev/null +++ b/prepare/r-ctc/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-amap +update_on: +- regex: ctc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ctc diff --git a/prepare/r-ctdquerier/PKGBUILD b/prepare/r-ctdquerier/PKGBUILD new file mode 100644 index 0000000000..5c581c5d7d --- /dev/null +++ b/prepare/r-ctdquerier/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CTDquerier +_pkgver=2.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Package for CTDbase data query, visualization and downstream analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocfilecache + r-ggplot2 + r-gridextra + r-igraph + r-rcurl + r-s4vectors + r-stringdist + r-stringr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ctdquerier/lilac.py b/prepare/r-ctdquerier/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ctdquerier/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ctdquerier/lilac.yaml b/prepare/r-ctdquerier/lilac.yaml new file mode 100644 index 0000000000..2124438764 --- /dev/null +++ b/prepare/r-ctdquerier/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-ggplot2 +- r-gridextra +- r-igraph +- r-rcurl +- r-s4vectors +- r-stringdist +- r-stringr +update_on: +- regex: CTDquerier_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CTDquerier diff --git a/prepare/r-ctggem/PKGBUILD b/prepare/r-ctggem/PKGBUILD new file mode 100644 index 0000000000..67869d9966 --- /dev/null +++ b/prepare/r-ctggem/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ctgGEM +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generating Tree Hierarchy Visualizations from Gene Expression Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-igraph + r-monocle + r-sincell + r-summarizedexperiment + r-tscan +) +optdepends=( + r-biocstyle + r-biomart + r-hsmmsinglecell + r-irlba + r-knitr + r-rmarkdown + r-vgam +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ctggem/lilac.py b/prepare/r-ctggem/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ctggem/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ctggem/lilac.yaml b/prepare/r-ctggem/lilac.yaml new file mode 100644 index 0000000000..1feab41d7a --- /dev/null +++ b/prepare/r-ctggem/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-igraph +- r-monocle +- r-sincell +- r-summarizedexperiment +- r-tscan +update_on: +- regex: ctgGEM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ctgGEM diff --git a/prepare/r-ctrap/PKGBUILD b/prepare/r-ctrap/PKGBUILD new file mode 100644 index 0000000000..bbf227af22 --- /dev/null +++ b/prepare/r-ctrap/PKGBUILD @@ -0,0 +1,63 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cTRAP +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identification of candidate causal perturbations from differential gene expression data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-annotationhub + r-binr + r-cowplot + r-data.table + r-dplyr + r-dt + r-fastmatch + r-fgsea + r-ggplot2 + r-ggrepel + r-highcharter + r-htmltools + r-httr + r-limma + r-pbapply + r-purrr + r-qs + r-r.utils + r-readxl + r-reshape2 + r-rhdf5 + r-rlang + r-scales + r-shiny + r-shinycssloaders + r-tibble +) +optdepends=( + r-biomart + r-covr + r-knitr + r-remotes + r-rmarkdown + r-spelling + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ctrap/lilac.py b/prepare/r-ctrap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ctrap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ctrap/lilac.yaml b/prepare/r-ctrap/lilac.yaml new file mode 100644 index 0000000000..c998c7430d --- /dev/null +++ b/prepare/r-ctrap/lilac.yaml @@ -0,0 +1,36 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-binr +- r-cowplot +- r-data.table +- r-dplyr +- r-dt +- r-fastmatch +- r-fgsea +- r-ggplot2 +- r-ggrepel +- r-highcharter +- r-htmltools +- r-httr +- r-limma +- r-pbapply +- r-purrr +- r-qs +- r-r.utils +- r-readxl +- r-reshape2 +- r-rhdf5 +- r-rlang +- r-scales +- r-shiny +- r-shinycssloaders +- r-tibble +update_on: +- regex: cTRAP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cTRAP diff --git a/prepare/r-ctsge/PKGBUILD b/prepare/r-ctsge/PKGBUILD new file mode 100644 index 0000000000..180c0c9c7b --- /dev/null +++ b/prepare/r-ctsge/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ctsGE +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clustering of Time Series Gene Expression data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ccapp + r-ggplot2 + r-limma + r-reshape2 + r-shiny + r-stringr +) +optdepends=( + r-biocstyle + r-dplyr + r-dt + r-geoquery + r-knitr + r-pander + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ctsge/lilac.py b/prepare/r-ctsge/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ctsge/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ctsge/lilac.yaml b/prepare/r-ctsge/lilac.yaml new file mode 100644 index 0000000000..d56279568d --- /dev/null +++ b/prepare/r-ctsge/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ccapp +- r-ggplot2 +- r-limma +- r-reshape2 +- r-shiny +- r-stringr +update_on: +- regex: ctsGE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ctsGE diff --git a/prepare/r-cubature/PKGBUILD b/prepare/r-cubature/PKGBUILD new file mode 100644 index 0000000000..5b7be2dbee --- /dev/null +++ b/prepare/r-cubature/PKGBUILD @@ -0,0 +1,35 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=cubature +_pkgver=2.0.4.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Adaptive Multivariate Integration over Hypercubes' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-benchr + r-knitr + r-mvtnorm + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cubature/lilac.py b/prepare/r-cubature/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cubature/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cubature/lilac.yaml b/prepare/r-cubature/lilac.yaml new file mode 100644 index 0000000000..05510dbc3b --- /dev/null +++ b/prepare/r-cubature/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: cubature_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=cubature diff --git a/prepare/r-cubist/PKGBUILD b/prepare/r-cubist/PKGBUILD new file mode 100644 index 0000000000..8a9e9a283d --- /dev/null +++ b/prepare/r-cubist/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Cubist +_pkgver=0.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Rule- And Instance-Based Regression Modeling' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-reshape2 +) +optdepends=( + r-dplyr + r-knitr + r-mlbench + r-modeldata + r-rlang + r-rmarkdown + r-tidyrules +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cubist/lilac.py b/prepare/r-cubist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cubist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cubist/lilac.yaml b/prepare/r-cubist/lilac.yaml new file mode 100644 index 0000000000..9f2093e03a --- /dev/null +++ b/prepare/r-cubist/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-reshape2 +update_on: +- regex: Cubist_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Cubist diff --git a/prepare/r-cummerbund/PKGBUILD b/prepare/r-cummerbund/PKGBUILD new file mode 100644 index 0000000000..26be855e05 --- /dev/null +++ b/prepare/r-cummerbund/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cummeRbund +_pkgver=2.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-fastcluster + r-ggplot2 + r-gviz + r-plyr + r-reshape2 + r-rsqlite + r-rtracklayer + r-s4vectors +) +optdepends=( + r-cluster + r-genomicfeatures + r-genomicranges + r-nmfn + r-plyr + r-rjson + r-stringr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cummerbund/lilac.py b/prepare/r-cummerbund/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cummerbund/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cummerbund/lilac.yaml b/prepare/r-cummerbund/lilac.yaml new file mode 100644 index 0000000000..af8551f8ce --- /dev/null +++ b/prepare/r-cummerbund/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-fastcluster +- r-ggplot2 +- r-gviz +- r-plyr +- r-reshape2 +- r-rsqlite +- r-rtracklayer +- r-s4vectors +update_on: +- regex: cummeRbund_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cummeRbund diff --git a/prepare/r-curatedtcgadata/PKGBUILD b/prepare/r-curatedtcgadata/PKGBUILD new file mode 100644 index 0000000000..d9c8fe73f2 --- /dev/null +++ b/prepare/r-curatedtcgadata/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=curatedTCGAData +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationhub + r-experimenthub + r-hdf5array + r-multiassayexperiment + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-raggedexperiment + r-readr + r-rmarkdown + r-tcgautils + r-testthat +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-curatedtcgadata/lilac.py b/prepare/r-curatedtcgadata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-curatedtcgadata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-curatedtcgadata/lilac.yaml b/prepare/r-curatedtcgadata/lilac.yaml new file mode 100644 index 0000000000..495d3758c6 --- /dev/null +++ b/prepare/r-curatedtcgadata/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-experimenthub +- r-hdf5array +- r-multiassayexperiment +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: curatedTCGAData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/curatedTCGAData diff --git a/prepare/r-curry/PKGBUILD b/prepare/r-curry/PKGBUILD new file mode 100644 index 0000000000..3524b2096e --- /dev/null +++ b/prepare/r-curry/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=curry +_pkgver=0.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Partial Function Application with %<%, %-<%, and %><%' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-curry/lilac.py b/prepare/r-curry/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-curry/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-curry/lilac.yaml b/prepare/r-curry/lilac.yaml new file mode 100644 index 0000000000..f31ad15234 --- /dev/null +++ b/prepare/r-curry/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: curry_(\d+.\d+.\d+).tar.gz + source: regex + url: https://cran.r-project.org/package=curry diff --git a/prepare/r-customcmpdb/PKGBUILD b/prepare/r-customcmpdb/PKGBUILD new file mode 100644 index 0000000000..09ea68c148 --- /dev/null +++ b/prepare/r-customcmpdb/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=customCMPdb +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Customize and Query Compound Annotation Database' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationhub + r-biocfilecache + r-chemminer + r-rappdirs + r-rsqlite + r-xml +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-customcmpdb/lilac.py b/prepare/r-customcmpdb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-customcmpdb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-customcmpdb/lilac.yaml b/prepare/r-customcmpdb/lilac.yaml new file mode 100644 index 0000000000..e592167c8e --- /dev/null +++ b/prepare/r-customcmpdb/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-biocfilecache +- r-chemminer +- r-rappdirs +- r-rsqlite +- r-xml +update_on: +- regex: customCMPdb_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/customCMPdb diff --git a/prepare/r-customprodb/PKGBUILD b/prepare/r-customprodb/PKGBUILD new file mode 100644 index 0000000000..ae7ba61cbe --- /dev/null +++ b/prepare/r-customprodb/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=customProDB +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ahocorasicktrie + r-annotationdbi + r-biomart + r-biostrings + r-dbi + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-plyr + r-rcurl + r-rsamtools + r-rsqlite + r-rtracklayer + r-s4vectors + r-stringr + r-variantannotation +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg19 + r-rmariadb +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-customprodb/lilac.py b/prepare/r-customprodb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-customprodb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-customprodb/lilac.yaml b/prepare/r-customprodb/lilac.yaml new file mode 100644 index 0000000000..26d9e7c49f --- /dev/null +++ b/prepare/r-customprodb/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ahocorasicktrie +- r-annotationdbi +- r-biomart +- r-biostrings +- r-dbi +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-plyr +- r-rcurl +- r-rsamtools +- r-rsqlite +- r-rtracklayer +- r-s4vectors +- r-stringr +- r-variantannotation +update_on: +- regex: customProDB_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/customProDB diff --git a/prepare/r-cvauc/PKGBUILD b/prepare/r-cvauc/PKGBUILD new file mode 100644 index 0000000000..dc376a47e3 --- /dev/null +++ b/prepare/r-cvauc/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cvAUC +_pkgver=1.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cross-Validated Area Under the ROC Curve Confidence Intervals' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-data.table + r-rocr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cvauc/lilac.py b/prepare/r-cvauc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cvauc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cvauc/lilac.yaml b/prepare/r-cvauc/lilac.yaml new file mode 100644 index 0000000000..a7bdd739fb --- /dev/null +++ b/prepare/r-cvauc/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-rocr +update_on: +- regex: cvAUC_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=cvAUC diff --git a/prepare/r-cyanofilter/PKGBUILD b/prepare/r-cyanofilter/PKGBUILD new file mode 100644 index 0000000000..1acf5faddc --- /dev/null +++ b/prepare/r-cyanofilter/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cyanoFilter +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Phytoplankton Population Identification using Cell Pigmentation and/or Complexity' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-cytometree + r-flowclust + r-flowcore + r-flowdensity + r-ggally + r-ggplot2 + r-mrfdepth +) +optdepends=( + r-dplyr + r-knitr + r-magrittr + r-purrr + r-rmarkdown + r-stringr + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cyanofilter/lilac.py b/prepare/r-cyanofilter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cyanofilter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cyanofilter/lilac.yaml b/prepare/r-cyanofilter/lilac.yaml new file mode 100644 index 0000000000..715595b36e --- /dev/null +++ b/prepare/r-cyanofilter/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-cytometree +- r-flowclust +- r-flowcore +- r-flowdensity +- r-ggally +- r-ggplot2 +- r-mrfdepth +update_on: +- regex: cyanoFilter_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cyanoFilter diff --git a/prepare/r-cycle/PKGBUILD b/prepare/r-cycle/PKGBUILD new file mode 100644 index 0000000000..43d55da526 --- /dev/null +++ b/prepare/r-cycle/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cycle +_pkgver=1.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Significance of periodic expression pattern in time-series data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-mfuzz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cycle/lilac.py b/prepare/r-cycle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cycle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cycle/lilac.yaml b/prepare/r-cycle/lilac.yaml new file mode 100644 index 0000000000..3bb19c5c84 --- /dev/null +++ b/prepare/r-cycle/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-mfuzz +update_on: +- regex: cycle_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cycle diff --git a/prepare/r-cydar/PKGBUILD b/prepare/r-cydar/PKGBUILD new file mode 100644 index 0000000000..58983abe0d --- /dev/null +++ b/prepare/r-cydar/PKGBUILD @@ -0,0 +1,49 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=cydar +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Using Mass Cytometry for Differential Abundance Analyses' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-biocneighbors + r-biocparallel + r-flowcore + r-rcpp + r-s4vectors + r-shiny + r-singlecellexperiment + r-summarizedexperiment + r-viridis +) +optdepends=( + r-biocstyle + r-edger + r-flowstats + r-glmnet + r-knitr + r-limma + r-ncdfflow + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cydar/lilac.py b/prepare/r-cydar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cydar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cydar/lilac.yaml b/prepare/r-cydar/lilac.yaml new file mode 100644 index 0000000000..28d3f17217 --- /dev/null +++ b/prepare/r-cydar/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocneighbors +- r-biocparallel +- r-flowcore +- r-rcpp +- r-s4vectors +- r-shiny +- r-singlecellexperiment +- r-summarizedexperiment +- r-viridis +update_on: +- regex: cydar_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cydar diff --git a/prepare/r-cytodx/PKGBUILD b/prepare/r-cytodx/PKGBUILD new file mode 100644 index 0000000000..b5b618508e --- /dev/null +++ b/prepare/r-cytodx/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CytoDx +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Robust prediction of clinical outcomes using cytometry data without cell gating' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-doparallel + r-dplyr + r-flowcore + r-glmnet + r-rpart.plot +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cytodx/lilac.py b/prepare/r-cytodx/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cytodx/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cytodx/lilac.yaml b/prepare/r-cytodx/lilac.yaml new file mode 100644 index 0000000000..9d48654675 --- /dev/null +++ b/prepare/r-cytodx/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-dplyr +- r-flowcore +- r-glmnet +- r-rpart.plot +update_on: +- regex: CytoDx_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CytoDx diff --git a/prepare/r-cytofpower/PKGBUILD b/prepare/r-cytofpower/PKGBUILD new file mode 100644 index 0000000000..b522b450f2 --- /dev/null +++ b/prepare/r-cytofpower/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CyTOFpower +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Power analysis for CyTOF experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-cytoglmm + r-diffcyt + r-dplyr + r-dt + r-ggplot2 + r-magrittr + r-rlang + r-shiny + r-shinyfeedback + r-shinyjs + r-shinymatrix + r-summarizedexperiment + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cytofpower/lilac.py b/prepare/r-cytofpower/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cytofpower/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cytofpower/lilac.yaml b/prepare/r-cytofpower/lilac.yaml new file mode 100644 index 0000000000..bfe2e24ba1 --- /dev/null +++ b/prepare/r-cytofpower/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cytoglmm +- r-diffcyt +- r-dplyr +- r-dt +- r-ggplot2 +- r-magrittr +- r-rlang +- r-shiny +- r-shinyfeedback +- r-shinyjs +- r-shinymatrix +- r-summarizedexperiment +- r-tibble +- r-tidyr +update_on: +- regex: CyTOFpower_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CyTOFpower diff --git a/prepare/r-cytoglmm/PKGBUILD b/prepare/r-cytoglmm/PKGBUILD new file mode 100644 index 0000000000..d25d05bf10 --- /dev/null +++ b/prepare/r-cytoglmm/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CytoGLMM +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Conditional Differential Analysis for Flow and Mass Cytometry Experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biocparallel + r-caret + r-cowplot + r-doparallel + r-dplyr + r-factoextra + r-flexmix + r-ggplot2 + r-ggrepel + r-logging + r-magrittr + r-mbest + r-pheatmap + r-rcolorbrewer + r-rlang + r-speedglm + r-stringr + r-strucchange + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cytoglmm/lilac.py b/prepare/r-cytoglmm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cytoglmm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cytoglmm/lilac.yaml b/prepare/r-cytoglmm/lilac.yaml new file mode 100644 index 0000000000..8c33943625 --- /dev/null +++ b/prepare/r-cytoglmm/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-caret +- r-cowplot +- r-doparallel +- r-dplyr +- r-factoextra +- r-flexmix +- r-ggplot2 +- r-ggrepel +- r-logging +- r-magrittr +- r-mbest +- r-pheatmap +- r-rcolorbrewer +- r-rlang +- r-speedglm +- r-stringr +- r-strucchange +- r-tibble +- r-tidyr +update_on: +- regex: CytoGLMM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CytoGLMM diff --git a/prepare/r-cytokernel/PKGBUILD b/prepare/r-cytokernel/PKGBUILD new file mode 100644 index 0000000000..269cbcc097 --- /dev/null +++ b/prepare/r-cytokernel/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cytoKernel +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential expression using kernel-based score test' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ashr + r-biocparallel + r-circlize + r-complexheatmap + r-data.table + r-dplyr + r-magrittr + r-rcpp + r-rlang + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cytokernel/lilac.py b/prepare/r-cytokernel/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cytokernel/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cytokernel/lilac.yaml b/prepare/r-cytokernel/lilac.yaml new file mode 100644 index 0000000000..85e411803b --- /dev/null +++ b/prepare/r-cytokernel/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ashr +- r-biocparallel +- r-circlize +- r-complexheatmap +- r-data.table +- r-dplyr +- r-magrittr +- r-rcpp +- r-rlang +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: cytoKernel_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cytoKernel diff --git a/prepare/r-cytolib/PKGBUILD b/prepare/r-cytolib/PKGBUILD new file mode 100644 index 0000000000..674fa3e4b3 --- /dev/null +++ b/prepare/r-cytolib/PKGBUILD @@ -0,0 +1,38 @@ +# system requirements: GNU make, C++11 +# Maintainer: Guoyi Zhang + +_pkgname=cytolib +_pkgver=2.6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='C++ infrastructure for representing and interacting with the gated cytometry data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-bh + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-rhdf5lib + r-rprotobuflib +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cytolib/lilac.py b/prepare/r-cytolib/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cytolib/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cytolib/lilac.yaml b/prepare/r-cytolib/lilac.yaml new file mode 100644 index 0000000000..1f053bb3b8 --- /dev/null +++ b/prepare/r-cytolib/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-rcpp +- r-rcpparmadillo +- r-rcppparallel +- r-rhdf5lib +- r-rprotobuflib +update_on: +- regex: cytolib_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cytolib diff --git a/prepare/r-cytomapper/PKGBUILD b/prepare/r-cytomapper/PKGBUILD new file mode 100644 index 0000000000..bfbd19eea5 --- /dev/null +++ b/prepare/r-cytomapper/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cytomapper +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization of highly multiplexed imaging data in R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-delayedarray + r-ebimage + r-ggbeeswarm + r-ggplot2 + r-hdf5array + r-matrixstats + r-raster + r-rcolorbrewer + r-rhdf5 + r-s4vectors + r-shiny + r-shinydashboard + r-singlecellexperiment + r-summarizedexperiment + r-svglite + r-svgpanzoom + r-viridis +) +optdepends=( + r-biocstyle + r-cowplot + r-knitr + r-markdown + r-rmarkdown + r-shinytest + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cytomapper/lilac.py b/prepare/r-cytomapper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cytomapper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cytomapper/lilac.yaml b/prepare/r-cytomapper/lilac.yaml new file mode 100644 index 0000000000..e5056b81b6 --- /dev/null +++ b/prepare/r-cytomapper/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-delayedarray +- r-ebimage +- r-ggbeeswarm +- r-ggplot2 +- r-hdf5array +- r-matrixstats +- r-raster +- r-rcolorbrewer +- r-rhdf5 +- r-s4vectors +- r-shiny +- r-shinydashboard +- r-singlecellexperiment +- r-summarizedexperiment +- r-svglite +- r-svgpanzoom +- r-viridis +update_on: +- regex: cytomapper_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/cytomapper diff --git a/prepare/r-cytometree/PKGBUILD b/prepare/r-cytometree/PKGBUILD new file mode 100644 index 0000000000..3ebd776155 --- /dev/null +++ b/prepare/r-cytometree/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=cytometree +_pkgver=2.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automated Cytometry Gating and Annotation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-cowplot + r-ggplot2 + r-gofkernel + r-igraph + r-mclust + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-formatr + r-knitr + r-rmarkdown + r-viridis +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cytometree/lilac.py b/prepare/r-cytometree/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cytometree/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cytometree/lilac.yaml b/prepare/r-cytometree/lilac.yaml new file mode 100644 index 0000000000..a3b7dea5ea --- /dev/null +++ b/prepare/r-cytometree/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cowplot +- r-ggplot2 +- r-gofkernel +- r-igraph +- r-mclust +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: cytometree_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=cytometree diff --git a/prepare/r-cytoml/PKGBUILD b/prepare/r-cytoml/PKGBUILD new file mode 100644 index 0000000000..b427d8ebe9 --- /dev/null +++ b/prepare/r-cytoml/PKGBUILD @@ -0,0 +1,61 @@ +# system requirements: xml2, GNU make, C++11 +# Maintainer: Guoyi Zhang + +_pkgname=CytoML +_pkgver=2.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A GatingML Interface for Cross Platform Cytometry Data Sharing' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-base64enc + r-bh + r-biobase + r-corpcor + r-cytolib + r-data.table + r-dplyr + r-flowcore + r-flowworkspace + r-ggcyto + r-graph + r-jsonlite + r-opencyto + r-plyr + r-rbgl + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-rgraphviz + r-rhdf5lib + r-rprotobuflib + r-runit + r-tibble + r-xml + r-xml2 + r-yaml +) +optdepends=( + r-flowworkspacedata + r-knitr + r-parallel + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cytoml/lilac.py b/prepare/r-cytoml/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cytoml/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cytoml/lilac.yaml b/prepare/r-cytoml/lilac.yaml new file mode 100644 index 0000000000..7432c4daf1 --- /dev/null +++ b/prepare/r-cytoml/lilac.yaml @@ -0,0 +1,35 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-bh +- r-biobase +- r-corpcor +- r-cytolib +- r-data.table +- r-dplyr +- r-flowcore +- r-flowworkspace +- r-ggcyto +- r-graph +- r-jsonlite +- r-opencyto +- r-plyr +- r-rbgl +- r-rcpp +- r-rcpparmadillo +- r-rcppparallel +- r-rgraphviz +- r-rhdf5lib +- r-rprotobuflib +- r-runit +- r-tibble +- r-xml +- r-xml2 +- r-yaml +update_on: +- regex: CytoML_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CytoML diff --git a/prepare/r-cytotree/PKGBUILD b/prepare/r-cytotree/PKGBUILD new file mode 100644 index 0000000000..78125296db --- /dev/null +++ b/prepare/r-cytotree/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=CytoTree +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Toolkit for Flow And Mass Cytometry Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocneighbors + r-destiny + r-flowcore + r-flowsom + r-flowutils + r-ggplot2 + r-gmodels + r-igraph + r-limma + r-matrixstats + r-mclust + r-pheatmap + r-prettydoc + r-rann + r-rcpp + r-rtsne + r-scatterpie + r-scatterplot3d + r-stringr + r-sva + r-umap +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rcolorbrewer + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-cytotree/lilac.py b/prepare/r-cytotree/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-cytotree/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-cytotree/lilac.yaml b/prepare/r-cytotree/lilac.yaml new file mode 100644 index 0000000000..ebc8b7f893 --- /dev/null +++ b/prepare/r-cytotree/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocneighbors +- r-destiny +- r-flowcore +- r-flowsom +- r-flowutils +- r-ggplot2 +- r-gmodels +- r-igraph +- r-limma +- r-matrixstats +- r-mclust +- r-pheatmap +- r-prettydoc +- r-rann +- r-rcpp +- r-rtsne +- r-scatterpie +- r-scatterplot3d +- r-stringr +- r-sva +- r-umap +update_on: +- regex: CytoTree_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/CytoTree diff --git a/prepare/r-dada2/PKGBUILD b/prepare/r-dada2/PKGBUILD new file mode 100644 index 0000000000..38550bdee4 --- /dev/null +++ b/prepare/r-dada2/PKGBUILD @@ -0,0 +1,41 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=dada2 +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Accurate, high-resolution sample inference from amplicon sequencing data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biocgenerics + r-biostrings + r-ggplot2 + r-iranges + r-rcpp + r-rcppparallel + r-reshape2 + r-shortread + r-xvector +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dada2/lilac.py b/prepare/r-dada2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dada2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dada2/lilac.yaml b/prepare/r-dada2/lilac.yaml new file mode 100644 index 0000000000..f371696e6f --- /dev/null +++ b/prepare/r-dada2/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-ggplot2 +- r-iranges +- r-rcpp +- r-rcppparallel +- r-reshape2 +- r-shortread +- r-xvector +update_on: +- regex: dada2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/dada2 diff --git a/prepare/r-daglogo/PKGBUILD b/prepare/r-daglogo/PKGBUILD new file mode 100644 index 0000000000..811c967f48 --- /dev/null +++ b/prepare/r-daglogo/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dagLogo +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biomart + r-biostrings + r-motifstack + r-pheatmap + r-uniprot.ws +) +optdepends=( + r-biocstyle + r-grimport + r-grimport2 + r-knitr + r-rmarkdown + r-testthat + r-xml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-daglogo/lilac.py b/prepare/r-daglogo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-daglogo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-daglogo/lilac.yaml b/prepare/r-daglogo/lilac.yaml new file mode 100644 index 0000000000..2bf6bca428 --- /dev/null +++ b/prepare/r-daglogo/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biomart +- r-biostrings +- r-motifstack +- r-pheatmap +- r-uniprot.ws +update_on: +- regex: dagLogo_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/dagLogo diff --git a/prepare/r-dama/PKGBUILD b/prepare/r-dama/PKGBUILD new file mode 100644 index 0000000000..5a8be68d03 --- /dev/null +++ b/prepare/r-dama/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=daMA +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Efficient design and analysis of factorial two-colour microarray data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dama/lilac.py b/prepare/r-dama/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dama/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dama/lilac.yaml b/prepare/r-dama/lilac.yaml new file mode 100644 index 0000000000..6bf6ffd30d --- /dev/null +++ b/prepare/r-dama/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: daMA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/daMA diff --git a/prepare/r-damefinder/PKGBUILD b/prepare/r-damefinder/PKGBUILD new file mode 100644 index 0000000000..6330be04fa --- /dev/null +++ b/prepare/r-damefinder/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DAMEfinder +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Finds DAMEs - Differential Allelicly MEthylated regions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-biostrings + r-bumphunter + r-cowplot + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-limma + r-plyr + r-readr + r-reshape2 + r-rsamtools + r-s4vectors + r-stringr + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-knitr + r-rmarkdown + r-rtracklayer + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-damefinder/lilac.py b/prepare/r-damefinder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-damefinder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-damefinder/lilac.yaml b/prepare/r-damefinder/lilac.yaml new file mode 100644 index 0000000000..40db254bb7 --- /dev/null +++ b/prepare/r-damefinder/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-bumphunter +- r-cowplot +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-limma +- r-plyr +- r-readr +- r-reshape2 +- r-rsamtools +- r-s4vectors +- r-stringr +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: DAMEfinder_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DAMEfinder diff --git a/prepare/r-damirseq/PKGBUILD b/prepare/r-damirseq/PKGBUILD new file mode 100644 index 0000000000..3a1da406f4 --- /dev/null +++ b/prepare/r-damirseq/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DaMiRseq +_pkgver=2.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data Mining for RNA-seq data: normalization, feature selection and classification' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-arm + r-caret + r-corrplot + r-deseq2 + r-e1071 + r-edaseq + r-edger + r-factominer + r-fselector + r-ggplot2 + r-hmisc + r-ineq + r-kknn + r-limma + r-lubridate + r-pheatmap + r-pls + r-plsvarsel + r-plyr + r-randomforest + r-rcolorbrewer + r-reshape2 + r-rsnns + r-summarizedexperiment + r-sva +) +optdepends=( + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-damirseq/lilac.py b/prepare/r-damirseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-damirseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-damirseq/lilac.yaml b/prepare/r-damirseq/lilac.yaml new file mode 100644 index 0000000000..b589aaf808 --- /dev/null +++ b/prepare/r-damirseq/lilac.yaml @@ -0,0 +1,34 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-arm +- r-caret +- r-corrplot +- r-deseq2 +- r-e1071 +- r-edaseq +- r-edger +- r-factominer +- r-fselector +- r-ggplot2 +- r-hmisc +- r-ineq +- r-kknn +- r-limma +- r-lubridate +- r-pheatmap +- r-pls +- r-plsvarsel +- r-plyr +- r-randomforest +- r-rcolorbrewer +- r-reshape2 +- r-rsnns +- r-summarizedexperiment +- r-sva +update_on: +- regex: DaMiRseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DaMiRseq diff --git a/prepare/r-dapar/PKGBUILD b/prepare/r-dapar/PKGBUILD new file mode 100644 index 0000000000..612a6fe1fa --- /dev/null +++ b/prepare/r-dapar/PKGBUILD @@ -0,0 +1,78 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DAPAR +_pkgver=1.26.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for the Differential Analysis of Proteins Abundance with R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-apcluster + r-biobase + r-cairo + r-clusterprofiler + r-cp4p + r-dapardata + r-dendextend + r-diptest + r-doparallel + r-dplyr + r-factoextra + r-factominer + r-forcats + r-foreach + r-ggplot2 + r-gplots + r-graph + r-highcharter + r-igraph + r-imp4p + r-impute + r-knitr + r-limma + r-lme4 + r-mfuzz + r-msnbase + r-multcomp + r-norm + r-openxlsx + r-pcamethods + r-png + r-preprocesscore + r-purrr + r-rcolorbrewer + r-readxl + r-reshape2 + r-scales + r-siggenes + r-stringr + r-tibble + r-tidyr + r-tidyverse + r-tmvtnorm + r-vioplot + r-visnetwork + r-vsn +) +optdepends=( + r-biocgenerics + r-biocstyle + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dapar/lilac.py b/prepare/r-dapar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dapar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dapar/lilac.yaml b/prepare/r-dapar/lilac.yaml new file mode 100644 index 0000000000..48b7b8b5fd --- /dev/null +++ b/prepare/r-dapar/lilac.yaml @@ -0,0 +1,56 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-apcluster +- r-biobase +- r-cairo +- r-clusterprofiler +- r-cp4p +- r-dapardata +- r-dendextend +- r-diptest +- r-doparallel +- r-dplyr +- r-factoextra +- r-factominer +- r-forcats +- r-foreach +- r-ggplot2 +- r-gplots +- r-graph +- r-highcharter +- r-igraph +- r-imp4p +- r-impute +- r-knitr +- r-limma +- r-lme4 +- r-mfuzz +- r-msnbase +- r-multcomp +- r-norm +- r-openxlsx +- r-pcamethods +- r-png +- r-preprocesscore +- r-purrr +- r-rcolorbrewer +- r-readxl +- r-reshape2 +- r-scales +- r-siggenes +- r-stringr +- r-tibble +- r-tidyr +- r-tidyverse +- r-tmvtnorm +- r-vioplot +- r-visnetwork +- r-vsn +update_on: +- regex: DAPAR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DAPAR diff --git a/prepare/r-dapardata/PKGBUILD b/prepare/r-dapardata/PKGBUILD new file mode 100644 index 0000000000..26d35ee73c --- /dev/null +++ b/prepare/r-dapardata/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DAPARdata +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data accompanying the DAPAR and Prostar packages' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-knitr + r-msnbase +) +optdepends=( + r-dapar +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dapardata/lilac.py b/prepare/r-dapardata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dapardata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dapardata/lilac.yaml b/prepare/r-dapardata/lilac.yaml new file mode 100644 index 0000000000..f2084dffae --- /dev/null +++ b/prepare/r-dapardata/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-knitr +- r-msnbase +update_on: +- regex: DAPARdata_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DAPARdata diff --git a/prepare/r-dart/PKGBUILD b/prepare/r-dart/PKGBUILD new file mode 100644 index 0000000000..62e6a568d5 --- /dev/null +++ b/prepare/r-dart/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DART +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Denoising Algorithm based on Relevance network Topology' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-igraph +) +optdepends=( + r-biobase + r-breastcancermainz + r-breastcancervdx +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dart/lilac.py b/prepare/r-dart/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dart/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dart/lilac.yaml b/prepare/r-dart/lilac.yaml new file mode 100644 index 0000000000..60f302a06c --- /dev/null +++ b/prepare/r-dart/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +update_on: +- regex: DART_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DART diff --git a/prepare/r-dasper/PKGBUILD b/prepare/r-dasper/PKGBUILD new file mode 100644 index 0000000000..c8daa1d61a --- /dev/null +++ b/prepare/r-dasper/PKGBUILD @@ -0,0 +1,64 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dasper +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detecting abberant splicing events from RNA-sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-basilisk + r-biocfilecache + r-biocparallel + r-data.table + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggpubr + r-ggrepel + r-iranges + r-magrittr + r-megadepth + r-plyranges + r-readr + r-reticulate + r-rtracklayer + r-s4vectors + r-stringr + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-annotationfilter + r-biocstyle + r-covr + r-ensembldb + r-genomicstate + r-knitr + r-lifecycle + r-markdown + r-recount + r-refmanager + r-rmarkdown + r-sessioninfo + r-testthat + r-tibble +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dasper/lilac.py b/prepare/r-dasper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dasper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dasper/lilac.yaml b/prepare/r-dasper/lilac.yaml new file mode 100644 index 0000000000..7d3c29bd2c --- /dev/null +++ b/prepare/r-dasper/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-basilisk +- r-biocfilecache +- r-biocparallel +- r-data.table +- r-dplyr +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-ggpubr +- r-ggrepel +- r-iranges +- r-magrittr +- r-megadepth +- r-plyranges +- r-readr +- r-reticulate +- r-rtracklayer +- r-s4vectors +- r-stringr +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: dasper_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/dasper diff --git a/prepare/r-data.table/PKGBUILD b/prepare/r-data.table/PKGBUILD new file mode 100644 index 0000000000..2d8b011c3b --- /dev/null +++ b/prepare/r-data.table/PKGBUILD @@ -0,0 +1,39 @@ +# system requirements: zlib +# Maintainer: Guoyi Zhang + +_pkgname=data.table +_pkgver=1.14.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Extension of `data.frame`' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MPL2') +depends=( + r +) +optdepends=( + r-bit + r-bit64 + r-curl + r-knitr + r-nanotime + r-r.utils + r-rmarkdown + r-xts + r-yaml + r-zoo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-data.table/lilac.py b/prepare/r-data.table/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-data.table/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-data.table/lilac.yaml b/prepare/r-data.table/lilac.yaml new file mode 100644 index 0000000000..df8da32efa --- /dev/null +++ b/prepare/r-data.table/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: data.table_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=data.table diff --git a/prepare/r-data.tree/PKGBUILD b/prepare/r-data.tree/PKGBUILD new file mode 100644 index 0000000000..c83669f2a7 --- /dev/null +++ b/prepare/r-data.tree/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=data.tree +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='General Purpose Hierarchical Data Structure' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-r6 + r-stringi +) +optdepends=( + r-ape + r-diagrammer + r-doparallel + r-foreach + r-formula + r-graphics + r-htmlwidgets + r-igraph + r-jsonlite + r-knitr + r-mockery + r-networkd3 + r-party + r-partykit + r-rmarkdown + r-rpart + r-testthat + r-treemap + r-yaml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-data.tree/lilac.py b/prepare/r-data.tree/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-data.tree/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-data.tree/lilac.yaml b/prepare/r-data.tree/lilac.yaml new file mode 100644 index 0000000000..88dc87f8f2 --- /dev/null +++ b/prepare/r-data.tree/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-r6 +- r-stringi +update_on: +- regex: data.tree_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=data.tree diff --git a/prepare/r-datavisualizations/PKGBUILD b/prepare/r-datavisualizations/PKGBUILD new file mode 100644 index 0000000000..941f13d496 --- /dev/null +++ b/prepare/r-datavisualizations/PKGBUILD @@ -0,0 +1,57 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=DataVisualizations +_pkgver=1.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualizations of High-Dimensional Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-pracma + r-rcpp + r-rcpparmadillo + r-reshape2 + r-sp +) +optdepends=( + r-abcanalysis + r-choroplethr + r-databionicswarm + r-diptest + r-dplyr + r-ggextra + r-ggmap + r-ggrepel + r-htmlwidgets + r-knitr + r-mba + r-moments + r-paralleldist + r-plotly + r-plotrix + r-plyr + r-r6 + r-rgl + r-rmarkdown + r-rworldmap + r-signal + r-vioplot +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-datavisualizations/lilac.py b/prepare/r-datavisualizations/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-datavisualizations/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-datavisualizations/lilac.yaml b/prepare/r-datavisualizations/lilac.yaml new file mode 100644 index 0000000000..91924a0057 --- /dev/null +++ b/prepare/r-datavisualizations/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-pracma +- r-rcpp +- r-rcpparmadillo +- r-reshape2 +- r-sp +update_on: +- regex: DataVisualizations_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=DataVisualizations diff --git a/prepare/r-dbscan/PKGBUILD b/prepare/r-dbscan/PKGBUILD new file mode 100644 index 0000000000..4f9760c0b0 --- /dev/null +++ b/prepare/r-dbscan/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=dbscan +_pkgver=1.1-8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Density Based Clustering of Applications with Noise (DBSCAN) and Related Algorithms' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-dendextend + r-fpc + r-igraph + r-knitr + r-microbenchmark + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dbscan/lilac.py b/prepare/r-dbscan/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dbscan/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dbscan/lilac.yaml b/prepare/r-dbscan/lilac.yaml new file mode 100644 index 0000000000..33560c866b --- /dev/null +++ b/prepare/r-dbscan/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: dbscan_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dbscan diff --git a/prepare/r-dcanr/PKGBUILD b/prepare/r-dcanr/PKGBUILD new file mode 100644 index 0000000000..7d6b082dcc --- /dev/null +++ b/prepare/r-dcanr/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dcanr +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential co-expression/association network analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-circlize + r-dorng + r-foreach + r-igraph + r-plyr + r-rcolorbrewer + r-reshape2 + r-stringr +) +optdepends=( + r-biobase + r-biocstyle + r-cosine + r-doparallel + r-dosnow + r-ebarrays + r-ebcoexpress + r-edger + r-genenet + r-knitr + r-mclust + r-minqa + r-parallel + r-rmarkdown + r-summarizedexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dcanr/lilac.py b/prepare/r-dcanr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dcanr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dcanr/lilac.yaml b/prepare/r-dcanr/lilac.yaml new file mode 100644 index 0000000000..a0550e481a --- /dev/null +++ b/prepare/r-dcanr/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circlize +- r-dorng +- r-foreach +- r-igraph +- r-plyr +- r-rcolorbrewer +- r-reshape2 +- r-stringr +update_on: +- regex: dcanr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/dcanr diff --git a/prepare/r-dce/PKGBUILD b/prepare/r-dce/PKGBUILD new file mode 100644 index 0000000000..c7159576ab --- /dev/null +++ b/prepare/r-dce/PKGBUILD @@ -0,0 +1,68 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dce +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pathway Enrichment Based on Differential Causal Effects' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-combinepvalue + r-dplyr + r-edger + r-epinem + r-expm + r-ggplot2 + r-ggraph + r-glm2 + r-glue + r-graph + r-graphite + r-harmonicmeanp + r-igraph + r-logger + r-metap + r-mnem + r-naturalsort + r-org.hs.eg.db + r-pcalg + r-ppcor + r-purrr + r-reshape2 + r-rgraphviz + r-rlang + r-tidygraph + r-tidyverse +) +optdepends=( + r-biocstyle + r-cowplot + r-curatedtcgadata + r-dagitty + r-devtools + r-formatr + r-knitr + r-lmtest + r-rmarkdown + r-sandwich + r-summarizedexperiment + r-tcgautils + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dce/lilac.py b/prepare/r-dce/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dce/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dce/lilac.yaml b/prepare/r-dce/lilac.yaml new file mode 100644 index 0000000000..15fd080968 --- /dev/null +++ b/prepare/r-dce/lilac.yaml @@ -0,0 +1,36 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-combinepvalue +- r-dplyr +- r-edger +- r-epinem +- r-expm +- r-ggplot2 +- r-ggraph +- r-glm2 +- r-glue +- r-graph +- r-graphite +- r-harmonicmeanp +- r-igraph +- r-logger +- r-metap +- r-mnem +- r-naturalsort +- r-org.hs.eg.db +- r-pcalg +- r-ppcor +- r-purrr +- r-reshape2 +- r-rgraphviz +- r-rlang +- r-tidygraph +- r-tidyverse +update_on: +- regex: dce_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/dce diff --git a/prepare/r-dcgsa/PKGBUILD b/prepare/r-dcgsa/PKGBUILD new file mode 100644 index 0000000000..6c4a4cb2a2 --- /dev/null +++ b/prepare/r-dcgsa/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dcGSA +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dcgsa/lilac.py b/prepare/r-dcgsa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dcgsa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dcgsa/lilac.yaml b/prepare/r-dcgsa/lilac.yaml new file mode 100644 index 0000000000..f004072375 --- /dev/null +++ b/prepare/r-dcgsa/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +update_on: +- regex: dcGSA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/dcGSA diff --git a/prepare/r-ddct/PKGBUILD b/prepare/r-ddct/PKGBUILD new file mode 100644 index 0000000000..2391984806 --- /dev/null +++ b/prepare/r-ddct/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ddCt +_pkgver=1.50.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-biocgenerics + r-rcolorbrewer + r-xtable +) +optdepends=( + r-runit + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ddct/lilac.py b/prepare/r-ddct/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ddct/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ddct/lilac.yaml b/prepare/r-ddct/lilac.yaml new file mode 100644 index 0000000000..62d7fac707 --- /dev/null +++ b/prepare/r-ddct/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-rcolorbrewer +- r-xtable +update_on: +- regex: ddCt_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ddCt diff --git a/prepare/r-ddpcr/PKGBUILD b/prepare/r-ddpcr/PKGBUILD new file mode 100644 index 0000000000..b906d1f303 --- /dev/null +++ b/prepare/r-ddpcr/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ddpcr +_pkgver=1.15 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis and Visualization of Droplet Digital PCR in R and on the Web' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-dt + r-ggplot2 + r-lazyeval + r-magrittr + r-mixtools + r-plyr + r-readr + r-shiny + r-shinyjs + r-tibble +) +optdepends=( + r-ggextra + r-graphics + r-grid + r-gridextra + r-knitr + r-rmarkdown + r-stats + r-testthat + r-utils +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ddpcr/lilac.py b/prepare/r-ddpcr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ddpcr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ddpcr/lilac.yaml b/prepare/r-ddpcr/lilac.yaml new file mode 100644 index 0000000000..9126be9b3c --- /dev/null +++ b/prepare/r-ddpcr/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-dt +- r-ggplot2 +- r-lazyeval +- r-magrittr +- r-mixtools +- r-plyr +- r-readr +- r-shiny +- r-shinyjs +- r-tibble +update_on: +- regex: ddpcr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ddpcr diff --git a/prepare/r-ddpcrclust/PKGBUILD b/prepare/r-ddpcrclust/PKGBUILD new file mode 100644 index 0000000000..9fc2cd8aba --- /dev/null +++ b/prepare/r-ddpcrclust/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ddPCRclust +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clustering algorithm for ddPCR data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-clue + r-flowcore + r-flowdensity + r-flowpeaks + r-ggplot2 + r-openxlsx + r-plotrix + r-r.utils + r-samspectral +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ddpcrclust/lilac.py b/prepare/r-ddpcrclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ddpcrclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ddpcrclust/lilac.yaml b/prepare/r-ddpcrclust/lilac.yaml new file mode 100644 index 0000000000..01f806e631 --- /dev/null +++ b/prepare/r-ddpcrclust/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clue +- r-flowcore +- r-flowdensity +- r-flowpeaks +- r-ggplot2 +- r-openxlsx +- r-plotrix +- r-r.utils +- r-samspectral +update_on: +- regex: ddPCRclust_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ddPCRclust diff --git a/prepare/r-ddrtree/PKGBUILD b/prepare/r-ddrtree/PKGBUILD new file mode 100644 index 0000000000..5162100475 --- /dev/null +++ b/prepare/r-ddrtree/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=DDRTree +_pkgver=0.1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Learning Principal Graphs with DDRTree' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bh + r-irlba + r-rcpp + r-rcppeigen +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ddrtree/lilac.py b/prepare/r-ddrtree/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ddrtree/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ddrtree/lilac.yaml b/prepare/r-ddrtree/lilac.yaml new file mode 100644 index 0000000000..daee8e8b0e --- /dev/null +++ b/prepare/r-ddrtree/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-irlba +- r-rcpp +- r-rcppeigen +update_on: +- regex: DDRTree_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=DDRTree diff --git a/prepare/r-dearseq/PKGBUILD b/prepare/r-dearseq/PKGBUILD new file mode 100644 index 0000000000..c37ff4c8ed --- /dev/null +++ b/prepare/r-dearseq/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dearseq +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential Expression Analysis for RNA-seq data through a robust variance component test' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-matrixstats + r-patchwork + r-pbapply + r-statmod + r-survey + r-viridislite +) +optdepends=( + r-biobase + r-biocmanager + r-biocset + r-covr + r-deseq2 + r-edger + r-geoquery + r-gsa + r-knitr + r-limma + r-readxl + r-rmarkdown + r-s4vectors + r-summarizedexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dearseq/lilac.py b/prepare/r-dearseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dearseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dearseq/lilac.yaml b/prepare/r-dearseq/lilac.yaml new file mode 100644 index 0000000000..355b5db3cd --- /dev/null +++ b/prepare/r-dearseq/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-matrixstats +- r-patchwork +- r-pbapply +- r-statmod +- r-survey +- r-viridislite +update_on: +- regex: dearseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/dearseq diff --git a/prepare/r-debcam/PKGBUILD b/prepare/r-debcam/PKGBUILD new file mode 100644 index 0000000000..14adedde38 --- /dev/null +++ b/prepare/r-debcam/PKGBUILD @@ -0,0 +1,46 @@ +# system requirements: Java (>= 1.8) +# Maintainer: Guoyi Zhang + +_pkgname=debCAM +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Deconvolution by Convex Analysis of Mixtures' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-apcluster + r-biobase + r-biocparallel + r-corpcor + r-dmwr2 + r-geometry + r-nmf + r-nnls + r-pcapp + r-rjava + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-geoquery + r-knitr + r-rgl + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-debcam/lilac.py b/prepare/r-debcam/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-debcam/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-debcam/lilac.yaml b/prepare/r-debcam/lilac.yaml new file mode 100644 index 0000000000..9199e85686 --- /dev/null +++ b/prepare/r-debcam/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-apcluster +- r-biobase +- r-biocparallel +- r-corpcor +- r-dmwr2 +- r-geometry +- r-nmf +- r-nnls +- r-pcapp +- r-rjava +- r-summarizedexperiment +update_on: +- regex: debCAM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/debCAM diff --git a/prepare/r-debrowser/PKGBUILD b/prepare/r-debrowser/PKGBUILD new file mode 100644 index 0000000000..2bd5e26378 --- /dev/null +++ b/prepare/r-debrowser/PKGBUILD @@ -0,0 +1,66 @@ +# Maintainer: Guoyi Zhang + +_pkgname=debrowser +_pkgver=1.22.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive Differential Expresion Analysis Browser' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotate + r-annotationdbi + r-apeglm + r-ashr + r-clusterprofiler + r-colourpicker + r-deseq2 + r-dose + r-dt + r-edger + r-enrichplot + r-genomicranges + r-ggplot2 + r-gplots + r-harman + r-heatmaply + r-igraph + r-iranges + r-jsonlite + r-limma + r-org.hs.eg.db + r-org.mm.eg.db + r-pathview + r-plotly + r-rcolorbrewer + r-rcurl + r-reshape2 + r-s4vectors + r-shiny + r-shinybs + r-shinydashboard + r-shinyjs + r-stringi + r-summarizedexperiment + r-sva +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-debrowser/lilac.py b/prepare/r-debrowser/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-debrowser/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-debrowser/lilac.yaml b/prepare/r-debrowser/lilac.yaml new file mode 100644 index 0000000000..d5b4d52987 --- /dev/null +++ b/prepare/r-debrowser/lilac.yaml @@ -0,0 +1,44 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-apeglm +- r-ashr +- r-clusterprofiler +- r-colourpicker +- r-deseq2 +- r-dose +- r-dt +- r-edger +- r-enrichplot +- r-genomicranges +- r-ggplot2 +- r-gplots +- r-harman +- r-heatmaply +- r-igraph +- r-iranges +- r-jsonlite +- r-limma +- r-org.hs.eg.db +- r-org.mm.eg.db +- r-pathview +- r-plotly +- r-rcolorbrewer +- r-rcurl +- r-reshape2 +- r-s4vectors +- r-shiny +- r-shinybs +- r-shinydashboard +- r-shinyjs +- r-stringi +- r-summarizedexperiment +- r-sva +update_on: +- regex: debrowser_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/debrowser diff --git a/prepare/r-decipher/PKGBUILD b/prepare/r-decipher/PKGBUILD new file mode 100644 index 0000000000..4532104ac7 --- /dev/null +++ b/prepare/r-decipher/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DECIPHER +_pkgver=2.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for curating, analyzing, and manipulating biological sequences' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-dbi + r-iranges + r-rsqlite + r-s4vectors + r-xvector +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-decipher/lilac.py b/prepare/r-decipher/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-decipher/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-decipher/lilac.yaml b/prepare/r-decipher/lilac.yaml new file mode 100644 index 0000000000..b77bd79e66 --- /dev/null +++ b/prepare/r-decipher/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-dbi +- r-iranges +- r-rsqlite +- r-s4vectors +- r-xvector +update_on: +- regex: DECIPHER_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DECIPHER diff --git a/prepare/r-deco/PKGBUILD b/prepare/r-deco/PKGBUILD new file mode 100644 index 0000000000..e8e7527f2c --- /dev/null +++ b/prepare/r-deco/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=deco +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Decomposing Heterogeneous Cohorts using Omic Data Profiling' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ade4 + r-annotationdbi + r-biobase + r-biocparallel + r-biocstyle + r-gdata + r-ggplot2 + r-gplots + r-gridextra + r-limma + r-locfit + r-made4 + r-rcolorbrewer + r-reshape2 + r-scatterplot3d + r-sfsmisc + r-summarizedexperiment +) +optdepends=( + r-curatedtcgadata + r-homo.sapiens + r-knitr + r-multiassayexperiment + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-deco/lilac.py b/prepare/r-deco/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-deco/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-deco/lilac.yaml b/prepare/r-deco/lilac.yaml new file mode 100644 index 0000000000..dfde58c70d --- /dev/null +++ b/prepare/r-deco/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ade4 +- r-annotationdbi +- r-biobase +- r-biocparallel +- r-biocstyle +- r-gdata +- r-ggplot2 +- r-gplots +- r-gridextra +- r-limma +- r-locfit +- r-made4 +- r-rcolorbrewer +- r-reshape2 +- r-scatterplot3d +- r-sfsmisc +- r-summarizedexperiment +update_on: +- regex: deco_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/deco diff --git a/prepare/r-decomplexdisease/PKGBUILD b/prepare/r-decomplexdisease/PKGBUILD new file mode 100644 index 0000000000..6032961cea --- /dev/null +++ b/prepare/r-decomplexdisease/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DEComplexDisease +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-complexheatmap + r-deseq2 + r-edger + r-rcpp + r-summarizedexperiment +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-decomplexdisease/lilac.py b/prepare/r-decomplexdisease/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-decomplexdisease/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-decomplexdisease/lilac.yaml b/prepare/r-decomplexdisease/lilac.yaml new file mode 100644 index 0000000000..2500aedfb2 --- /dev/null +++ b/prepare/r-decomplexdisease/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-complexheatmap +- r-deseq2 +- r-edger +- r-rcpp +- r-summarizedexperiment +update_on: +- regex: DEComplexDisease_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DEComplexDisease diff --git a/prepare/r-decomptumor2sig/PKGBUILD b/prepare/r-decomptumor2sig/PKGBUILD new file mode 100644 index 0000000000..8d991731da --- /dev/null +++ b/prepare/r-decomptumor2sig/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=decompTumor2Sig +_pkgver=2.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Decomposition of individual tumors into mutational signatures by signature refitting' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-bsgenome.hsapiens.ucsc.hg19 + r-data.table + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggseqlogo + r-gridextra + r-plyr + r-quadprog + r-readxl + r-s4vectors + r-summarizedexperiment + r-txdb.hsapiens.ucsc.hg19.knowngene + r-variantannotation +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-decomptumor2sig/lilac.py b/prepare/r-decomptumor2sig/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-decomptumor2sig/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-decomptumor2sig/lilac.yaml b/prepare/r-decomptumor2sig/lilac.yaml new file mode 100644 index 0000000000..c57eb03b24 --- /dev/null +++ b/prepare/r-decomptumor2sig/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-bsgenome.hsapiens.ucsc.hg19 +- r-data.table +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-ggseqlogo +- r-gridextra +- r-plyr +- r-quadprog +- r-readxl +- r-s4vectors +- r-summarizedexperiment +- r-txdb.hsapiens.ucsc.hg19.knowngene +- r-variantannotation +update_on: +- regex: decompTumor2Sig_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/decompTumor2Sig diff --git a/prepare/r-deconrnaseq/PKGBUILD b/prepare/r-deconrnaseq/PKGBUILD new file mode 100644 index 0000000000..f5baae3c77 --- /dev/null +++ b/prepare/r-deconrnaseq/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DeconRNASeq +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-limsolve + r-pcamethods +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-deconrnaseq/lilac.py b/prepare/r-deconrnaseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-deconrnaseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-deconrnaseq/lilac.yaml b/prepare/r-deconrnaseq/lilac.yaml new file mode 100644 index 0000000000..247d02b139 --- /dev/null +++ b/prepare/r-deconrnaseq/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-limsolve +- r-pcamethods +update_on: +- regex: DeconRNASeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DeconRNASeq diff --git a/prepare/r-decontam/PKGBUILD b/prepare/r-decontam/PKGBUILD new file mode 100644 index 0000000000..2653e8596d --- /dev/null +++ b/prepare/r-decontam/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=decontam +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identify Contaminants in Marker-gene and Metagenomics Sequencing Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ggplot2 + r-reshape2 +) +optdepends=( + r-biocstyle + r-knitr + r-phyloseq + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-decontam/lilac.py b/prepare/r-decontam/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-decontam/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-decontam/lilac.yaml b/prepare/r-decontam/lilac.yaml new file mode 100644 index 0000000000..b960c49249 --- /dev/null +++ b/prepare/r-decontam/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-reshape2 +update_on: +- regex: decontam_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/decontam diff --git a/prepare/r-deconvr/PKGBUILD b/prepare/r-deconvr/PKGBUILD new file mode 100644 index 0000000000..e1dc247862 --- /dev/null +++ b/prepare/r-deconvr/PKGBUILD @@ -0,0 +1,58 @@ +# Maintainer: Guoyi Zhang + +_pkgname=deconvR +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Simulation and Deconvolution of Omic Profiles' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-assertthat + r-biocgenerics + r-data.table + r-dplyr + r-e1071 + r-foreach + r-genomicranges + r-iranges + r-magrittr + r-matrixstats + r-methylkit + r-nnls + r-quadprog + r-rsq + r-s4vectors + r-tidyr +) +optdepends=( + r-biocstyle + r-covr + r-devtools + r-doparallel + r-ggplot2 + r-granulator + r-knitr + r-parallel + r-refmanager + r-reshape2 + r-rmarkdown + r-roxygen2 + r-sessioninfo + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-deconvr/lilac.py b/prepare/r-deconvr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-deconvr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-deconvr/lilac.yaml b/prepare/r-deconvr/lilac.yaml new file mode 100644 index 0000000000..18aea280b0 --- /dev/null +++ b/prepare/r-deconvr/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biocgenerics +- r-data.table +- r-dplyr +- r-e1071 +- r-foreach +- r-genomicranges +- r-iranges +- r-magrittr +- r-matrixstats +- r-methylkit +- r-nnls +- r-quadprog +- r-rsq +- r-s4vectors +- r-tidyr +update_on: +- regex: deconvR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/deconvR diff --git a/prepare/r-decoupler/PKGBUILD b/prepare/r-decoupler/PKGBUILD new file mode 100644 index 0000000000..359d9387e5 --- /dev/null +++ b/prepare/r-decoupler/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=decoupleR +_pkgver=2.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='decoupleR: Inferring biological activities from omics data using a collection of methods' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-aucell + r-broom + r-dplyr + r-fgsea + r-gsva + r-magrittr + r-purrr + r-ranger + r-rlang + r-robustrankaggreg + r-speedglm + r-stringr + r-summarizedexperiment + r-tibble + r-tidyr + r-tidyselect + r-viper + r-withr +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-pkgdown + r-refmanager + r-rmarkdown + r-roxygen2 + r-sessioninfo + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-decoupler/lilac.py b/prepare/r-decoupler/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-decoupler/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-decoupler/lilac.yaml b/prepare/r-decoupler/lilac.yaml new file mode 100644 index 0000000000..518f9c4ac3 --- /dev/null +++ b/prepare/r-decoupler/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aucell +- r-broom +- r-dplyr +- r-fgsea +- r-gsva +- r-magrittr +- r-purrr +- r-ranger +- r-rlang +- r-robustrankaggreg +- r-speedglm +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-tidyr +- r-tidyselect +- r-viper +- r-withr +update_on: +- regex: decoupleR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/decoupleR diff --git a/prepare/r-deepbluer/PKGBUILD b/prepare/r-deepbluer/PKGBUILD new file mode 100644 index 0000000000..0d7fd95ce0 --- /dev/null +++ b/prepare/r-deepbluer/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DeepBlueR +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='DeepBlueR' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-diffr + r-dplyr + r-filehash + r-foreach + r-genomeinfodb + r-genomicranges + r-r.utils + r-rcurl + r-rjson + r-rtracklayer + r-settings + r-stringr + r-withr + r-xml +) +optdepends=( + r-ggplot2 + r-gplots + r-gviz + r-knitr + r-lola + r-matrixstats + r-rcolorbrewer + r-rmarkdown + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-deepbluer/lilac.py b/prepare/r-deepbluer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-deepbluer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-deepbluer/lilac.yaml b/prepare/r-deepbluer/lilac.yaml new file mode 100644 index 0000000000..3ccfe0702c --- /dev/null +++ b/prepare/r-deepbluer/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-diffr +- r-dplyr +- r-filehash +- r-foreach +- r-genomeinfodb +- r-genomicranges +- r-r.utils +- r-rcurl +- r-rjson +- r-rtracklayer +- r-settings +- r-stringr +- r-withr +- r-xml +update_on: +- regex: DeepBlueR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DeepBlueR diff --git a/prepare/r-deeppincs/PKGBUILD b/prepare/r-deeppincs/PKGBUILD new file mode 100644 index 0000000000..1dd1f66de0 --- /dev/null +++ b/prepare/r-deeppincs/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DeepPINCS +_pkgver=1.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Protein Interactions and Networks with Compounds based on Sequences using Deep Learning' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-catencoders + r-keras + r-matlab + r-prroc + r-purrr + r-rcdk + r-reticulate + r-stringdist + r-tensorflow + r-tokenizers + r-ttgsea + r-webchem +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-deeppincs/lilac.py b/prepare/r-deeppincs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-deeppincs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-deeppincs/lilac.yaml b/prepare/r-deeppincs/lilac.yaml new file mode 100644 index 0000000000..70e461fd5e --- /dev/null +++ b/prepare/r-deeppincs/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-catencoders +- r-keras +- r-matlab +- r-prroc +- r-purrr +- r-rcdk +- r-reticulate +- r-stringdist +- r-tensorflow +- r-tokenizers +- r-ttgsea +- r-webchem +update_on: +- regex: DeepPINCS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DeepPINCS diff --git a/prepare/r-deepsnv/PKGBUILD b/prepare/r-deepsnv/PKGBUILD new file mode 100644 index 0000000000..907074ccd3 --- /dev/null +++ b/prepare/r-deepsnv/PKGBUILD @@ -0,0 +1,39 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=deepSNV +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detection of subclonal SNVs in deep sequencing data.' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-genomicranges + r-iranges + r-rhtslib + r-summarizedexperiment + r-variantannotation + r-vgam +) +optdepends=( + r-knitr + r-rcolorbrewer + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-deepsnv/lilac.py b/prepare/r-deepsnv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-deepsnv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-deepsnv/lilac.yaml b/prepare/r-deepsnv/lilac.yaml new file mode 100644 index 0000000000..1f0aff339b --- /dev/null +++ b/prepare/r-deepsnv/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-genomicranges +- r-iranges +- r-rhtslib +- r-summarizedexperiment +- r-variantannotation +- r-vgam +update_on: +- regex: deepSNV_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/deepSNV diff --git a/prepare/r-deformats/PKGBUILD b/prepare/r-deformats/PKGBUILD new file mode 100644 index 0000000000..8c64f4d59b --- /dev/null +++ b/prepare/r-deformats/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DEFormats +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential gene expression data formats converter' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-checkmate + r-data.table + r-deseq2 + r-edger + r-genomicranges + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-deformats/lilac.py b/prepare/r-deformats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-deformats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-deformats/lilac.yaml b/prepare/r-deformats/lilac.yaml new file mode 100644 index 0000000000..08d00924c2 --- /dev/null +++ b/prepare/r-deformats/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-checkmate +- r-data.table +- r-deseq2 +- r-edger +- r-genomicranges +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: DEFormats_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DEFormats diff --git a/prepare/r-degnorm/PKGBUILD b/prepare/r-degnorm/PKGBUILD new file mode 100644 index 0000000000..c945cd8396 --- /dev/null +++ b/prepare/r-degnorm/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DegNorm +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='DegNorm: degradation normalization for RNA-seq data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-data.table + r-doparallel + r-foreach + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-heatmaply + r-iranges + r-plotly + r-plyr + r-rcpp + r-rcpparmadillo + r-rsamtools + r-s4vectors + r-viridis +) +optdepends=( + r-formatr + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-degnorm/lilac.py b/prepare/r-degnorm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-degnorm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-degnorm/lilac.yaml b/prepare/r-degnorm/lilac.yaml new file mode 100644 index 0000000000..1508c129c0 --- /dev/null +++ b/prepare/r-degnorm/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-doparallel +- r-foreach +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-heatmaply +- r-iranges +- r-plotly +- r-plyr +- r-rcpp +- r-rcpparmadillo +- r-rsamtools +- r-s4vectors +- r-viridis +update_on: +- regex: DegNorm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DegNorm diff --git a/prepare/r-degraph/PKGBUILD b/prepare/r-degraph/PKGBUILD new file mode 100644 index 0000000000..319ea82496 --- /dev/null +++ b/prepare/r-degraph/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DEGraph +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Two-sample tests on a graph' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-graph + r-kegggraph + r-mvtnorm + r-ncigraph + r-r.methodss3 + r-r.utils + r-rbgl + r-rgraphviz + r-rrcov +) +optdepends=( + r-corpcor + r-fields + r-graph + r-kegggraph + r-lattice + r-marray + r-ncigraph + r-rbgl + r-rgraphviz + r-rrcov +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-degraph/lilac.py b/prepare/r-degraph/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-degraph/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-degraph/lilac.yaml b/prepare/r-degraph/lilac.yaml new file mode 100644 index 0000000000..222b03b1a6 --- /dev/null +++ b/prepare/r-degraph/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +- r-kegggraph +- r-mvtnorm +- r-ncigraph +- r-r.methodss3 +- r-r.utils +- r-rbgl +- r-rgraphviz +- r-rrcov +update_on: +- regex: DEGraph_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DEGraph diff --git a/prepare/r-degreport/PKGBUILD b/prepare/r-degreport/PKGBUILD new file mode 100644 index 0000000000..337be462f6 --- /dev/null +++ b/prepare/r-degreport/PKGBUILD @@ -0,0 +1,64 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DEGreport +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Report of DEG analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-biocgenerics + r-broom + r-circlize + r-complexheatmap + r-consensusclusterplus + r-cowplot + r-deseq2 + r-dplyr + r-edger + r-ggdendro + r-ggplot2 + r-ggrepel + r-knitr + r-lasso2 + r-logging + r-magrittr + r-nozzle.r1 + r-psych + r-rcolorbrewer + r-reshape + r-rlang + r-s4vectors + r-scales + r-stringr + r-summarizedexperiment + r-tibble + r-tidyr +) +optdepends=( + r-annotationdbi + r-biocstyle + r-limma + r-pheatmap + r-rmarkdown + r-statmod + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-degreport/lilac.py b/prepare/r-degreport/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-degreport/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-degreport/lilac.yaml b/prepare/r-degreport/lilac.yaml new file mode 100644 index 0000000000..7ed2b24d51 --- /dev/null +++ b/prepare/r-degreport/lilac.yaml @@ -0,0 +1,37 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-broom +- r-circlize +- r-complexheatmap +- r-consensusclusterplus +- r-cowplot +- r-deseq2 +- r-dplyr +- r-edger +- r-ggdendro +- r-ggplot2 +- r-ggrepel +- r-knitr +- r-lasso2 +- r-logging +- r-magrittr +- r-nozzle.r1 +- r-psych +- r-rcolorbrewer +- r-reshape +- r-rlang +- r-s4vectors +- r-scales +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-tidyr +update_on: +- regex: DEGreport_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DEGreport diff --git a/prepare/r-degseq/PKGBUILD b/prepare/r-degseq/PKGBUILD new file mode 100644 index 0000000000..0926cbf2bd --- /dev/null +++ b/prepare/r-degseq/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DEGseq +_pkgver=1.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identify Differentially Expressed Genes from RNA-seq data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-qvalue +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-degseq/lilac.py b/prepare/r-degseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-degseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-degseq/lilac.yaml b/prepare/r-degseq/lilac.yaml new file mode 100644 index 0000000000..b3f5fc209d --- /dev/null +++ b/prepare/r-degseq/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-qvalue +update_on: +- regex: DEGseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DEGseq diff --git a/prepare/r-delaporte/PKGBUILD b/prepare/r-delaporte/PKGBUILD new file mode 100644 index 0000000000..643a5fe182 --- /dev/null +++ b/prepare/r-delaporte/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Delaporte +_pkgver=8.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Functions for the Delaporte Distribution' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-delaporte/lilac.py b/prepare/r-delaporte/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-delaporte/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-delaporte/lilac.yaml b/prepare/r-delaporte/lilac.yaml new file mode 100644 index 0000000000..2f1efb4684 --- /dev/null +++ b/prepare/r-delaporte/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Delaporte_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Delaporte diff --git a/prepare/r-delayedarray/PKGBUILD b/prepare/r-delayedarray/PKGBUILD new file mode 100644 index 0000000000..1b65582178 --- /dev/null +++ b/prepare/r-delayedarray/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DelayedArray +_pkgver=0.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A unified framework for working transparently with on-disk and in-memory array-like datasets' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-iranges + r-matrixgenerics + r-s4vectors +) +optdepends=( + r-airway + r-biocparallel + r-biocstyle + r-delayedmatrixstats + r-genefilter + r-hdf5array + r-knitr + r-lobstr + r-rmarkdown + r-runit + r-summarizedexperiment +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-delayedarray/lilac.py b/prepare/r-delayedarray/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-delayedarray/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-delayedarray/lilac.yaml b/prepare/r-delayedarray/lilac.yaml new file mode 100644 index 0000000000..f620d34a8c --- /dev/null +++ b/prepare/r-delayedarray/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-iranges +- r-matrixgenerics +- r-s4vectors +update_on: +- regex: DelayedArray_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DelayedArray diff --git a/prepare/r-delayeddataframe/PKGBUILD b/prepare/r-delayeddataframe/PKGBUILD new file mode 100644 index 0000000000..de5a97d69f --- /dev/null +++ b/prepare/r-delayeddataframe/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DelayedDataFrame +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Delayed operation on DataFrame using standard DataFrame metaphor' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-delayedarray + r-s4vectors +) +optdepends=( + r-gdsarray + r-knitr + r-rmarkdown + r-seqarray + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-delayeddataframe/lilac.py b/prepare/r-delayeddataframe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-delayeddataframe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-delayeddataframe/lilac.yaml b/prepare/r-delayeddataframe/lilac.yaml new file mode 100644 index 0000000000..af9f5829e7 --- /dev/null +++ b/prepare/r-delayeddataframe/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-delayedarray +- r-s4vectors +update_on: +- regex: DelayedDataFrame_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DelayedDataFrame diff --git a/prepare/r-delayedmatrixstats/PKGBUILD b/prepare/r-delayedmatrixstats/PKGBUILD new file mode 100644 index 0000000000..fe01e2f476 --- /dev/null +++ b/prepare/r-delayedmatrixstats/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DelayedMatrixStats +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-delayedarray + r-iranges + r-matrixgenerics + r-matrixstats + r-s4vectors + r-sparsematrixstats +) +optdepends=( + r-biocstyle + r-covr + r-hdf5array + r-knitr + r-microbenchmark + r-profmem + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-delayedmatrixstats/lilac.py b/prepare/r-delayedmatrixstats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-delayedmatrixstats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-delayedmatrixstats/lilac.yaml b/prepare/r-delayedmatrixstats/lilac.yaml new file mode 100644 index 0000000000..2fc32d9cf8 --- /dev/null +++ b/prepare/r-delayedmatrixstats/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-delayedarray +- r-iranges +- r-matrixgenerics +- r-matrixstats +- r-s4vectors +- r-sparsematrixstats +update_on: +- regex: DelayedMatrixStats_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DelayedMatrixStats diff --git a/prepare/r-delayedrandomarray/PKGBUILD b/prepare/r-delayedrandomarray/PKGBUILD new file mode 100644 index 0000000000..e10d7a1d70 --- /dev/null +++ b/prepare/r-delayedrandomarray/PKGBUILD @@ -0,0 +1,38 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=DelayedRandomArray +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Delayed Arrays of Random Values' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bh + r-delayedarray + r-dqrng + r-rcpp +) +optdepends=( + r-biocstyle + r-knitr + r-matrix + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-delayedrandomarray/lilac.py b/prepare/r-delayedrandomarray/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-delayedrandomarray/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-delayedrandomarray/lilac.yaml b/prepare/r-delayedrandomarray/lilac.yaml new file mode 100644 index 0000000000..5878e49a88 --- /dev/null +++ b/prepare/r-delayedrandomarray/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-delayedarray +- r-dqrng +- r-rcpp +update_on: +- regex: DelayedRandomArray_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DelayedRandomArray diff --git a/prepare/r-delayedtensor/PKGBUILD b/prepare/r-delayedtensor/PKGBUILD new file mode 100644 index 0000000000..58d2e5e6c2 --- /dev/null +++ b/prepare/r-delayedtensor/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DelayedTensor +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R package for sparse and out-of-core arithmetic and decomposition of Tensor' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocsingular + r-delayedarray + r-delayedrandomarray + r-einsum + r-hdf5array + r-irlba + r-rtensor +) +optdepends=( + r-biocstyle + r-dplyr + r-knitr + r-magrittr + r-markdown + r-reticulate + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-delayedtensor/lilac.py b/prepare/r-delayedtensor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-delayedtensor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-delayedtensor/lilac.yaml b/prepare/r-delayedtensor/lilac.yaml new file mode 100644 index 0000000000..48f434acbe --- /dev/null +++ b/prepare/r-delayedtensor/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocsingular +- r-delayedarray +- r-delayedrandomarray +- r-einsum +- r-hdf5array +- r-irlba +- r-rtensor +update_on: +- regex: DelayedTensor_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DelayedTensor diff --git a/prepare/r-deldir/PKGBUILD b/prepare/r-deldir/PKGBUILD new file mode 100644 index 0000000000..0b3c56ab53 --- /dev/null +++ b/prepare/r-deldir/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=deldir +_pkgver=1.0-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Delaunay Triangulation and Dirichlet (Voronoi) Tessellation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-polyclip +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-deldir/lilac.py b/prepare/r-deldir/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-deldir/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-deldir/lilac.yaml b/prepare/r-deldir/lilac.yaml new file mode 100644 index 0000000000..590b0e4723 --- /dev/null +++ b/prepare/r-deldir/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: deldir_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=deldir diff --git a/prepare/r-deltacapturec/PKGBUILD b/prepare/r-deltacapturec/PKGBUILD new file mode 100644 index 0000000000..24781ba5f6 --- /dev/null +++ b/prepare/r-deltacapturec/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=deltaCaptureC +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='This Package Discovers Meso-scale Chromatin Remodeling from 3C Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-deseq2 + r-genomicranges + r-ggplot2 + r-iranges + r-summarizedexperiment + r-tictoc +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-deltacapturec/lilac.py b/prepare/r-deltacapturec/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-deltacapturec/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-deltacapturec/lilac.yaml b/prepare/r-deltacapturec/lilac.yaml new file mode 100644 index 0000000000..a34fded1f4 --- /dev/null +++ b/prepare/r-deltacapturec/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-deseq2 +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-summarizedexperiment +- r-tictoc +update_on: +- regex: deltaCaptureC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/deltaCaptureC diff --git a/prepare/r-deltagseg/PKGBUILD b/prepare/r-deltagseg/PKGBUILD new file mode 100644 index 0000000000..0e2a26b80f --- /dev/null +++ b/prepare/r-deltagseg/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=deltaGseg +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='deltaGseg' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-changepoint + r-fbasics + r-ggplot2 + r-pvclust + r-reshape + r-scales + r-tseries + r-wavethresh +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-deltagseg/lilac.py b/prepare/r-deltagseg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-deltagseg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-deltagseg/lilac.yaml b/prepare/r-deltagseg/lilac.yaml new file mode 100644 index 0000000000..fd03951f34 --- /dev/null +++ b/prepare/r-deltagseg/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-changepoint +- r-fbasics +- r-ggplot2 +- r-pvclust +- r-reshape +- r-scales +- r-tseries +- r-wavethresh +update_on: +- regex: deltaGseg_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/deltaGseg diff --git a/prepare/r-demand/PKGBUILD b/prepare/r-demand/PKGBUILD new file mode 100644 index 0000000000..a40c471be7 --- /dev/null +++ b/prepare/r-demand/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DeMAND +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='DeMAND' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-demand/lilac.py b/prepare/r-demand/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-demand/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-demand/lilac.yaml b/prepare/r-demand/lilac.yaml new file mode 100644 index 0000000000..6bcbdc43c8 --- /dev/null +++ b/prepare/r-demand/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: DeMAND_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DeMAND diff --git a/prepare/r-demixt/PKGBUILD b/prepare/r-demixt/PKGBUILD new file mode 100644 index 0000000000..86364f5d8b --- /dev/null +++ b/prepare/r-demixt/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DeMixT +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-base64enc + r-ggplot2 + r-knitr + r-matrixcalc + r-matrixstats + r-rcpp + r-rmarkdown + r-summarizedexperiment + r-truncdist +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-demixt/lilac.py b/prepare/r-demixt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-demixt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-demixt/lilac.yaml b/prepare/r-demixt/lilac.yaml new file mode 100644 index 0000000000..6db8b57016 --- /dev/null +++ b/prepare/r-demixt/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-ggplot2 +- r-knitr +- r-matrixcalc +- r-matrixstats +- r-rcpp +- r-rmarkdown +- r-summarizedexperiment +- r-truncdist +update_on: +- regex: DeMixT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DeMixT diff --git a/prepare/r-dendextend/PKGBUILD b/prepare/r-dendextend/PKGBUILD new file mode 100644 index 0000000000..e623116238 --- /dev/null +++ b/prepare/r-dendextend/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dendextend +_pkgver=1.15.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Extending 'dendrogram' Functionality in R" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-magrittr + r-viridis +) +optdepends=( + r-ape + r-circlize + r-cluster + r-colorspace + r-corrplot + r-covr + r-data.table + r-dendroextras + r-dendser + r-dynamictreecut + r-fpc + r-ggdendro + r-gplots + r-heatmaply + r-hmisc + r-knitr + r-mass + r-microbenchmark + r-pvclust + r-rmarkdown + r-rpart + r-seriation + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dendextend/lilac.py b/prepare/r-dendextend/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dendextend/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dendextend/lilac.yaml b/prepare/r-dendextend/lilac.yaml new file mode 100644 index 0000000000..a933f7c80b --- /dev/null +++ b/prepare/r-dendextend/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-magrittr +- r-viridis +update_on: +- regex: dendextend_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dendextend diff --git a/prepare/r-densestbayes/PKGBUILD b/prepare/r-densestbayes/PKGBUILD new file mode 100644 index 0000000000..6465f21713 --- /dev/null +++ b/prepare/r-densestbayes/PKGBUILD @@ -0,0 +1,34 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=densEstBayes +_pkgver=1.0-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Density Estimation via Bayesian Inference Engines' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bh + r-rcpp + r-rcpparmadillo + r-rcppeigen + r-rcppparallel + r-rstan + r-stanheaders +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-densestbayes/lilac.py b/prepare/r-densestbayes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-densestbayes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-densestbayes/lilac.yaml b/prepare/r-densestbayes/lilac.yaml new file mode 100644 index 0000000000..acb3cb007f --- /dev/null +++ b/prepare/r-densestbayes/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-rcpp +- r-rcpparmadillo +- r-rcppeigen +- r-rcppparallel +- r-rstan +- r-stanheaders +update_on: +- regex: densEstBayes_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=densEstBayes diff --git a/prepare/r-densityclust/PKGBUILD b/prepare/r-densityclust/PKGBUILD new file mode 100644 index 0000000000..2d3599ace3 --- /dev/null +++ b/prepare/r-densityclust/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=densityClust +_pkgver=0.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clustering by Fast Search and Find of Density Peaks' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-fnn + r-ggplot2 + r-ggrepel + r-gridextra + r-rcolorbrewer + r-rcpp + r-rtsne +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-densityclust/lilac.py b/prepare/r-densityclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-densityclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-densityclust/lilac.yaml b/prepare/r-densityclust/lilac.yaml new file mode 100644 index 0000000000..b45034d706 --- /dev/null +++ b/prepare/r-densityclust/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fnn +- r-ggplot2 +- r-ggrepel +- r-gridextra +- r-rcolorbrewer +- r-rcpp +- r-rtsne +update_on: +- regex: densityClust_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=densityClust diff --git a/prepare/r-densvis/PKGBUILD b/prepare/r-densvis/PKGBUILD new file mode 100644 index 0000000000..1a976c15e9 --- /dev/null +++ b/prepare/r-densvis/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=densvis +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-assertthat + r-basilisk + r-rcpp + r-reticulate +) +optdepends=( + r-biocstyle + r-ggplot2 + r-knitr + r-rmarkdown + r-rtsne + r-testthat + r-uwot +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-densvis/lilac.py b/prepare/r-densvis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-densvis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-densvis/lilac.yaml b/prepare/r-densvis/lilac.yaml new file mode 100644 index 0000000000..698e092707 --- /dev/null +++ b/prepare/r-densvis/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-basilisk +- r-rcpp +- r-reticulate +update_on: +- regex: densvis_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/densvis diff --git a/prepare/r-deoptimr/PKGBUILD b/prepare/r-deoptimr/PKGBUILD new file mode 100644 index 0000000000..bd4e840bce --- /dev/null +++ b/prepare/r-deoptimr/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DEoptimR +_pkgver=1.0-10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential Evolution Optimization in Pure R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-robustbase +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-deoptimr/lilac.py b/prepare/r-deoptimr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-deoptimr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-deoptimr/lilac.yaml b/prepare/r-deoptimr/lilac.yaml new file mode 100644 index 0000000000..9d1f430cb7 --- /dev/null +++ b/prepare/r-deoptimr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: DEoptimR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=DEoptimR diff --git a/prepare/r-dep/PKGBUILD b/prepare/r-dep/PKGBUILD new file mode 100644 index 0000000000..188fdb493e --- /dev/null +++ b/prepare/r-dep/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DEP +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential Enrichment analysis of Proteomics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-assertthat + r-circlize + r-complexheatmap + r-dplyr + r-dt + r-fdrtool + r-ggplot2 + r-ggrepel + r-gridextra + r-imputelcmd + r-limma + r-msnbase + r-purrr + r-rcolorbrewer + r-readr + r-rmarkdown + r-shiny + r-shinydashboard + r-summarizedexperiment + r-tibble + r-tidyr + r-vsn +) +optdepends=( + r-biocstyle + r-enrichr + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dep/lilac.py b/prepare/r-dep/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dep/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dep/lilac.yaml b/prepare/r-dep/lilac.yaml new file mode 100644 index 0000000000..633721f71d --- /dev/null +++ b/prepare/r-dep/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-circlize +- r-complexheatmap +- r-dplyr +- r-dt +- r-fdrtool +- r-ggplot2 +- r-ggrepel +- r-gridextra +- r-imputelcmd +- r-limma +- r-msnbase +- r-purrr +- r-rcolorbrewer +- r-readr +- r-rmarkdown +- r-shiny +- r-shinydashboard +- r-summarizedexperiment +- r-tibble +- r-tidyr +- r-vsn +update_on: +- regex: DEP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DEP diff --git a/prepare/r-depecher/PKGBUILD b/prepare/r-depecher/PKGBUILD new file mode 100644 index 0000000000..d9b6b3fad3 --- /dev/null +++ b/prepare/r-depecher/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DepecheR +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Determination of essential phenotypic elements of clusters in high-dimensional entities' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-beanplot + r-dosnow + r-dplyr + r-fnn + r-foreach + r-ggplot2 + r-gmodels + r-gplots + r-matrixstats + r-mixomics + r-moments + r-rcpp + r-rcppeigen + r-reshape2 + r-robustbase + r-viridis +) +optdepends=( + r-biocstyle + r-knitr + r-reshape2 + r-rmarkdown + r-testthat + r-uwot +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-depecher/lilac.py b/prepare/r-depecher/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-depecher/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-depecher/lilac.yaml b/prepare/r-depecher/lilac.yaml new file mode 100644 index 0000000000..12a191e2e4 --- /dev/null +++ b/prepare/r-depecher/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beanplot +- r-dosnow +- r-dplyr +- r-fnn +- r-foreach +- r-ggplot2 +- r-gmodels +- r-gplots +- r-matrixstats +- r-mixomics +- r-moments +- r-rcpp +- r-rcppeigen +- r-reshape2 +- r-robustbase +- r-viridis +update_on: +- regex: DepecheR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DepecheR diff --git a/prepare/r-depmixs4/PKGBUILD b/prepare/r-depmixs4/PKGBUILD new file mode 100644 index 0000000000..9aa94daf21 --- /dev/null +++ b/prepare/r-depmixs4/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=depmixS4 +_pkgver=1.5-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dependent Mixture Models - Hidden Markov Models of GLMs and Other Distributions in S4' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rsolnp +) +optdepends=( + r-gamlss + r-gamlss.dist + r-rdonlp2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-depmixs4/lilac.py b/prepare/r-depmixs4/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-depmixs4/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-depmixs4/lilac.yaml b/prepare/r-depmixs4/lilac.yaml new file mode 100644 index 0000000000..fde0ccfac3 --- /dev/null +++ b/prepare/r-depmixs4/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rsolnp +update_on: +- regex: depmixS4_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=depmixS4 diff --git a/prepare/r-deqms/PKGBUILD b/prepare/r-deqms/PKGBUILD new file mode 100644 index 0000000000..cad126106e --- /dev/null +++ b/prepare/r-deqms/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DEqMS +_pkgver=1.11.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-ggplot2 + r-limma + r-matrixstats +) +optdepends=( + r-biocstyle + r-experimenthub + r-farms + r-ggrepel + r-knitr + r-lsd + r-markdown + r-plyr + r-reshape2 + r-rmarkdown + r-utils +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-deqms/lilac.py b/prepare/r-deqms/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-deqms/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-deqms/lilac.yaml b/prepare/r-deqms/lilac.yaml new file mode 100644 index 0000000000..34136c4dd7 --- /dev/null +++ b/prepare/r-deqms/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-limma +- r-matrixstats +update_on: +- regex: DEqMS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DEqMS diff --git a/prepare/r-derfinder/PKGBUILD b/prepare/r-derfinder/PKGBUILD new file mode 100644 index 0000000000..4776d67d6b --- /dev/null +++ b/prepare/r-derfinder/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=derfinder +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biocgenerics + r-biocparallel + r-bumphunter + r-derfinderhelper + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicfiles + r-genomicranges + r-hmisc + r-iranges + r-qvalue + r-rsamtools + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocstyle + r-covr + r-derfinderdata + r-derfinderplot + r-deseq2 + r-ggplot2 + r-knitr + r-limma + r-refmanager + r-rmarkdown + r-sessioninfo + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-derfinder/lilac.py b/prepare/r-derfinder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-derfinder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-derfinder/lilac.yaml b/prepare/r-derfinder/lilac.yaml new file mode 100644 index 0000000000..68dc267fc8 --- /dev/null +++ b/prepare/r-derfinder/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-biocparallel +- r-bumphunter +- r-derfinderhelper +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicfiles +- r-genomicranges +- r-hmisc +- r-iranges +- r-qvalue +- r-rsamtools +- r-rtracklayer +- r-s4vectors +update_on: +- regex: derfinder_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/derfinder diff --git a/prepare/r-derfinderhelper/PKGBUILD b/prepare/r-derfinderhelper/PKGBUILD new file mode 100644 index 0000000000..8f88db9f22 --- /dev/null +++ b/prepare/r-derfinderhelper/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=derfinderHelper +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='derfinder helper package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-iranges + r-s4vectors +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-refmanager + r-rmarkdown + r-sessioninfo + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-derfinderhelper/lilac.py b/prepare/r-derfinderhelper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-derfinderhelper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-derfinderhelper/lilac.yaml b/prepare/r-derfinderhelper/lilac.yaml new file mode 100644 index 0000000000..f13a8ffe67 --- /dev/null +++ b/prepare/r-derfinderhelper/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-iranges +- r-s4vectors +update_on: +- regex: derfinderHelper_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/derfinderHelper diff --git a/prepare/r-derfinderplot/PKGBUILD b/prepare/r-derfinderplot/PKGBUILD new file mode 100644 index 0000000000..030af6ca80 --- /dev/null +++ b/prepare/r-derfinderplot/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=derfinderPlot +_pkgver=1.28.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Plotting functions for derfinder' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-derfinder + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggbio + r-ggplot2 + r-iranges + r-limma + r-plyr + r-rcolorbrewer + r-reshape2 + r-s4vectors + r-scales +) +optdepends=( + r-biocstyle + r-biovizbase + r-bumphunter + r-covr + r-derfinderdata + r-knitr + r-org.hs.eg.db + r-refmanager + r-rmarkdown + r-sessioninfo + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-derfinderplot/lilac.py b/prepare/r-derfinderplot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-derfinderplot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-derfinderplot/lilac.yaml b/prepare/r-derfinderplot/lilac.yaml new file mode 100644 index 0000000000..446d807d03 --- /dev/null +++ b/prepare/r-derfinderplot/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-derfinder +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggbio +- r-ggplot2 +- r-iranges +- r-limma +- r-plyr +- r-rcolorbrewer +- r-reshape2 +- r-s4vectors +- r-scales +update_on: +- regex: derfinderPlot_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/derfinderPlot diff --git a/prepare/r-deriv/PKGBUILD b/prepare/r-deriv/PKGBUILD new file mode 100644 index 0000000000..9e81d0bbf1 --- /dev/null +++ b/prepare/r-deriv/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Deriv +_pkgver=4.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Symbolic Differentiation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-deriv/lilac.py b/prepare/r-deriv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-deriv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-deriv/lilac.yaml b/prepare/r-deriv/lilac.yaml new file mode 100644 index 0000000000..1254c7deb9 --- /dev/null +++ b/prepare/r-deriv/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Deriv_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Deriv diff --git a/prepare/r-desc/PKGBUILD b/prepare/r-desc/PKGBUILD new file mode 100644 index 0000000000..6b372e1f2d --- /dev/null +++ b/prepare/r-desc/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=desc +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Manipulate DESCRIPTION Files' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-crayon + r-r6 + r-rprojroot +) +optdepends=( + r-covr + r-gh + r-spelling + r-testthat + r-whoami + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-desc/lilac.py b/prepare/r-desc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-desc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-desc/lilac.yaml b/prepare/r-desc/lilac.yaml new file mode 100644 index 0000000000..ab89a07f1f --- /dev/null +++ b/prepare/r-desc/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-crayon +- r-r6 +- r-rprojroot +update_on: +- regex: desc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=desc diff --git a/prepare/r-descan2/PKGBUILD b/prepare/r-descan2/PKGBUILD new file mode 100644 index 0000000000..e9da1b7527 --- /dev/null +++ b/prepare/r-descan2/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DEScan2 +_pkgver=1.14.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential Enrichment Scan 2' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biocparallel + r-chippeakanno + r-data.table + r-delayedarray + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-glue + r-iranges + r-plyr + r-rcpp + r-rcpparmadillo + r-rtracklayer + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-edaseq + r-edger + r-knitr + r-limma + r-rcolorbrewer + r-rmarkdown + r-ruvseq + r-statmod + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-descan2/lilac.py b/prepare/r-descan2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-descan2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-descan2/lilac.yaml b/prepare/r-descan2/lilac.yaml new file mode 100644 index 0000000000..2cd101ef39 --- /dev/null +++ b/prepare/r-descan2/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-chippeakanno +- r-data.table +- r-delayedarray +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-glue +- r-iranges +- r-plyr +- r-rcpp +- r-rcpparmadillo +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: DEScan2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DEScan2 diff --git a/prepare/r-desctools/PKGBUILD b/prepare/r-desctools/PKGBUILD new file mode 100644 index 0000000000..42a44c44f8 --- /dev/null +++ b/prepare/r-desctools/PKGBUILD @@ -0,0 +1,44 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=DescTools +_pkgver=0.99.44 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Descriptive Statistics' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bh + r-data.table + r-exact + r-expm + r-gld + r-mvtnorm + r-rcpp + r-rstudioapi +) +optdepends=( + r-r.rsp + r-rdcomclient + r-tcltk + r-vgam +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-desctools/lilac.py b/prepare/r-desctools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-desctools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-desctools/lilac.yaml b/prepare/r-desctools/lilac.yaml new file mode 100644 index 0000000000..b401b01a27 --- /dev/null +++ b/prepare/r-desctools/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-data.table +- r-exact +- r-expm +- r-gld +- r-mvtnorm +- r-rcpp +- r-rstudioapi +update_on: +- regex: DescTools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=DescTools diff --git a/prepare/r-deseq2/PKGBUILD b/prepare/r-deseq2/PKGBUILD new file mode 100644 index 0000000000..522b8a4f21 --- /dev/null +++ b/prepare/r-deseq2/PKGBUILD @@ -0,0 +1,58 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DESeq2 +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential gene expression analysis based on the negative binomial distribution' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-genefilter + r-geneplotter + r-genomicranges + r-ggplot2 + r-iranges + r-locfit + r-rcpp + r-rcpparmadillo + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-airway + r-apeglm + r-ashr + r-biocmanager + r-glmgampoi + r-knitr + r-pasilla + r-pbapply + r-pheatmap + r-rcolorbrewer + r-readr + r-rmarkdown + r-testthat + r-tximeta + r-tximport + r-tximportdata + r-vsn +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-deseq2/lilac.py b/prepare/r-deseq2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-deseq2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-deseq2/lilac.yaml b/prepare/r-deseq2/lilac.yaml new file mode 100644 index 0000000000..7ce2b28f10 --- /dev/null +++ b/prepare/r-deseq2/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-genefilter +- r-geneplotter +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-locfit +- r-rcpp +- r-rcpparmadillo +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: DESeq2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DESeq2 diff --git a/prepare/r-desingle/PKGBUILD b/prepare/r-desingle/PKGBUILD new file mode 100644 index 0000000000..79b6fdb24c --- /dev/null +++ b/prepare/r-desingle/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DEsingle +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='DEsingle for detecting three types of differential expression in single-cell RNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bbmle + r-biocparallel + r-gamlss + r-maxlik + r-pscl + r-vgam +) +optdepends=( + r-knitr + r-rmarkdown + r-singlecellexperiment +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-desingle/lilac.py b/prepare/r-desingle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-desingle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-desingle/lilac.yaml b/prepare/r-desingle/lilac.yaml new file mode 100644 index 0000000000..8cdf362386 --- /dev/null +++ b/prepare/r-desingle/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bbmle +- r-biocparallel +- r-gamlss +- r-maxlik +- r-pscl +- r-vgam +update_on: +- regex: DEsingle_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DEsingle diff --git a/prepare/r-desolve/PKGBUILD b/prepare/r-desolve/PKGBUILD new file mode 100644 index 0000000000..2bdb7eceef --- /dev/null +++ b/prepare/r-desolve/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=deSolve +_pkgver=1.30 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Solvers for Initial Value Problems of Differential Equations ('ODE', 'DAE', 'DDE')" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-fme + r-scatterplot3d +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-desolve/lilac.py b/prepare/r-desolve/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-desolve/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-desolve/lilac.yaml b/prepare/r-desolve/lilac.yaml new file mode 100644 index 0000000000..6a40d1028f --- /dev/null +++ b/prepare/r-desolve/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: deSolve_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=deSolve diff --git a/prepare/r-destiny/PKGBUILD b/prepare/r-destiny/PKGBUILD new file mode 100644 index 0000000000..b685772e7d --- /dev/null +++ b/prepare/r-destiny/PKGBUILD @@ -0,0 +1,57 @@ +# system requirements: C++11, jupyter nbconvert (see nbconvertR’s INSTALLfile) +# Maintainer: Guoyi Zhang + +_pkgname=destiny +_pkgver=3.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Creates diffusion maps' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-ggplot.multistats + r-ggplot2 + r-ggthemes + r-irlba + r-knn.covertree + r-pcamethods + r-proxy + r-rcpp + r-rcppeigen + r-rcpphnsw + r-rspectra + r-scales + r-scatterplot3d + r-singlecellexperiment + r-smoother + r-summarizedexperiment + r-tidyr + r-tidyselect + r-vim +) +optdepends=( + r-fnn + r-igraph + r-nbconvertr + r-rgl + r-singlecellexperiment + r-testthat + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-destiny/lilac.py b/prepare/r-destiny/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-destiny/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-destiny/lilac.yaml b/prepare/r-destiny/lilac.yaml new file mode 100644 index 0000000000..e33050c9c0 --- /dev/null +++ b/prepare/r-destiny/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-ggplot.multistats +- r-ggplot2 +- r-ggthemes +- r-irlba +- r-knn.covertree +- r-pcamethods +- r-proxy +- r-rcpp +- r-rcppeigen +- r-rcpphnsw +- r-rspectra +- r-scales +- r-scatterplot3d +- r-singlecellexperiment +- r-smoother +- r-summarizedexperiment +- r-tidyr +- r-tidyselect +- r-vim +update_on: +- regex: destiny_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/destiny diff --git a/prepare/r-desubs/PKGBUILD b/prepare/r-desubs/PKGBUILD new file mode 100644 index 0000000000..fc0e918a1b --- /dev/null +++ b/prepare/r-desubs/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DEsubs +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-circlize + r-deseq2 + r-ebseq + r-edger + r-ggplot2 + r-graph + r-igraph + r-jsonlite + r-limma + r-locfit + r-nbpseq + r-pheatmap + r-rbgl +) +optdepends=( + r-biocgenerics + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-desubs/lilac.py b/prepare/r-desubs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-desubs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-desubs/lilac.yaml b/prepare/r-desubs/lilac.yaml new file mode 100644 index 0000000000..7129c10d1a --- /dev/null +++ b/prepare/r-desubs/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circlize +- r-deseq2 +- r-ebseq +- r-edger +- r-ggplot2 +- r-graph +- r-igraph +- r-jsonlite +- r-limma +- r-locfit +- r-nbpseq +- r-pheatmap +- r-rbgl +update_on: +- regex: DEsubs_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DEsubs diff --git a/prepare/r-detectseparation/PKGBUILD b/prepare/r-detectseparation/PKGBUILD new file mode 100644 index 0000000000..dc0096a396 --- /dev/null +++ b/prepare/r-detectseparation/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=detectseparation +_pkgver=0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detect and Check for Separation and Infinite Maximum Likelihood Estimates' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-lpsolveapi + r-pkgload + r-roi + r-roi.plugin.lpsolve +) +optdepends=( + r-aer + r-brglm2 + r-covr + r-knitr + r-rmarkdown + r-roi.plugin.alabama + r-roi.plugin.ecos + r-roi.plugin.glpk + r-roi.plugin.neos + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-detectseparation/lilac.py b/prepare/r-detectseparation/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-detectseparation/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-detectseparation/lilac.yaml b/prepare/r-detectseparation/lilac.yaml new file mode 100644 index 0000000000..fae387f873 --- /dev/null +++ b/prepare/r-detectseparation/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lpsolveapi +- r-pkgload +- r-roi +- r-roi.plugin.lpsolve +update_on: +- regex: detectseparation_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=detectseparation diff --git a/prepare/r-devtools/PKGBUILD b/prepare/r-devtools/PKGBUILD new file mode 100644 index 0000000000..c86da24325 --- /dev/null +++ b/prepare/r-devtools/PKGBUILD @@ -0,0 +1,66 @@ +# Maintainer: Guoyi Zhang + +_pkgname=devtools +_pkgver=2.4.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools to Make Developing R Packages Easier' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-callr + r-cli + r-desc + r-ellipsis + r-fs + r-httr + r-lifecycle + r-memoise + r-pkgbuild + r-pkgload + r-rcmdcheck + r-remotes + r-rlang + r-roxygen2 + r-rstudioapi + r-rversions + r-sessioninfo + r-testthat + r-usethis + r-withr +) +optdepends=( + r-biocmanager + r-covr + r-curl + r-digest + r-dt + r-foghorn + r-gh + r-gmailr + r-knitr + r-lintr + r-mass + r-mockery + r-pingr + r-pkgdown + r-rhub + r-rmarkdown + r-spelling +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-devtools/lilac.py b/prepare/r-devtools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-devtools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-devtools/lilac.yaml b/prepare/r-devtools/lilac.yaml new file mode 100644 index 0000000000..ffe7d0acac --- /dev/null +++ b/prepare/r-devtools/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-callr +- r-cli +- r-desc +- r-ellipsis +- r-fs +- r-httr +- r-lifecycle +- r-memoise +- r-pkgbuild +- r-pkgload +- r-rcmdcheck +- r-remotes +- r-rlang +- r-roxygen2 +- r-rstudioapi +- r-rversions +- r-sessioninfo +- r-testthat +- r-usethis +- r-withr +update_on: +- regex: devtools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=devtools diff --git a/prepare/r-dewseq/PKGBUILD b/prepare/r-dewseq/PKGBUILD new file mode 100644 index 0000000000..1b390959a5 --- /dev/null +++ b/prepare/r-dewseq/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DEWSeq +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential Expressed Windows Based on Negative Binomial Distribution' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-data.table + r-deseq2 + r-genomeinfodb + r-genomicranges + r-r.utils + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-ihw + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dewseq/lilac.py b/prepare/r-dewseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dewseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dewseq/lilac.yaml b/prepare/r-dewseq/lilac.yaml new file mode 100644 index 0000000000..46f4eedc63 --- /dev/null +++ b/prepare/r-dewseq/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-data.table +- r-deseq2 +- r-genomeinfodb +- r-genomicranges +- r-r.utils +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: DEWSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DEWSeq diff --git a/prepare/r-dexma/PKGBUILD b/prepare/r-dexma/PKGBUILD new file mode 100644 index 0000000000..2a76ce8a4e --- /dev/null +++ b/prepare/r-dexma/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DExMA +_pkgver=1.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential Expression Meta-Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-bnstruct + r-dexmadata + r-geoquery + r-impute + r-limma + r-pheatmap + r-plyr + r-scales + r-snpstats + r-sva + r-swamp +) +optdepends=( + r-biocgenerics + r-biocstyle + r-qpdf + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dexma/lilac.py b/prepare/r-dexma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dexma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dexma/lilac.yaml b/prepare/r-dexma/lilac.yaml new file mode 100644 index 0000000000..0a97ff4c76 --- /dev/null +++ b/prepare/r-dexma/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-bnstruct +- r-dexmadata +- r-geoquery +- r-impute +- r-limma +- r-pheatmap +- r-plyr +- r-scales +- r-snpstats +- r-sva +- r-swamp +update_on: +- regex: DExMA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DExMA diff --git a/prepare/r-dexmadata/PKGBUILD b/prepare/r-dexmadata/PKGBUILD new file mode 100644 index 0000000000..1d2f3be184 --- /dev/null +++ b/prepare/r-dexmadata/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DExMAdata +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data package for DExMA package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dexmadata/lilac.py b/prepare/r-dexmadata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dexmadata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dexmadata/lilac.yaml b/prepare/r-dexmadata/lilac.yaml new file mode 100644 index 0000000000..837ae40cfa --- /dev/null +++ b/prepare/r-dexmadata/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: DExMAdata_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DExMAdata diff --git a/prepare/r-dexseq/PKGBUILD b/prepare/r-dexseq/PKGBUILD new file mode 100644 index 0000000000..6f1a5d39b3 --- /dev/null +++ b/prepare/r-dexseq/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DEXSeq +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Inference of differential exon usage in RNA-Seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-biomart + r-deseq2 + r-genefilter + r-geneplotter + r-genomicranges + r-hwriter + r-iranges + r-rcolorbrewer + r-rsamtools + r-s4vectors + r-statmod + r-stringr + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-genomicfeatures + r-knitr + r-parathyroidse + r-pasilla + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dexseq/lilac.py b/prepare/r-dexseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dexseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dexseq/lilac.yaml b/prepare/r-dexseq/lilac.yaml new file mode 100644 index 0000000000..b5ecb030b0 --- /dev/null +++ b/prepare/r-dexseq/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-biomart +- r-deseq2 +- r-genefilter +- r-geneplotter +- r-genomicranges +- r-hwriter +- r-iranges +- r-rcolorbrewer +- r-rsamtools +- r-s4vectors +- r-statmod +- r-stringr +- r-summarizedexperiment +update_on: +- regex: DEXSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DEXSeq diff --git a/prepare/r-dfp/PKGBUILD b/prepare/r-dfp/PKGBUILD new file mode 100644 index 0000000000..18e6fa0c78 --- /dev/null +++ b/prepare/r-dfp/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DFP +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Selection' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dfp/lilac.py b/prepare/r-dfp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dfp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dfp/lilac.yaml b/prepare/r-dfp/lilac.yaml new file mode 100644 index 0000000000..4db8885753 --- /dev/null +++ b/prepare/r-dfp/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: DFP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DFP diff --git a/prepare/r-dgof/PKGBUILD b/prepare/r-dgof/PKGBUILD new file mode 100644 index 0000000000..305f7e980f --- /dev/null +++ b/prepare/r-dgof/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dgof +_pkgver=1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Discrete Goodness-of-Fit Tests' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dgof/lilac.py b/prepare/r-dgof/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dgof/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dgof/lilac.yaml b/prepare/r-dgof/lilac.yaml new file mode 100644 index 0000000000..7d72e6b21d --- /dev/null +++ b/prepare/r-dgof/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: dgof_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dgof diff --git a/prepare/r-diagram/PKGBUILD b/prepare/r-diagram/PKGBUILD new file mode 100644 index 0000000000..e08b25a1f5 --- /dev/null +++ b/prepare/r-diagram/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=diagram +_pkgver=1.6.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-shape +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-diagram/lilac.py b/prepare/r-diagram/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-diagram/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-diagram/lilac.yaml b/prepare/r-diagram/lilac.yaml new file mode 100644 index 0000000000..a9460bbf9e --- /dev/null +++ b/prepare/r-diagram/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-shape +update_on: +- regex: diagram_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=diagram diff --git a/prepare/r-diagrammer/PKGBUILD b/prepare/r-diagrammer/PKGBUILD new file mode 100644 index 0000000000..ab5e687858 --- /dev/null +++ b/prepare/r-diagrammer/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DiagrammeR +_pkgver=1.0.6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Graph/Network Visualization' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-downloader + r-dplyr + r-glue + r-htmltools + r-htmlwidgets + r-igraph + r-influencer + r-magrittr + r-purrr + r-rcolorbrewer + r-readr + r-rlang + r-rstudioapi + r-scales + r-stringr + r-tibble + r-tidyr + r-viridis + r-visnetwork +) +optdepends=( + r-covr + r-diagrammersvg + r-knitr + r-rmarkdown + r-rsvg + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-diagrammer/lilac.py b/prepare/r-diagrammer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-diagrammer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-diagrammer/lilac.yaml b/prepare/r-diagrammer/lilac.yaml new file mode 100644 index 0000000000..b587cb006b --- /dev/null +++ b/prepare/r-diagrammer/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-downloader +- r-dplyr +- r-glue +- r-htmltools +- r-htmlwidgets +- r-igraph +- r-influencer +- r-magrittr +- r-purrr +- r-rcolorbrewer +- r-readr +- r-rlang +- r-rstudioapi +- r-scales +- r-stringr +- r-tibble +- r-tidyr +- r-viridis +- r-visnetwork +update_on: +- regex: DiagrammeR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=DiagrammeR diff --git a/prepare/r-dialignr/PKGBUILD b/prepare/r-dialignr/PKGBUILD new file mode 100644 index 0000000000..7a54fe414b --- /dev/null +++ b/prepare/r-dialignr/PKGBUILD @@ -0,0 +1,58 @@ +# system requirements: C++14 +# Maintainer: Guoyi Zhang + +_pkgname=DIAlignR +_pkgver=2.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dynamic Programming Based Alignment of MS2 Chromatograms' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-bit64 + r-data.table + r-dbi + r-dplyr + r-ggplot2 + r-magrittr + r-mzr + r-phangorn + r-pracma + r-rcpp + r-rcppeigen + r-reticulate + r-rlang + r-rmsnumpress + r-rsqlite + r-signal + r-tidyr + r-zoo +) +optdepends=( + r-akima + r-biocparallel + r-biocstyle + r-gridextra + r-knitr + r-lattice + r-latticeextra + r-rmarkdown + r-scales + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dialignr/lilac.py b/prepare/r-dialignr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dialignr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dialignr/lilac.yaml b/prepare/r-dialignr/lilac.yaml new file mode 100644 index 0000000000..78b5fe31c5 --- /dev/null +++ b/prepare/r-dialignr/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-bit64 +- r-data.table +- r-dbi +- r-dplyr +- r-ggplot2 +- r-magrittr +- r-mzr +- r-phangorn +- r-pracma +- r-rcpp +- r-rcppeigen +- r-reticulate +- r-rlang +- r-rmsnumpress +- r-rsqlite +- r-signal +- r-tidyr +- r-zoo +update_on: +- regex: DIAlignR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DIAlignR diff --git a/prepare/r-dichromat/PKGBUILD b/prepare/r-dichromat/PKGBUILD new file mode 100644 index 0000000000..b8e2cd7acb --- /dev/null +++ b/prepare/r-dichromat/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dichromat +_pkgver=2.0-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Color Schemes for Dichromats' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dichromat/lilac.py b/prepare/r-dichromat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dichromat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dichromat/lilac.yaml b/prepare/r-dichromat/lilac.yaml new file mode 100644 index 0000000000..ac6c3dbfc9 --- /dev/null +++ b/prepare/r-dichromat/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: dichromat_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dichromat diff --git a/prepare/r-diffbind/PKGBUILD b/prepare/r-diffbind/PKGBUILD new file mode 100644 index 0000000000..bd86d28b7e --- /dev/null +++ b/prepare/r-diffbind/PKGBUILD @@ -0,0 +1,63 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=DiffBind +_pkgver=3.4.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential Binding Analysis of ChIP-Seq Peak Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-amap + r-apeglm + r-ashr + r-biocparallel + r-deseq2 + r-dplyr + r-genomicalignments + r-genomicranges + r-ggplot2 + r-ggrepel + r-gplots + r-greylistchip + r-iranges + r-limma + r-locfit + r-rcolorbrewer + r-rcpp + r-rhtslib + r-rsamtools + r-s4vectors + r-summarizedexperiment + r-systempiper +) +optdepends=( + r-biocstyle + r-bsgenome + r-csaw + r-edger + r-genomeinfodb + r-grid + r-profileplyr + r-rgl + r-rtracklayer + r-testthat + r-xlconnect + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-diffbind/lilac.py b/prepare/r-diffbind/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-diffbind/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-diffbind/lilac.yaml b/prepare/r-diffbind/lilac.yaml new file mode 100644 index 0000000000..7049d83469 --- /dev/null +++ b/prepare/r-diffbind/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-amap +- r-apeglm +- r-ashr +- r-biocparallel +- r-deseq2 +- r-dplyr +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-ggrepel +- r-gplots +- r-greylistchip +- r-iranges +- r-limma +- r-locfit +- r-rcolorbrewer +- r-rcpp +- r-rhtslib +- r-rsamtools +- r-s4vectors +- r-summarizedexperiment +- r-systempiper +update_on: +- regex: DiffBind_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DiffBind diff --git a/prepare/r-diffcoexp/PKGBUILD b/prepare/r-diffcoexp/PKGBUILD new file mode 100644 index 0000000000..ff4f3aefe7 --- /dev/null +++ b/prepare/r-diffcoexp/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=diffcoexp +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential Co-expression Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-diffcorr + r-igraph + r-psych + r-summarizedexperiment + r-wgcna +) +optdepends=( + r-geoquery +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-diffcoexp/lilac.py b/prepare/r-diffcoexp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-diffcoexp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-diffcoexp/lilac.yaml b/prepare/r-diffcoexp/lilac.yaml new file mode 100644 index 0000000000..efd8775cca --- /dev/null +++ b/prepare/r-diffcoexp/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-diffcorr +- r-igraph +- r-psych +- r-summarizedexperiment +- r-wgcna +update_on: +- regex: diffcoexp_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/diffcoexp diff --git a/prepare/r-diffcorr/PKGBUILD b/prepare/r-diffcorr/PKGBUILD new file mode 100644 index 0000000000..2492dcee03 --- /dev/null +++ b/prepare/r-diffcorr/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DiffCorr +_pkgver=0.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analyzing and Visualizing Differential Correlation Networks in Biological Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-fdrtool + r-igraph + r-multtest + r-pcamethods +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-diffcorr/lilac.py b/prepare/r-diffcorr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-diffcorr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-diffcorr/lilac.yaml b/prepare/r-diffcorr/lilac.yaml new file mode 100644 index 0000000000..11f1eb7602 --- /dev/null +++ b/prepare/r-diffcorr/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fdrtool +- r-igraph +- r-multtest +- r-pcamethods +update_on: +- regex: DiffCorr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=DiffCorr diff --git a/prepare/r-diffcyt/PKGBUILD b/prepare/r-diffcyt/PKGBUILD new file mode 100644 index 0000000000..8d2814f9b5 --- /dev/null +++ b/prepare/r-diffcyt/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=diffcyt +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential discovery in high-dimensional cytometry via high-resolution clustering' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-circlize + r-complexheatmap + r-dplyr + r-edger + r-flowcore + r-flowsom + r-limma + r-lme4 + r-magrittr + r-multcomp + r-reshape2 + r-s4vectors + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-biocstyle + r-catalyst + r-hdcytodata + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-diffcyt/lilac.py b/prepare/r-diffcyt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-diffcyt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-diffcyt/lilac.yaml b/prepare/r-diffcyt/lilac.yaml new file mode 100644 index 0000000000..8b066fe7a7 --- /dev/null +++ b/prepare/r-diffcyt/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circlize +- r-complexheatmap +- r-dplyr +- r-edger +- r-flowcore +- r-flowsom +- r-limma +- r-lme4 +- r-magrittr +- r-multcomp +- r-reshape2 +- r-s4vectors +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: diffcyt_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/diffcyt diff --git a/prepare/r-diffgeneanalysis/PKGBUILD b/prepare/r-diffgeneanalysis/PKGBUILD new file mode 100644 index 0000000000..2a759acc8f --- /dev/null +++ b/prepare/r-diffgeneanalysis/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=diffGeneAnalysis +_pkgver=1.76.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Performs differential gene expression Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-minpack.lm +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-diffgeneanalysis/lilac.py b/prepare/r-diffgeneanalysis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-diffgeneanalysis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-diffgeneanalysis/lilac.yaml b/prepare/r-diffgeneanalysis/lilac.yaml new file mode 100644 index 0000000000..d2f5369f09 --- /dev/null +++ b/prepare/r-diffgeneanalysis/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-minpack.lm +update_on: +- regex: diffGeneAnalysis_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/diffGeneAnalysis diff --git a/prepare/r-diffhic/PKGBUILD b/prepare/r-diffhic/PKGBUILD new file mode 100644 index 0000000000..aa2f214c56 --- /dev/null +++ b/prepare/r-diffhic/PKGBUILD @@ -0,0 +1,51 @@ +# system requirements: C++11, GNU make +# Maintainer: Guoyi Zhang + +_pkgname=diffHic +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential Analyis of Hi-C Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-bsgenome + r-csaw + r-edger + r-genomeinfodb + r-genomicranges + r-interactionset + r-iranges + r-limma + r-locfit + r-rcpp + r-rhdf5 + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-zlibbioc +) +optdepends=( + r-bsgenome.ecoli.ncbi.20080805 + r-matrix + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-diffhic/lilac.py b/prepare/r-diffhic/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-diffhic/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-diffhic/lilac.yaml b/prepare/r-diffhic/lilac.yaml new file mode 100644 index 0000000000..8056765990 --- /dev/null +++ b/prepare/r-diffhic/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-csaw +- r-edger +- r-genomeinfodb +- r-genomicranges +- r-interactionset +- r-iranges +- r-limma +- r-locfit +- r-rcpp +- r-rhdf5 +- r-rhtslib +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +- r-zlibbioc +update_on: +- regex: diffHic_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/diffHic diff --git a/prepare/r-difflogo/PKGBUILD b/prepare/r-difflogo/PKGBUILD new file mode 100644 index 0000000000..4e4dbdc4a6 --- /dev/null +++ b/prepare/r-difflogo/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DiffLogo +_pkgver=2.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='DiffLogo: A comparative visualisation of biooligomer motifs' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cba +) +optdepends=( + r-knitr + r-motifdb + r-seqlogo + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-difflogo/lilac.py b/prepare/r-difflogo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-difflogo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-difflogo/lilac.yaml b/prepare/r-difflogo/lilac.yaml new file mode 100644 index 0000000000..e25c0adcf9 --- /dev/null +++ b/prepare/r-difflogo/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cba +update_on: +- regex: DiffLogo_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DiffLogo diff --git a/prepare/r-diffloop/PKGBUILD b/prepare/r-diffloop/PKGBUILD new file mode 100644 index 0000000000..414aa9a9d5 --- /dev/null +++ b/prepare/r-diffloop/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=diffloop +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identifying differential DNA loops from chromatin topology data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-biomart + r-data.table + r-dplyr + r-edger + r-foreach + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-limma + r-locfit + r-matrixstats + r-pbapply + r-plyr + r-readr + r-reshape2 + r-rtracklayer + r-s4vectors + r-statmod + r-sushi +) +optdepends=( + r-deseq2 + r-diffloopdata + r-ggrepel + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-diffloop/lilac.py b/prepare/r-diffloop/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-diffloop/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-diffloop/lilac.yaml b/prepare/r-diffloop/lilac.yaml new file mode 100644 index 0000000000..ac7f0a647a --- /dev/null +++ b/prepare/r-diffloop/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biomart +- r-data.table +- r-dplyr +- r-edger +- r-foreach +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-limma +- r-locfit +- r-matrixstats +- r-pbapply +- r-plyr +- r-readr +- r-reshape2 +- r-rtracklayer +- r-s4vectors +- r-statmod +- r-sushi +update_on: +- regex: diffloop_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/diffloop diff --git a/prepare/r-diffobj/PKGBUILD b/prepare/r-diffobj/PKGBUILD new file mode 100644 index 0000000000..ecda708eac --- /dev/null +++ b/prepare/r-diffobj/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=diffobj +_pkgver=0.3.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Diffs for R Objects' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-crayon +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-diffobj/lilac.py b/prepare/r-diffobj/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-diffobj/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-diffobj/lilac.yaml b/prepare/r-diffobj/lilac.yaml new file mode 100644 index 0000000000..1b7bb2d89a --- /dev/null +++ b/prepare/r-diffobj/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-crayon +update_on: +- regex: diffobj_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=diffobj diff --git a/prepare/r-diffr/PKGBUILD b/prepare/r-diffr/PKGBUILD new file mode 100644 index 0000000000..f6b87a27d1 --- /dev/null +++ b/prepare/r-diffr/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=diffr +_pkgver=0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Display Differences Between Two Files using Codediff Library' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-htmlwidgets +) +optdepends=( + r-shiny +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-diffr/lilac.py b/prepare/r-diffr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-diffr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-diffr/lilac.yaml b/prepare/r-diffr/lilac.yaml new file mode 100644 index 0000000000..7830d9505c --- /dev/null +++ b/prepare/r-diffr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmlwidgets +update_on: +- regex: diffr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=diffr diff --git a/prepare/r-diffusr/PKGBUILD b/prepare/r-diffusr/PKGBUILD new file mode 100644 index 0000000000..96c2aad2c9 --- /dev/null +++ b/prepare/r-diffusr/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=diffusr +_pkgver=0.1.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Network Diffusion Algorithms' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-igraph + r-rcpp + r-rcppeigen +) +optdepends=( + r-knitr + r-lintr + r-matrix + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-diffusr/lilac.py b/prepare/r-diffusr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-diffusr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-diffusr/lilac.yaml b/prepare/r-diffusr/lilac.yaml new file mode 100644 index 0000000000..614bcfbb73 --- /dev/null +++ b/prepare/r-diffusr/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +- r-rcpp +- r-rcppeigen +update_on: +- regex: diffusr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=diffusr diff --git a/prepare/r-diffustats/PKGBUILD b/prepare/r-diffustats/PKGBUILD new file mode 100644 index 0000000000..75ea948330 --- /dev/null +++ b/prepare/r-diffustats/PKGBUILD @@ -0,0 +1,46 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=diffuStats +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Diffusion scores on biological networks' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-checkmate + r-expm + r-igraph + r-plyr + r-precrec + r-rcpp + r-rcpparmadillo + r-rcppparallel +) +optdepends=( + r-biocstyle + r-ggplot2 + r-ggsci + r-igraphdata + r-knitr + r-reshape2 + r-rmarkdown + r-testthat + r-utils +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-diffustats/lilac.py b/prepare/r-diffustats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-diffustats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-diffustats/lilac.yaml b/prepare/r-diffustats/lilac.yaml new file mode 100644 index 0000000000..4f7e82176c --- /dev/null +++ b/prepare/r-diffustats/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-checkmate +- r-expm +- r-igraph +- r-plyr +- r-precrec +- r-rcpp +- r-rcpparmadillo +- r-rcppparallel +update_on: +- regex: diffuStats_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/diffuStats diff --git a/prepare/r-diffutr/PKGBUILD b/prepare/r-diffutr/PKGBUILD new file mode 100644 index 0000000000..6293f5a5fc --- /dev/null +++ b/prepare/r-diffutr/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=diffUTR +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="diffUTR: Streamlining differential exon and 3' UTR usage" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-complexheatmap + r-dexseq + r-dplyr + r-edger + r-ensembldb + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-ggrepel + r-iranges + r-limma + r-matrixstats + r-rsubread + r-rtracklayer + r-s4vectors + r-stringi + r-summarizedexperiment + r-viridislite +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-diffutr/lilac.py b/prepare/r-diffutr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-diffutr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-diffutr/lilac.yaml b/prepare/r-diffutr/lilac.yaml new file mode 100644 index 0000000000..cb9d9ee18a --- /dev/null +++ b/prepare/r-diffutr/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-complexheatmap +- r-dexseq +- r-dplyr +- r-edger +- r-ensembldb +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-ggrepel +- r-iranges +- r-limma +- r-matrixstats +- r-rsubread +- r-rtracklayer +- r-s4vectors +- r-stringi +- r-summarizedexperiment +- r-viridislite +update_on: +- regex: diffUTR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/diffUTR diff --git a/prepare/r-diggit/PKGBUILD b/prepare/r-diggit/PKGBUILD new file mode 100644 index 0000000000..261ac0e53e --- /dev/null +++ b/prepare/r-diggit/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=diggit +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Inference of Genetic Variants Driving Cellular Phenotypes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-biobase + r-ks + r-viper +) +optdepends=( + r-diggitdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-diggit/lilac.py b/prepare/r-diggit/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-diggit/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-diggit/lilac.yaml b/prepare/r-diggit/lilac.yaml new file mode 100644 index 0000000000..1e35584300 --- /dev/null +++ b/prepare/r-diggit/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-ks +- r-viper +update_on: +- regex: diggit_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/diggit diff --git a/prepare/r-dino/PKGBUILD b/prepare/r-dino/PKGBUILD new file mode 100644 index 0000000000..5ece3ff777 --- /dev/null +++ b/prepare/r-dino/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Dino +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Normalization of Single-Cell mRNA Sequencing Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-biocsingular + r-matrixstats + r-s4vectors + r-scran + r-seurat + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-devtools + r-ggplot2 + r-ggpubr + r-grid + r-gridextra + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dino/lilac.py b/prepare/r-dino/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dino/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dino/lilac.yaml b/prepare/r-dino/lilac.yaml new file mode 100644 index 0000000000..e8fc9fa42c --- /dev/null +++ b/prepare/r-dino/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-biocsingular +- r-matrixstats +- r-s4vectors +- r-scran +- r-seurat +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: Dino_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Dino diff --git a/prepare/r-diptest/PKGBUILD b/prepare/r-diptest/PKGBUILD new file mode 100644 index 0000000000..372d6e5966 --- /dev/null +++ b/prepare/r-diptest/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=diptest +_pkgver=0.76-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Hartigan's Dip Test Statistic for Unimodality - Corrected" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-diptest/lilac.py b/prepare/r-diptest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-diptest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-diptest/lilac.yaml b/prepare/r-diptest/lilac.yaml new file mode 100644 index 0000000000..2715cc7caa --- /dev/null +++ b/prepare/r-diptest/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: diptest_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=diptest diff --git a/prepare/r-dir.expiry/PKGBUILD b/prepare/r-dir.expiry/PKGBUILD new file mode 100644 index 0000000000..e9bcb0a176 --- /dev/null +++ b/prepare/r-dir.expiry/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dir.expiry +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Managing Expiration for Cache Directories' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-filelock +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dir.expiry/lilac.py b/prepare/r-dir.expiry/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dir.expiry/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dir.expiry/lilac.yaml b/prepare/r-dir.expiry/lilac.yaml new file mode 100644 index 0000000000..2334f272bb --- /dev/null +++ b/prepare/r-dir.expiry/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-filelock +update_on: +- regex: dir.expiry_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/dir.expiry diff --git a/prepare/r-director/PKGBUILD b/prepare/r-director/PKGBUILD new file mode 100644 index 0000000000..36ce2e0664 --- /dev/null +++ b/prepare/r-director/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Director +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A dynamic visualization tool of multi-level data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-htmltools +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-director/lilac.py b/prepare/r-director/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-director/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-director/lilac.yaml b/prepare/r-director/lilac.yaml new file mode 100644 index 0000000000..2fd76e5225 --- /dev/null +++ b/prepare/r-director/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +update_on: +- regex: Director_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Director diff --git a/prepare/r-dirichletmultinomial/PKGBUILD b/prepare/r-dirichletmultinomial/PKGBUILD new file mode 100644 index 0000000000..7dc0b6f96f --- /dev/null +++ b/prepare/r-dirichletmultinomial/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: gsl +# Maintainer: Guoyi Zhang + +_pkgname=DirichletMultinomial +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biocgenerics + r-iranges + r-s4vectors +) +optdepends=( + r-lattice + r-mass + r-parallel + r-rcolorbrewer + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dirichletmultinomial/lilac.py b/prepare/r-dirichletmultinomial/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dirichletmultinomial/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dirichletmultinomial/lilac.yaml b/prepare/r-dirichletmultinomial/lilac.yaml new file mode 100644 index 0000000000..73557a0558 --- /dev/null +++ b/prepare/r-dirichletmultinomial/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-iranges +- r-s4vectors +update_on: +- regex: DirichletMultinomial_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DirichletMultinomial diff --git a/prepare/r-dirichletreg/PKGBUILD b/prepare/r-dirichletreg/PKGBUILD new file mode 100644 index 0000000000..d89c47846d --- /dev/null +++ b/prepare/r-dirichletreg/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DirichletReg +_pkgver=0.7-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dirichlet Regression' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-formula + r-maxlik +) +optdepends=( + r-formatr + r-knitr + r-rgl + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dirichletreg/lilac.py b/prepare/r-dirichletreg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dirichletreg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dirichletreg/lilac.yaml b/prepare/r-dirichletreg/lilac.yaml new file mode 100644 index 0000000000..190d474192 --- /dev/null +++ b/prepare/r-dirichletreg/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-formula +- r-maxlik +update_on: +- regex: DirichletReg_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=DirichletReg diff --git a/prepare/r-dirmult/PKGBUILD b/prepare/r-dirmult/PKGBUILD new file mode 100644 index 0000000000..d243766944 --- /dev/null +++ b/prepare/r-dirmult/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dirmult +_pkgver=0.1.3-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimation in Dirichlet-Multinomial distribution.' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dirmult/lilac.py b/prepare/r-dirmult/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dirmult/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dirmult/lilac.yaml b/prepare/r-dirmult/lilac.yaml new file mode 100644 index 0000000000..1f0f554b21 --- /dev/null +++ b/prepare/r-dirmult/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: dirmult_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dirmult diff --git a/prepare/r-discordant/PKGBUILD b/prepare/r-discordant/PKGBUILD new file mode 100644 index 0000000000..69094f2803 --- /dev/null +++ b/prepare/r-discordant/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=discordant +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The Discordant Method: A Novel Approach for Differential Correlation' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biwt + r-gtools +) +optdepends=( + r-biocstyle + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-discordant/lilac.py b/prepare/r-discordant/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-discordant/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-discordant/lilac.yaml b/prepare/r-discordant/lilac.yaml new file mode 100644 index 0000000000..3e7259d1aa --- /dev/null +++ b/prepare/r-discordant/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biwt +- r-gtools +update_on: +- regex: discordant_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/discordant diff --git a/prepare/r-discorhythm/PKGBUILD b/prepare/r-discorhythm/PKGBUILD new file mode 100644 index 0000000000..f9825dc707 --- /dev/null +++ b/prepare/r-discorhythm/PKGBUILD @@ -0,0 +1,60 @@ +# system requirements: To generate html reports pandoc(http://pandoc.org/installing.html) is required. +# Maintainer: Guoyi Zhang + +_pkgname=DiscoRhythm +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive Workflow for Discovering Rhythmicity in Biological Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocstyle + r-broom + r-data.table + r-dplyr + r-dt + r-ggextra + r-ggplot2 + r-gridextra + r-heatmaply + r-kableextra + r-knitr + r-magick + r-matrixstats + r-matrixtests + r-metacycle + r-plotly + r-reshape2 + r-rmarkdown + r-s4vectors + r-shiny + r-shinybs + r-shinycssloaders + r-shinydashboard + r-shinyjs + r-summarizedexperiment + r-upsetr + r-venndiagram + r-viridis + r-zip +) +optdepends=( + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-discorhythm/lilac.py b/prepare/r-discorhythm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-discorhythm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-discorhythm/lilac.yaml b/prepare/r-discorhythm/lilac.yaml new file mode 100644 index 0000000000..297a2fd0f8 --- /dev/null +++ b/prepare/r-discorhythm/lilac.yaml @@ -0,0 +1,39 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocstyle +- r-broom +- r-data.table +- r-dplyr +- r-dt +- r-ggextra +- r-ggplot2 +- r-gridextra +- r-heatmaply +- r-kableextra +- r-knitr +- r-magick +- r-matrixstats +- r-matrixtests +- r-metacycle +- r-plotly +- r-reshape2 +- r-rmarkdown +- r-s4vectors +- r-shiny +- r-shinybs +- r-shinycssloaders +- r-shinydashboard +- r-shinyjs +- r-summarizedexperiment +- r-upsetr +- r-venndiagram +- r-viridis +- r-zip +update_on: +- regex: DiscoRhythm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DiscoRhythm diff --git a/prepare/r-discretecdalgorithm/PKGBUILD b/prepare/r-discretecdalgorithm/PKGBUILD new file mode 100644 index 0000000000..3adf499804 --- /dev/null +++ b/prepare/r-discretecdalgorithm/PKGBUILD @@ -0,0 +1,34 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=discretecdAlgorithm +_pkgver=0.0.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Coordinate-Descent Algorithm for Learning Sparse Discrete Bayesian Networks' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-igraph + r-rcpp + r-rcppeigen + r-sparsebnutils +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-discretecdalgorithm/lilac.py b/prepare/r-discretecdalgorithm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-discretecdalgorithm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-discretecdalgorithm/lilac.yaml b/prepare/r-discretecdalgorithm/lilac.yaml new file mode 100644 index 0000000000..77020eb23e --- /dev/null +++ b/prepare/r-discretecdalgorithm/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +- r-rcpp +- r-rcppeigen +- r-sparsebnutils +update_on: +- regex: discretecdAlgorithm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=discretecdAlgorithm diff --git a/prepare/r-discriminer/PKGBUILD b/prepare/r-discriminer/PKGBUILD new file mode 100644 index 0000000000..8121a2cdca --- /dev/null +++ b/prepare/r-discriminer/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DiscriMiner +_pkgver=0.1-29 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools of the Trade for Discriminant Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-factominer + r-mass +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-discriminer/lilac.py b/prepare/r-discriminer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-discriminer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-discriminer/lilac.yaml b/prepare/r-discriminer/lilac.yaml new file mode 100644 index 0000000000..4806c38e24 --- /dev/null +++ b/prepare/r-discriminer/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: DiscriMiner_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=DiscriMiner diff --git a/prepare/r-distances/PKGBUILD b/prepare/r-distances/PKGBUILD new file mode 100644 index 0000000000..f3678c2d51 --- /dev/null +++ b/prepare/r-distances/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=distances +_pkgver=0.1.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Distance Metrics' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-distances/lilac.py b/prepare/r-distances/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-distances/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-distances/lilac.yaml b/prepare/r-distances/lilac.yaml new file mode 100644 index 0000000000..a9e5bf2897 --- /dev/null +++ b/prepare/r-distances/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: distances_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=distances diff --git a/prepare/r-distillery/PKGBUILD b/prepare/r-distillery/PKGBUILD new file mode 100644 index 0000000000..9900eb7659 --- /dev/null +++ b/prepare/r-distillery/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=distillery +_pkgver=1.2-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Method Functions for Confidence Intervals and to Distill Information from an Object' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-distillery/lilac.py b/prepare/r-distillery/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-distillery/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-distillery/lilac.yaml b/prepare/r-distillery/lilac.yaml new file mode 100644 index 0000000000..af7640f17f --- /dev/null +++ b/prepare/r-distillery/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: distillery_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=distillery diff --git a/prepare/r-distinct/PKGBUILD b/prepare/r-distinct/PKGBUILD new file mode 100644 index 0000000000..695032bebd --- /dev/null +++ b/prepare/r-distinct/PKGBUILD @@ -0,0 +1,43 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=distinct +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='distinct: a method for differential analyses via hierarchical permutation tests' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-doparallel + r-dorng + r-foreach + r-ggplot2 + r-limma + r-rcpp + r-rcpparmadillo + r-scater + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat + r-upsetr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-distinct/lilac.py b/prepare/r-distinct/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-distinct/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-distinct/lilac.yaml b/prepare/r-distinct/lilac.yaml new file mode 100644 index 0000000000..ccc34cd2ba --- /dev/null +++ b/prepare/r-distinct/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-dorng +- r-foreach +- r-ggplot2 +- r-limma +- r-rcpp +- r-rcpparmadillo +- r-scater +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: distinct_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/distinct diff --git a/prepare/r-distr/PKGBUILD b/prepare/r-distr/PKGBUILD new file mode 100644 index 0000000000..d8222ae83e --- /dev/null +++ b/prepare/r-distr/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=distr +_pkgver=2.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Object Oriented Implementation of Distributions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-sfsmisc + r-startupmsg +) +optdepends=( + r-distrex + r-knitr + r-svunit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-distr/lilac.py b/prepare/r-distr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-distr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-distr/lilac.yaml b/prepare/r-distr/lilac.yaml new file mode 100644 index 0000000000..22a813c616 --- /dev/null +++ b/prepare/r-distr/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-sfsmisc +- r-startupmsg +update_on: +- regex: distr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=distr diff --git a/prepare/r-distrex/PKGBUILD b/prepare/r-distrex/PKGBUILD new file mode 100644 index 0000000000..2a1f4851f4 --- /dev/null +++ b/prepare/r-distrex/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=distrEx +_pkgver=2.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Extensions of Package 'distr'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-distr + r-startupmsg +) +optdepends=( + r-tcltk +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-distrex/lilac.py b/prepare/r-distrex/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-distrex/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-distrex/lilac.yaml b/prepare/r-distrex/lilac.yaml new file mode 100644 index 0000000000..2848bf8d9e --- /dev/null +++ b/prepare/r-distrex/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-distr +- r-startupmsg +update_on: +- regex: distrEx_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=distrEx diff --git a/prepare/r-distributional/PKGBUILD b/prepare/r-distributional/PKGBUILD new file mode 100644 index 0000000000..8c8be500ed --- /dev/null +++ b/prepare/r-distributional/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=distributional +_pkgver=0.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Vectorised Probability Distributions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-digest + r-ellipsis + r-farver + r-generics + r-ggplot2 + r-lifecycle + r-numderiv + r-rlang + r-scales + r-vctrs +) +optdepends=( + r-actuar + r-covr + r-ggdist + r-mvtnorm + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-distributional/lilac.py b/prepare/r-distributional/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-distributional/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-distributional/lilac.yaml b/prepare/r-distributional/lilac.yaml new file mode 100644 index 0000000000..96c8bbdae5 --- /dev/null +++ b/prepare/r-distributional/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-ellipsis +- r-farver +- r-generics +- r-ggplot2 +- r-lifecycle +- r-numderiv +- r-rlang +- r-scales +- r-vctrs +update_on: +- regex: distributional_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=distributional diff --git a/prepare/r-dittoseq/PKGBUILD b/prepare/r-dittoseq/PKGBUILD new file mode 100644 index 0000000000..db79abe2ad --- /dev/null +++ b/prepare/r-dittoseq/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dittoSeq +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='User Friendly Single-Cell and Bulk RNA Sequencing Visualization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-colorspace + r-cowplot + r-ggplot2 + r-ggrepel + r-ggridges + r-gridextra + r-pheatmap + r-reshape2 + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-bluster + r-complexheatmap + r-deseq2 + r-edger + r-ggplot.multistats + r-ggrastr + r-knitr + r-plotly + r-rmarkdown + r-scater + r-scran + r-scrnaseq + r-seurat + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dittoseq/lilac.py b/prepare/r-dittoseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dittoseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dittoseq/lilac.yaml b/prepare/r-dittoseq/lilac.yaml new file mode 100644 index 0000000000..00d0c1d34e --- /dev/null +++ b/prepare/r-dittoseq/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colorspace +- r-cowplot +- r-ggplot2 +- r-ggrepel +- r-ggridges +- r-gridextra +- r-pheatmap +- r-reshape2 +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: dittoSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/dittoSeq diff --git a/prepare/r-divergence/PKGBUILD b/prepare/r-divergence/PKGBUILD new file mode 100644 index 0000000000..fb4d9e85fa --- /dev/null +++ b/prepare/r-divergence/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=divergence +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Divergence: Functionality for assessing omics data by divergence with respect to a baseline' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-summarizedexperiment +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-divergence/lilac.py b/prepare/r-divergence/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-divergence/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-divergence/lilac.yaml b/prepare/r-divergence/lilac.yaml new file mode 100644 index 0000000000..3728d99b1d --- /dev/null +++ b/prepare/r-divergence/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-summarizedexperiment +update_on: +- regex: divergence_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/divergence diff --git a/prepare/r-dks/PKGBUILD b/prepare/r-dks/PKGBUILD new file mode 100644 index 0000000000..8a6ac94657 --- /dev/null +++ b/prepare/r-dks/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dks +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cubature +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dks/lilac.py b/prepare/r-dks/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dks/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dks/lilac.yaml b/prepare/r-dks/lilac.yaml new file mode 100644 index 0000000000..b7ec149e35 --- /dev/null +++ b/prepare/r-dks/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cubature +update_on: +- regex: dks_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/dks diff --git a/prepare/r-dmcfb/PKGBUILD b/prepare/r-dmcfb/PKGBUILD new file mode 100644 index 0000000000..88785f00a7 --- /dev/null +++ b/prepare/r-dmcfb/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DMCFB +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differentially Methylated Cytosines via a Bayesian Functional Approach' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-arm + r-benchmarkme + r-biocparallel + r-data.table + r-fastdummies + r-genomicranges + r-iranges + r-matrixstats + r-rtracklayer + r-s4vectors + r-speedglm + r-summarizedexperiment + r-tibble +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dmcfb/lilac.py b/prepare/r-dmcfb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dmcfb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dmcfb/lilac.yaml b/prepare/r-dmcfb/lilac.yaml new file mode 100644 index 0000000000..3073924bb7 --- /dev/null +++ b/prepare/r-dmcfb/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-arm +- r-benchmarkme +- r-biocparallel +- r-data.table +- r-fastdummies +- r-genomicranges +- r-iranges +- r-matrixstats +- r-rtracklayer +- r-s4vectors +- r-speedglm +- r-summarizedexperiment +- r-tibble +update_on: +- regex: DMCFB_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DMCFB diff --git a/prepare/r-dmchmm/PKGBUILD b/prepare/r-dmchmm/PKGBUILD new file mode 100644 index 0000000000..5786389428 --- /dev/null +++ b/prepare/r-dmchmm/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DMCHMM +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differentially Methylated CpG using Hidden Markov Model' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-calibrate + r-fdrtool + r-genomicranges + r-iranges + r-multcomp + r-rtracklayer + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dmchmm/lilac.py b/prepare/r-dmchmm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dmchmm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dmchmm/lilac.yaml b/prepare/r-dmchmm/lilac.yaml new file mode 100644 index 0000000000..01bd9fb534 --- /dev/null +++ b/prepare/r-dmchmm/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-calibrate +- r-fdrtool +- r-genomicranges +- r-iranges +- r-multcomp +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: DMCHMM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DMCHMM diff --git a/prepare/r-dml/PKGBUILD b/prepare/r-dml/PKGBUILD new file mode 100644 index 0000000000..5343e1d04d --- /dev/null +++ b/prepare/r-dml/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dml +_pkgver=1.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Distance Metric Learning in R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-lfda +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dml/lilac.py b/prepare/r-dml/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dml/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dml/lilac.yaml b/prepare/r-dml/lilac.yaml new file mode 100644 index 0000000000..65077a1c15 --- /dev/null +++ b/prepare/r-dml/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lfda +update_on: +- regex: dml_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dml diff --git a/prepare/r-dmrcaller/PKGBUILD b/prepare/r-dmrcaller/PKGBUILD new file mode 100644 index 0000000000..cfb33da417 --- /dev/null +++ b/prepare/r-dmrcaller/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DMRcaller +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differentially Methylated Regions caller' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-betareg + r-genomicranges + r-iranges + r-rcpp + r-rcpproll + r-s4vectors +) +optdepends=( + r-biocgenerics + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dmrcaller/lilac.py b/prepare/r-dmrcaller/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dmrcaller/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dmrcaller/lilac.yaml b/prepare/r-dmrcaller/lilac.yaml new file mode 100644 index 0000000000..2ea01f0b05 --- /dev/null +++ b/prepare/r-dmrcaller/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-betareg +- r-genomicranges +- r-iranges +- r-rcpp +- r-rcpproll +- r-s4vectors +update_on: +- regex: DMRcaller_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DMRcaller diff --git a/prepare/r-dmrcate/PKGBUILD b/prepare/r-dmrcate/PKGBUILD new file mode 100644 index 0000000000..055db1ea4f --- /dev/null +++ b/prepare/r-dmrcate/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DMRcate +_pkgver=2.8.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methylation array and sequencing spatial analysis methods' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-bsseq + r-dss + r-edger + r-experimenthub + r-genomeinfodb + r-genomicranges + r-gviz + r-iranges + r-limma + r-minfi + r-missmethyl + r-plyr + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocgenerics + r-illuminahumanmethylation450kanno.ilmn12.hg19 + r-illuminahumanmethylationepicanno.ilm10b4.hg19 + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dmrcate/lilac.py b/prepare/r-dmrcate/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dmrcate/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dmrcate/lilac.yaml b/prepare/r-dmrcate/lilac.yaml new file mode 100644 index 0000000000..9c9d6b465b --- /dev/null +++ b/prepare/r-dmrcate/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsseq +- r-dss +- r-edger +- r-experimenthub +- r-genomeinfodb +- r-genomicranges +- r-gviz +- r-iranges +- r-limma +- r-minfi +- r-missmethyl +- r-plyr +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: DMRcate_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DMRcate diff --git a/prepare/r-dmrforpairs/PKGBUILD b/prepare/r-dmrforpairs/PKGBUILD new file mode 100644 index 0000000000..e40a873ad2 --- /dev/null +++ b/prepare/r-dmrforpairs/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DMRforPairs +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicranges + r-gviz + r-r2html +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dmrforpairs/lilac.py b/prepare/r-dmrforpairs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dmrforpairs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dmrforpairs/lilac.yaml b/prepare/r-dmrforpairs/lilac.yaml new file mode 100644 index 0000000000..9fb1b16b09 --- /dev/null +++ b/prepare/r-dmrforpairs/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-gviz +- r-r2html +update_on: +- regex: DMRforPairs_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DMRforPairs diff --git a/prepare/r-dmrscan/PKGBUILD b/prepare/r-dmrscan/PKGBUILD new file mode 100644 index 0000000000..f278774d58 --- /dev/null +++ b/prepare/r-dmrscan/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DMRScan +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detection of Differentially Methylated Regions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomeinfodb + r-genomicranges + r-iranges + r-mvtnorm + r-rcpproll +) +optdepends=( + r-biocmanager + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dmrscan/lilac.py b/prepare/r-dmrscan/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dmrscan/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dmrscan/lilac.yaml b/prepare/r-dmrscan/lilac.yaml new file mode 100644 index 0000000000..d258996e0d --- /dev/null +++ b/prepare/r-dmrscan/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-mvtnorm +- r-rcpproll +update_on: +- regex: DMRScan_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DMRScan diff --git a/prepare/r-dmrseq/PKGBUILD b/prepare/r-dmrseq/PKGBUILD new file mode 100644 index 0000000000..2c6dc04209 --- /dev/null +++ b/prepare/r-dmrseq/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dmrseq +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationhub + r-annotatr + r-biocparallel + r-bsseq + r-bumphunter + r-delayedmatrixstats + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-locfit + r-matrixstats + r-outliers + r-rcolorbrewer + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dmrseq/lilac.py b/prepare/r-dmrseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dmrseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dmrseq/lilac.yaml b/prepare/r-dmrseq/lilac.yaml new file mode 100644 index 0000000000..6089170f4e --- /dev/null +++ b/prepare/r-dmrseq/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-annotatr +- r-biocparallel +- r-bsseq +- r-bumphunter +- r-delayedmatrixstats +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-locfit +- r-matrixstats +- r-outliers +- r-rcolorbrewer +- r-rtracklayer +- r-s4vectors +update_on: +- regex: dmrseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/dmrseq diff --git a/prepare/r-dmt/PKGBUILD b/prepare/r-dmt/PKGBUILD new file mode 100644 index 0000000000..442112be7e --- /dev/null +++ b/prepare/r-dmt/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dmt +_pkgver=0.8.20 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dependency Modeling Toolkit' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-mvtnorm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dmt/lilac.py b/prepare/r-dmt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dmt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dmt/lilac.yaml b/prepare/r-dmt/lilac.yaml new file mode 100644 index 0000000000..1da98bb33e --- /dev/null +++ b/prepare/r-dmt/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mvtnorm +update_on: +- regex: dmt_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dmt diff --git a/prepare/r-dmwr2/PKGBUILD b/prepare/r-dmwr2/PKGBUILD new file mode 100644 index 0000000000..d04c899c62 --- /dev/null +++ b/prepare/r-dmwr2/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DMwR2 +_pkgver=0.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions and Data for the Second Edition of "Data Mining with R"' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dbi + r-dplyr + r-quantmod + r-readr + r-xts + r-zoo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dmwr2/lilac.py b/prepare/r-dmwr2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dmwr2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dmwr2/lilac.yaml b/prepare/r-dmwr2/lilac.yaml new file mode 100644 index 0000000000..e500951cb9 --- /dev/null +++ b/prepare/r-dmwr2/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dbi +- r-dplyr +- r-quantmod +- r-readr +- r-xts +- r-zoo +update_on: +- regex: DMwR2_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=DMwR2 diff --git a/prepare/r-dnabarcodecompatibility/PKGBUILD b/prepare/r-dnabarcodecompatibility/PKGBUILD new file mode 100644 index 0000000000..970c50b063 --- /dev/null +++ b/prepare/r-dnabarcodecompatibility/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DNABarcodeCompatibility +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-dnabarcodes + r-dplyr + r-numbers + r-purrr + r-stringr + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dnabarcodecompatibility/lilac.py b/prepare/r-dnabarcodecompatibility/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dnabarcodecompatibility/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dnabarcodecompatibility/lilac.yaml b/prepare/r-dnabarcodecompatibility/lilac.yaml new file mode 100644 index 0000000000..111485ede7 --- /dev/null +++ b/prepare/r-dnabarcodecompatibility/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dnabarcodes +- r-dplyr +- r-numbers +- r-purrr +- r-stringr +- r-tidyr +update_on: +- regex: DNABarcodeCompatibility_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DNABarcodeCompatibility diff --git a/prepare/r-dnabarcodes/PKGBUILD b/prepare/r-dnabarcodes/PKGBUILD new file mode 100644 index 0000000000..5808389313 --- /dev/null +++ b/prepare/r-dnabarcodes/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DNABarcodes +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bh + r-rcpp +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dnabarcodes/lilac.py b/prepare/r-dnabarcodes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dnabarcodes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dnabarcodes/lilac.yaml b/prepare/r-dnabarcodes/lilac.yaml new file mode 100644 index 0000000000..305bb01c68 --- /dev/null +++ b/prepare/r-dnabarcodes/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-rcpp +update_on: +- regex: DNABarcodes_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DNABarcodes diff --git a/prepare/r-dnacopy/PKGBUILD b/prepare/r-dnacopy/PKGBUILD new file mode 100644 index 0000000000..52c34cb303 --- /dev/null +++ b/prepare/r-dnacopy/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DNAcopy +_pkgver=1.68.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='DNA copy number data analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dnacopy/lilac.py b/prepare/r-dnacopy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dnacopy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dnacopy/lilac.yaml b/prepare/r-dnacopy/lilac.yaml new file mode 100644 index 0000000000..f05997e9aa --- /dev/null +++ b/prepare/r-dnacopy/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: DNAcopy_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DNAcopy diff --git a/prepare/r-dnashaper/PKGBUILD b/prepare/r-dnashaper/PKGBUILD new file mode 100644 index 0000000000..fc16e9f3a6 --- /dev/null +++ b/prepare/r-dnashaper/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DNAshapeR +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='High-throughput prediction of DNA shape features' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-fields + r-genomicranges + r-rcpp +) +optdepends=( + r-annotationhub + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.scerevisiae.ucsc.saccer3 + r-caret + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dnashaper/lilac.py b/prepare/r-dnashaper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dnashaper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dnashaper/lilac.yaml b/prepare/r-dnashaper/lilac.yaml new file mode 100644 index 0000000000..57d182980c --- /dev/null +++ b/prepare/r-dnashaper/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-fields +- r-genomicranges +- r-rcpp +update_on: +- regex: DNAshapeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DNAshapeR diff --git a/prepare/r-dnet/PKGBUILD b/prepare/r-dnet/PKGBUILD new file mode 100644 index 0000000000..705a226db8 --- /dev/null +++ b/prepare/r-dnet/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dnet +_pkgver=1.1.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-graph + r-igraph + r-rgraphviz + r-suprahex +) +optdepends=( + r-biobase + r-doparallel + r-foreach + r-limma + r-survival +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dnet/lilac.py b/prepare/r-dnet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dnet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dnet/lilac.yaml b/prepare/r-dnet/lilac.yaml new file mode 100644 index 0000000000..45226ac55a --- /dev/null +++ b/prepare/r-dnet/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +- r-igraph +- r-rgraphviz +- r-suprahex +update_on: +- regex: dnet_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dnet diff --git a/prepare/r-do.db/PKGBUILD b/prepare/r-do.db/PKGBUILD new file mode 100644 index 0000000000..e3fb32ce80 --- /dev/null +++ b/prepare/r-do.db/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DO.db +_pkgver=2.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A set of annotation maps describing the entire Disease Ontology' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-do.db/lilac.py b/prepare/r-do.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-do.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-do.db/lilac.yaml b/prepare/r-do.db/lilac.yaml new file mode 100644 index 0000000000..c925a3eaa0 --- /dev/null +++ b/prepare/r-do.db/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +update_on: +- regex: DO.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DO.db diff --git a/prepare/r-doby/PKGBUILD b/prepare/r-doby/PKGBUILD new file mode 100644 index 0000000000..cf070f8778 --- /dev/null +++ b/prepare/r-doby/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=doBy +_pkgver=4.6.11 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Groupwise Statistics, LSmeans, Linear Contrasts, Utilities' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-broom + r-curry + r-deriv + r-dplyr + r-ggplot2 + r-magrittr + r-microbenchmark + r-pbkrtest + r-tibble +) +optdepends=( + r-geepack + r-knitr + r-lme4 + r-multcomp + r-survival + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-doby/lilac.py b/prepare/r-doby/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-doby/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-doby/lilac.yaml b/prepare/r-doby/lilac.yaml new file mode 100644 index 0000000000..5ce11edf08 --- /dev/null +++ b/prepare/r-doby/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-broom +- r-curry +- r-deriv +- r-dplyr +- r-ggplot2 +- r-magrittr +- r-microbenchmark +- r-pbkrtest +- r-tibble +update_on: +- regex: doBy_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=doBy diff --git a/prepare/r-dockerfiler/PKGBUILD b/prepare/r-dockerfiler/PKGBUILD new file mode 100644 index 0000000000..ee5e130532 --- /dev/null +++ b/prepare/r-dockerfiler/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dockerfiler +_pkgver=0.1.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Easy Dockerfile Creation from R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-attempt + r-cli + r-desc + r-fs + r-glue + r-jsonlite + r-pkgbuild + r-r6 + r-remotes + r-usethis +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dockerfiler/lilac.py b/prepare/r-dockerfiler/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dockerfiler/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dockerfiler/lilac.yaml b/prepare/r-dockerfiler/lilac.yaml new file mode 100644 index 0000000000..c976fe41fc --- /dev/null +++ b/prepare/r-dockerfiler/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-attempt +- r-cli +- r-desc +- r-fs +- r-glue +- r-jsonlite +- r-pkgbuild +- r-r6 +- r-remotes +- r-usethis +update_on: +- regex: dockerfiler_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dockerfiler diff --git a/prepare/r-docopt/PKGBUILD b/prepare/r-docopt/PKGBUILD new file mode 100644 index 0000000000..6134064c55 --- /dev/null +++ b/prepare/r-docopt/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=docopt +_pkgver=0.7.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Command-Line Interface Specification Language' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-docopt/lilac.py b/prepare/r-docopt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-docopt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-docopt/lilac.yaml b/prepare/r-docopt/lilac.yaml new file mode 100644 index 0000000000..083fd734c4 --- /dev/null +++ b/prepare/r-docopt/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: docopt_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=docopt diff --git a/prepare/r-dominoeffect/PKGBUILD b/prepare/r-dominoeffect/PKGBUILD new file mode 100644 index 0000000000..0c09b6f4e1 --- /dev/null +++ b/prepare/r-dominoeffect/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DominoEffect +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identification and Annotation of Protein Hotspot Residues' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biomart + r-biostrings + r-data.table + r-genomeinfodb + r-genomicranges + r-iranges + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dominoeffect/lilac.py b/prepare/r-dominoeffect/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dominoeffect/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dominoeffect/lilac.yaml b/prepare/r-dominoeffect/lilac.yaml new file mode 100644 index 0000000000..5f9dbc3fc5 --- /dev/null +++ b/prepare/r-dominoeffect/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biomart +- r-biostrings +- r-data.table +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: DominoEffect_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DominoEffect diff --git a/prepare/r-doparallel/PKGBUILD b/prepare/r-doparallel/PKGBUILD new file mode 100644 index 0000000000..f7925a85a1 --- /dev/null +++ b/prepare/r-doparallel/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=doParallel +_pkgver=1.0.16 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Foreach Parallel Adaptor for the 'parallel' Package" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-foreach + r-iterators +) +optdepends=( + r-caret + r-compiler + r-mlbench + r-rpart + r-runit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-doparallel/lilac.py b/prepare/r-doparallel/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-doparallel/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-doparallel/lilac.yaml b/prepare/r-doparallel/lilac.yaml new file mode 100644 index 0000000000..fad28132ed --- /dev/null +++ b/prepare/r-doparallel/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-foreach +- r-iterators +update_on: +- regex: doParallel_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=doParallel diff --git a/prepare/r-doppelgangr/PKGBUILD b/prepare/r-doppelgangr/PKGBUILD new file mode 100644 index 0000000000..99d3c55368 --- /dev/null +++ b/prepare/r-doppelgangr/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=doppelgangR +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identify likely duplicate samples from genomic or meta-data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocparallel + r-digest + r-impute + r-mnormt + r-summarizedexperiment + r-sva +) +optdepends=( + r-biocstyle + r-curatedovariandata + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-doppelgangr/lilac.py b/prepare/r-doppelgangr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-doppelgangr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-doppelgangr/lilac.yaml b/prepare/r-doppelgangr/lilac.yaml new file mode 100644 index 0000000000..a6e2f4b399 --- /dev/null +++ b/prepare/r-doppelgangr/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocparallel +- r-digest +- r-impute +- r-mnormt +- r-summarizedexperiment +- r-sva +update_on: +- regex: doppelgangR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/doppelgangR diff --git a/prepare/r-dorng/PKGBUILD b/prepare/r-dorng/PKGBUILD new file mode 100644 index 0000000000..0d96993967 --- /dev/null +++ b/prepare/r-dorng/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=doRNG +_pkgver=1.8.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Generic Reproducible Parallel Backend for 'foreach' Loops" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-foreach + r-iterators + r-rngtools +) +optdepends=( + r-bibtex + r-devtools + r-dompi + r-doparallel + r-doredis + r-knitr + r-pkgmaker + r-rbenchmark + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dorng/lilac.py b/prepare/r-dorng/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dorng/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dorng/lilac.yaml b/prepare/r-dorng/lilac.yaml new file mode 100644 index 0000000000..1e3040fb1b --- /dev/null +++ b/prepare/r-dorng/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-foreach +- r-iterators +- r-rngtools +update_on: +- regex: doRNG_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=doRNG diff --git a/prepare/r-dorothea/PKGBUILD b/prepare/r-dorothea/PKGBUILD new file mode 100644 index 0000000000..1f17e85e0b --- /dev/null +++ b/prepare/r-dorothea/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dorothea +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Collection Of Human And Mouse TF Regulons' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bcellviper + r-dplyr + r-magrittr + r-viper +) +optdepends=( + r-biobase + r-biocstyle + r-knitr + r-pheatmap + r-pkgdown + r-rmarkdown + r-seurat + r-singlecellexperiment + r-summarizedexperiment + r-testthat + r-tibble + r-tidyr + r-utils +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dorothea/lilac.py b/prepare/r-dorothea/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dorothea/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dorothea/lilac.yaml b/prepare/r-dorothea/lilac.yaml new file mode 100644 index 0000000000..e31613077d --- /dev/null +++ b/prepare/r-dorothea/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bcellviper +- r-dplyr +- r-magrittr +- r-viper +update_on: +- regex: dorothea_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/dorothea diff --git a/prepare/r-doscheda/PKGBUILD b/prepare/r-doscheda/PKGBUILD new file mode 100644 index 0000000000..0c1d8af036 --- /dev/null +++ b/prepare/r-doscheda/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Doscheda +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A DownStream Chemo-Proteomics Analysis Pipeline' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-calibrate + r-corrgram + r-drc + r-dt + r-ggplot2 + r-gridextra + r-httr + r-jsonlite + r-limma + r-matrixstats + r-prodlim + r-readxl + r-reshape2 + r-shiny + r-shinydashboard + r-stringr + r-vsn +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-doscheda/lilac.py b/prepare/r-doscheda/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-doscheda/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-doscheda/lilac.yaml b/prepare/r-doscheda/lilac.yaml new file mode 100644 index 0000000000..10c2a3af98 --- /dev/null +++ b/prepare/r-doscheda/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-calibrate +- r-corrgram +- r-drc +- r-dt +- r-ggplot2 +- r-gridextra +- r-httr +- r-jsonlite +- r-limma +- r-matrixstats +- r-prodlim +- r-readxl +- r-reshape2 +- r-shiny +- r-shinydashboard +- r-stringr +- r-vsn +update_on: +- regex: Doscheda_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Doscheda diff --git a/prepare/r-dose/PKGBUILD b/prepare/r-dose/PKGBUILD new file mode 100644 index 0000000000..3a7a16cb14 --- /dev/null +++ b/prepare/r-dose/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DOSE +_pkgver=3.20.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Disease Ontology Semantic and Enrichment analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biocparallel + r-do.db + r-fgsea + r-ggplot2 + r-gosemsim + r-qvalue + r-reshape2 +) +optdepends=( + r-clusterprofiler + r-knitr + r-org.hs.eg.db + r-prettydoc + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dose/lilac.py b/prepare/r-dose/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dose/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dose/lilac.yaml b/prepare/r-dose/lilac.yaml new file mode 100644 index 0000000000..f3dea74ee3 --- /dev/null +++ b/prepare/r-dose/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocparallel +- r-do.db +- r-fgsea +- r-ggplot2 +- r-gosemsim +- r-qvalue +- r-reshape2 +update_on: +- regex: DOSE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DOSE diff --git a/prepare/r-doser/PKGBUILD b/prepare/r-doser/PKGBUILD new file mode 100644 index 0000000000..89cb81ab11 --- /dev/null +++ b/prepare/r-doser/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=doseR +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='doseR' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-digest + r-edger + r-lme4 + r-matrixstats + r-mclust + r-runit + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-doser/lilac.py b/prepare/r-doser/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-doser/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-doser/lilac.yaml b/prepare/r-doser/lilac.yaml new file mode 100644 index 0000000000..ff1b70e431 --- /dev/null +++ b/prepare/r-doser/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-edger +- r-lme4 +- r-matrixstats +- r-mclust +- r-runit +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: doseR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/doseR diff --git a/prepare/r-dosnow/PKGBUILD b/prepare/r-dosnow/PKGBUILD new file mode 100644 index 0000000000..8c1aa46282 --- /dev/null +++ b/prepare/r-dosnow/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=doSNOW +_pkgver=1.0.19 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Foreach Parallel Adaptor for the 'snow' Package" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-foreach + r-iterators + r-snow +) +optdepends=( + r-caret + r-compiler + r-mlbench + r-parallel + r-rpart + r-runit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dosnow/lilac.py b/prepare/r-dosnow/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dosnow/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dosnow/lilac.yaml b/prepare/r-dosnow/lilac.yaml new file mode 100644 index 0000000000..0d9ea15f8d --- /dev/null +++ b/prepare/r-dosnow/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-foreach +- r-iterators +- r-snow +update_on: +- regex: doSNOW_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=doSNOW diff --git a/prepare/r-dotcall64/PKGBUILD b/prepare/r-dotcall64/PKGBUILD new file mode 100644 index 0000000000..9c1cc6a3a4 --- /dev/null +++ b/prepare/r-dotcall64/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dotCall64 +_pkgver=1.0-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Enhanced Foreign Function Interface Supporting Long Vectors' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-microbenchmark + r-openmpcontroller + r-rcolorbrewer + r-roxygen2 + r-spam + r-testthat +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dotcall64/lilac.py b/prepare/r-dotcall64/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dotcall64/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dotcall64/lilac.yaml b/prepare/r-dotcall64/lilac.yaml new file mode 100644 index 0000000000..00c85b58f4 --- /dev/null +++ b/prepare/r-dotcall64/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: dotCall64_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dotCall64 diff --git a/prepare/r-downloader/PKGBUILD b/prepare/r-downloader/PKGBUILD new file mode 100644 index 0000000000..f57940ba77 --- /dev/null +++ b/prepare/r-downloader/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=downloader +_pkgver=0.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Download Files over HTTP and HTTPS' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-digest +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-downloader/lilac.py b/prepare/r-downloader/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-downloader/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-downloader/lilac.yaml b/prepare/r-downloader/lilac.yaml new file mode 100644 index 0000000000..b4609b064d --- /dev/null +++ b/prepare/r-downloader/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +update_on: +- regex: downloader_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=downloader diff --git a/prepare/r-dpeak/PKGBUILD b/prepare/r-dpeak/PKGBUILD new file mode 100644 index 0000000000..1c486dbb49 --- /dev/null +++ b/prepare/r-dpeak/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: GNU make, meme, fimo +# Maintainer: Guoyi Zhang + +_pkgname=dpeak +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='dPeak (Deconvolution of Peaks in ChIP-seq Analysis)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bsgenome + r-iranges + r-rcpp +) +optdepends=( + r-bsgenome.ecoli.ncbi.20080805 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dpeak/lilac.py b/prepare/r-dpeak/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dpeak/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dpeak/lilac.yaml b/prepare/r-dpeak/lilac.yaml new file mode 100644 index 0000000000..41d5106af6 --- /dev/null +++ b/prepare/r-dpeak/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +- r-iranges +- r-rcpp +update_on: +- regex: dpeak_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/dpeak diff --git a/prepare/r-dplr/PKGBUILD b/prepare/r-dplr/PKGBUILD new file mode 100644 index 0000000000..8b41a03ffa --- /dev/null +++ b/prepare/r-dplr/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dplR +_pkgver=1.7.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dendrochronology Program Library in R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-digest + r-matrixstats + r-plyr + r-png + r-r.utils + r-signal + r-stringi + r-stringr + r-xml +) +optdepends=( + r-biobase + r-cairo + r-dichromat + r-foreach + r-forecast + r-gmp + r-iterators + r-knitr + r-rcolorbrewer + r-testthat + r-tikzdevice + r-waveslim +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dplr/lilac.py b/prepare/r-dplr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dplr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dplr/lilac.yaml b/prepare/r-dplr/lilac.yaml new file mode 100644 index 0000000000..ca8742175b --- /dev/null +++ b/prepare/r-dplr/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-matrixstats +- r-plyr +- r-png +- r-r.utils +- r-signal +- r-stringi +- r-stringr +- r-xml +update_on: +- regex: dplR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dplR diff --git a/prepare/r-dqrng/PKGBUILD b/prepare/r-dqrng/PKGBUILD new file mode 100644 index 0000000000..ce4d838476 --- /dev/null +++ b/prepare/r-dqrng/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dqrng +_pkgver=0.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast Pseudo Random Number Generators' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('AGPL') +depends=( + r + r-bh + r-rcpp + r-sitmo +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dqrng/lilac.py b/prepare/r-dqrng/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dqrng/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dqrng/lilac.yaml b/prepare/r-dqrng/lilac.yaml new file mode 100644 index 0000000000..1225c30964 --- /dev/null +++ b/prepare/r-dqrng/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-rcpp +- r-sitmo +update_on: +- regex: dqrng_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dqrng diff --git a/prepare/r-drawer/PKGBUILD b/prepare/r-drawer/PKGBUILD new file mode 100644 index 0000000000..94457b3247 --- /dev/null +++ b/prepare/r-drawer/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=drawer +_pkgver=0.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Interactive HTML Image Editing Tool' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bsplus + r-glue + r-htmltools + r-magrittr + r-shiny + r-stringr +) +optdepends=( + r-ggplot2 + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-drawer/lilac.py b/prepare/r-drawer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-drawer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-drawer/lilac.yaml b/prepare/r-drawer/lilac.yaml new file mode 100644 index 0000000000..3f7eba956e --- /dev/null +++ b/prepare/r-drawer/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsplus +- r-glue +- r-htmltools +- r-magrittr +- r-shiny +- r-stringr +update_on: +- regex: drawer_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=drawer diff --git a/prepare/r-drawproteins/PKGBUILD b/prepare/r-drawproteins/PKGBUILD new file mode 100644 index 0000000000..16a0220ef1 --- /dev/null +++ b/prepare/r-drawproteins/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=drawProteins +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Package to Draw Protein Schematics from Uniprot API output' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-ggplot2 + r-httr + r-readr + r-tidyr +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-drawproteins/lilac.py b/prepare/r-drawproteins/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-drawproteins/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-drawproteins/lilac.yaml b/prepare/r-drawproteins/lilac.yaml new file mode 100644 index 0000000000..50a899233f --- /dev/null +++ b/prepare/r-drawproteins/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-httr +- r-readr +- r-tidyr +update_on: +- regex: drawProteins_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/drawProteins diff --git a/prepare/r-drawr/PKGBUILD b/prepare/r-drawr/PKGBUILD new file mode 100644 index 0000000000..71fc8681e1 --- /dev/null +++ b/prepare/r-drawr/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DRaWR +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Discriminative Random Walk with Restart' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rocr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-drawr/lilac.py b/prepare/r-drawr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-drawr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-drawr/lilac.yaml b/prepare/r-drawr/lilac.yaml new file mode 100644 index 0000000000..dbbc068394 --- /dev/null +++ b/prepare/r-drawr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rocr +update_on: +- regex: DRaWR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=DRaWR diff --git a/prepare/r-drc/PKGBUILD b/prepare/r-drc/PKGBUILD new file mode 100644 index 0000000000..d3e2eaa73d --- /dev/null +++ b/prepare/r-drc/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=drc +_pkgver=3.0-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Dose-Response Curves' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-car + r-gtools + r-multcomp + r-plotrix + r-scales +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-drc/lilac.py b/prepare/r-drc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-drc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-drc/lilac.yaml b/prepare/r-drc/lilac.yaml new file mode 100644 index 0000000000..006a2baf84 --- /dev/null +++ b/prepare/r-drc/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-car +- r-gtools +- r-multcomp +- r-plotrix +- r-scales +update_on: +- regex: drc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=drc diff --git a/prepare/r-drimpute/PKGBUILD b/prepare/r-drimpute/PKGBUILD new file mode 100644 index 0000000000..512b286fa7 --- /dev/null +++ b/prepare/r-drimpute/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DrImpute +_pkgver=1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Imputing Dropout Events in Single-Cell RNA-Sequencing Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-devtools + r-irlba + r-knitr + r-rmarkdown + r-roxygen2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-drimpute/lilac.py b/prepare/r-drimpute/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-drimpute/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-drimpute/lilac.yaml b/prepare/r-drimpute/lilac.yaml new file mode 100644 index 0000000000..1835b4b921 --- /dev/null +++ b/prepare/r-drimpute/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: DrImpute_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=DrImpute diff --git a/prepare/r-drimseq/PKGBUILD b/prepare/r-drimseq/PKGBUILD new file mode 100644 index 0000000000..4e881889ab --- /dev/null +++ b/prepare/r-drimseq/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DRIMSeq +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-edger + r-genomicranges + r-ggplot2 + r-iranges + r-limma + r-reshape2 + r-s4vectors +) +optdepends=( + r-biocstyle + r-geuvadistranscriptexpr + r-grid + r-knitr + r-pasillatranscriptexpr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-drimseq/lilac.py b/prepare/r-drimseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-drimseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-drimseq/lilac.yaml b/prepare/r-drimseq/lilac.yaml new file mode 100644 index 0000000000..29e7c8a9d7 --- /dev/null +++ b/prepare/r-drimseq/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-edger +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-limma +- r-reshape2 +- r-s4vectors +update_on: +- regex: DRIMSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DRIMSeq diff --git a/prepare/r-drivernet/PKGBUILD b/prepare/r-drivernet/PKGBUILD new file mode 100644 index 0000000000..ab2cd9e5c4 --- /dev/null +++ b/prepare/r-drivernet/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DriverNet +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-drivernet/lilac.py b/prepare/r-drivernet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-drivernet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-drivernet/lilac.yaml b/prepare/r-drivernet/lilac.yaml new file mode 100644 index 0000000000..6dd9411799 --- /dev/null +++ b/prepare/r-drivernet/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: DriverNet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DriverNet diff --git a/prepare/r-dropletutils/PKGBUILD b/prepare/r-dropletutils/PKGBUILD new file mode 100644 index 0000000000..17ce866ddb --- /dev/null +++ b/prepare/r-dropletutils/PKGBUILD @@ -0,0 +1,54 @@ +# system requirements: C++11, GNU make +# Maintainer: Guoyi Zhang + +_pkgname=DropletUtils +_pkgver=1.14.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities for Handling Single-Cell Droplet Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-beachmat + r-bh + r-biocgenerics + r-biocparallel + r-delayedarray + r-delayedmatrixstats + r-dqrng + r-edger + r-genomicranges + r-hdf5array + r-iranges + r-r.utils + r-rcpp + r-rhdf5 + r-rhdf5lib + r-s4vectors + r-scuttle + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-droplettestfiles + r-jsonlite + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dropletutils/lilac.py b/prepare/r-dropletutils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dropletutils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dropletutils/lilac.yaml b/prepare/r-dropletutils/lilac.yaml new file mode 100644 index 0000000000..7aa63c2d5c --- /dev/null +++ b/prepare/r-dropletutils/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beachmat +- r-bh +- r-biocgenerics +- r-biocparallel +- r-delayedarray +- r-delayedmatrixstats +- r-dqrng +- r-edger +- r-genomicranges +- r-hdf5array +- r-iranges +- r-r.utils +- r-rcpp +- r-rhdf5 +- r-rhdf5lib +- r-s4vectors +- r-scuttle +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: DropletUtils_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DropletUtils diff --git a/prepare/r-drtmle/PKGBUILD b/prepare/r-drtmle/PKGBUILD new file mode 100644 index 0000000000..10240219dd --- /dev/null +++ b/prepare/r-drtmle/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=drtmle +_pkgver=1.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Doubly-Robust Nonparametric Estimation and Inference' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-future.apply + r-np + r-superlearner +) +optdepends=( + r-earth + r-foreach + r-future.batchtools + r-gam + r-knitr + r-nloptr + r-parallel + r-quadprog + r-rmarkdown + r-stringi + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-drtmle/lilac.py b/prepare/r-drtmle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-drtmle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-drtmle/lilac.yaml b/prepare/r-drtmle/lilac.yaml new file mode 100644 index 0000000000..a9e2af2aea --- /dev/null +++ b/prepare/r-drtmle/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-future.apply +- r-np +- r-superlearner +update_on: +- regex: drtmle_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=drtmle diff --git a/prepare/r-drugtargetinteractions/PKGBUILD b/prepare/r-drugtargetinteractions/PKGBUILD new file mode 100644 index 0000000000..7b8152417b --- /dev/null +++ b/prepare/r-drugtargetinteractions/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=drugTargetInteractions +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Drug-Target Interactions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationfilter + r-biocfilecache + r-biomart + r-dplyr + r-ensembldb + r-rappdirs + r-rsqlite + r-s4vectors + r-uniprot.ws +) +optdepends=( + r-biocstyle + r-dt + r-ensdb.hsapiens.v86 + r-ggplot2 + r-knitr + r-reshape2 + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-drugtargetinteractions/lilac.py b/prepare/r-drugtargetinteractions/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-drugtargetinteractions/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-drugtargetinteractions/lilac.yaml b/prepare/r-drugtargetinteractions/lilac.yaml new file mode 100644 index 0000000000..98bda71ad0 --- /dev/null +++ b/prepare/r-drugtargetinteractions/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationfilter +- r-biocfilecache +- r-biomart +- r-dplyr +- r-ensembldb +- r-rappdirs +- r-rsqlite +- r-s4vectors +- r-uniprot.ws +update_on: +- regex: drugTargetInteractions_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/drugTargetInteractions diff --git a/prepare/r-drugvsdisease/PKGBUILD b/prepare/r-drugvsdisease/PKGBUILD new file mode 100644 index 0000000000..c26daed53f --- /dev/null +++ b/prepare/r-drugvsdisease/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DrugVsDisease +_pkgver=2.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Comparison of disease and drug profiles using Gene set Enrichment Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-annotate + r-arrayexpress + r-biocgenerics + r-biomart + r-cmap2data + r-drugvsdiseasedata + r-geoquery + r-hgu133a.db + r-hgu133a2.db + r-hgu133plus2.db + r-limma + r-qvalue + r-runit + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-drugvsdisease/lilac.py b/prepare/r-drugvsdisease/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-drugvsdisease/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-drugvsdisease/lilac.yaml b/prepare/r-drugvsdisease/lilac.yaml new file mode 100644 index 0000000000..1079370a7c --- /dev/null +++ b/prepare/r-drugvsdisease/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-annotate +- r-arrayexpress +- r-biocgenerics +- r-biomart +- r-cmap2data +- r-drugvsdiseasedata +- r-geoquery +- r-hgu133a.db +- r-hgu133a2.db +- r-hgu133plus2.db +- r-limma +- r-qvalue +- r-runit +- r-xtable +update_on: +- regex: DrugVsDisease_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DrugVsDisease diff --git a/prepare/r-drugvsdiseasedata/PKGBUILD b/prepare/r-drugvsdiseasedata/PKGBUILD new file mode 100644 index 0000000000..4dcf7fa98f --- /dev/null +++ b/prepare/r-drugvsdiseasedata/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DrugVsDiseasedata +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Drug versus Disease Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-drugvsdiseasedata/lilac.py b/prepare/r-drugvsdiseasedata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-drugvsdiseasedata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-drugvsdiseasedata/lilac.yaml b/prepare/r-drugvsdiseasedata/lilac.yaml new file mode 100644 index 0000000000..5212c2f00c --- /dev/null +++ b/prepare/r-drugvsdiseasedata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: DrugVsDiseasedata_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DrugVsDiseasedata diff --git a/prepare/r-dss/PKGBUILD b/prepare/r-dss/PKGBUILD new file mode 100644 index 0000000000..e501619244 --- /dev/null +++ b/prepare/r-dss/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DSS +_pkgver=2.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dispersion shrinkage for sequencing data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocparallel + r-bsseq + r-delayedarray +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dss/lilac.py b/prepare/r-dss/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dss/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dss/lilac.yaml b/prepare/r-dss/lilac.yaml new file mode 100644 index 0000000000..1a10995ade --- /dev/null +++ b/prepare/r-dss/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocparallel +- r-bsseq +- r-delayedarray +update_on: +- regex: DSS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DSS diff --git a/prepare/r-dstruct/PKGBUILD b/prepare/r-dstruct/PKGBUILD new file mode 100644 index 0000000000..e7f931707e --- /dev/null +++ b/prepare/r-dstruct/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dStruct +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identifying differentially reactive regions from RNA structurome profiling data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-iranges + r-purrr + r-reshape2 + r-rlang + r-s4vectors + r-zoo +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dstruct/lilac.py b/prepare/r-dstruct/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dstruct/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dstruct/lilac.yaml b/prepare/r-dstruct/lilac.yaml new file mode 100644 index 0000000000..198c29a50e --- /dev/null +++ b/prepare/r-dstruct/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-iranges +- r-purrr +- r-reshape2 +- r-rlang +- r-s4vectors +- r-zoo +update_on: +- regex: dStruct_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/dStruct diff --git a/prepare/r-dt/PKGBUILD b/prepare/r-dt/PKGBUILD new file mode 100644 index 0000000000..7e5eecfc56 --- /dev/null +++ b/prepare/r-dt/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DT +_pkgver=0.20 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="A Wrapper of the JavaScript Library 'DataTables'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-crosstalk + r-htmltools + r-htmlwidgets + r-jquerylib + r-jsonlite + r-magrittr + r-promises +) +optdepends=( + r-bslib + r-knitr + r-rmarkdown + r-shiny + r-testit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dt/lilac.py b/prepare/r-dt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dt/lilac.yaml b/prepare/r-dt/lilac.yaml new file mode 100644 index 0000000000..6cb48e73ce --- /dev/null +++ b/prepare/r-dt/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-crosstalk +- r-htmltools +- r-htmlwidgets +- r-jquerylib +- r-jsonlite +- r-magrittr +- r-promises +update_on: +- regex: DT_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=DT diff --git a/prepare/r-dta/PKGBUILD b/prepare/r-dta/PKGBUILD new file mode 100644 index 0000000000..052c585e62 --- /dev/null +++ b/prepare/r-dta/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DTA +_pkgver=2.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dynamic Transcriptome Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-lsd + r-scatterplot3d +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dta/lilac.py b/prepare/r-dta/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dta/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dta/lilac.yaml b/prepare/r-dta/lilac.yaml new file mode 100644 index 0000000000..25aad9fb0b --- /dev/null +++ b/prepare/r-dta/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lsd +- r-scatterplot3d +update_on: +- regex: DTA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DTA diff --git a/prepare/r-dtangle/PKGBUILD b/prepare/r-dtangle/PKGBUILD new file mode 100644 index 0000000000..bb29a4201a --- /dev/null +++ b/prepare/r-dtangle/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dtangle +_pkgver=2.0.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cell Type Deconvolution from Gene Expressions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-deoptimr +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dtangle/lilac.py b/prepare/r-dtangle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dtangle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dtangle/lilac.yaml b/prepare/r-dtangle/lilac.yaml new file mode 100644 index 0000000000..3fe49207b7 --- /dev/null +++ b/prepare/r-dtangle/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-deoptimr +update_on: +- regex: dtangle_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dtangle diff --git a/prepare/r-dtplyr/PKGBUILD b/prepare/r-dtplyr/PKGBUILD new file mode 100644 index 0000000000..b056bf1e02 --- /dev/null +++ b/prepare/r-dtplyr/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dtplyr +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Data Table Back-End for 'dplyr'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-crayon + r-data.table + r-dplyr + r-ellipsis + r-glue + r-lifecycle + r-rlang + r-tibble + r-tidyselect + r-vctrs +) +optdepends=( + r-bench + r-covr + r-knitr + r-rmarkdown + r-testthat + r-tidyr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dtplyr/lilac.py b/prepare/r-dtplyr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dtplyr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dtplyr/lilac.yaml b/prepare/r-dtplyr/lilac.yaml new file mode 100644 index 0000000000..d525c8d168 --- /dev/null +++ b/prepare/r-dtplyr/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-crayon +- r-data.table +- r-dplyr +- r-ellipsis +- r-glue +- r-lifecycle +- r-rlang +- r-tibble +- r-tidyselect +- r-vctrs +update_on: +- regex: dtplyr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dtplyr diff --git a/prepare/r-dtt/PKGBUILD b/prepare/r-dtt/PKGBUILD new file mode 100644 index 0000000000..3c1c982974 --- /dev/null +++ b/prepare/r-dtt/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dtt +_pkgver=0.1-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Discrete Trigonometric Transforms' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dtt/lilac.py b/prepare/r-dtt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dtt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dtt/lilac.yaml b/prepare/r-dtt/lilac.yaml new file mode 100644 index 0000000000..1f7fde5023 --- /dev/null +++ b/prepare/r-dtt/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: dtt_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dtt diff --git a/prepare/r-dtw/PKGBUILD b/prepare/r-dtw/PKGBUILD new file mode 100644 index 0000000000..a14fe736c8 --- /dev/null +++ b/prepare/r-dtw/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dtw +_pkgver=1.22-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dynamic Time Warping Algorithms' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-proxy +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dtw/lilac.py b/prepare/r-dtw/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dtw/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dtw/lilac.yaml b/prepare/r-dtw/lilac.yaml new file mode 100644 index 0000000000..1bba6a7916 --- /dev/null +++ b/prepare/r-dtw/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-proxy +update_on: +- regex: dtw_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dtw diff --git a/prepare/r-dualks/PKGBUILD b/prepare/r-dualks/PKGBUILD new file mode 100644 index 0000000000..45293225ad --- /dev/null +++ b/prepare/r-dualks/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dualKS +_pkgver=1.53.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dual KS Discriminant Analysis and Classification' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-affy + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dualks/lilac.py b/prepare/r-dualks/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dualks/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dualks/lilac.yaml b/prepare/r-dualks/lilac.yaml new file mode 100644 index 0000000000..4d095eb214 --- /dev/null +++ b/prepare/r-dualks/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +update_on: +- regex: dualKS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/dualKS diff --git a/prepare/r-dune/PKGBUILD b/prepare/r-dune/PKGBUILD new file mode 100644 index 0000000000..57c29fdc34 --- /dev/null +++ b/prepare/r-dune/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Dune +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Improving replicability in single-cell RNA-Seq cell type discovery' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-aricode + r-biocparallel + r-dplyr + r-gganimate + r-ggplot2 + r-magrittr + r-purrr + r-rcolorbrewer + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dune/lilac.py b/prepare/r-dune/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dune/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dune/lilac.yaml b/prepare/r-dune/lilac.yaml new file mode 100644 index 0000000000..418ebb9c48 --- /dev/null +++ b/prepare/r-dune/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aricode +- r-biocparallel +- r-dplyr +- r-gganimate +- r-ggplot2 +- r-magrittr +- r-purrr +- r-rcolorbrewer +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: Dune_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Dune diff --git a/prepare/r-dunn.test/PKGBUILD b/prepare/r-dunn.test/PKGBUILD new file mode 100644 index 0000000000..f9f7375f79 --- /dev/null +++ b/prepare/r-dunn.test/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dunn.test +_pkgver=1.3.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Dunn's Test of Multiple Comparisons Using Rank Sums" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dunn.test/lilac.py b/prepare/r-dunn.test/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dunn.test/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dunn.test/lilac.yaml b/prepare/r-dunn.test/lilac.yaml new file mode 100644 index 0000000000..764c20973d --- /dev/null +++ b/prepare/r-dunn.test/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: dunn.test_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dunn.test diff --git a/prepare/r-dupradar/PKGBUILD b/prepare/r-dupradar/PKGBUILD new file mode 100644 index 0000000000..3249a44bc2 --- /dev/null +++ b/prepare/r-dupradar/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dupRadar +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assessment of duplication rates in RNA-Seq datasets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rsubread +) +optdepends=( + r-annotationhub + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dupradar/lilac.py b/prepare/r-dupradar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dupradar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dupradar/lilac.yaml b/prepare/r-dupradar/lilac.yaml new file mode 100644 index 0000000000..cc06642b39 --- /dev/null +++ b/prepare/r-dupradar/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rsubread +update_on: +- regex: dupRadar_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/dupRadar diff --git a/prepare/r-dyebias/PKGBUILD b/prepare/r-dyebias/PKGBUILD new file mode 100644 index 0000000000..6c525a3f11 --- /dev/null +++ b/prepare/r-dyebias/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dyebias +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The GASSCO method for correcting for slide-dependent gene-specific dye bias' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-marray +) +optdepends=( + r-convert + r-dyebiasexamples + r-geoquery + r-limma + r-methods +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dyebias/lilac.py b/prepare/r-dyebias/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dyebias/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dyebias/lilac.yaml b/prepare/r-dyebias/lilac.yaml new file mode 100644 index 0000000000..22e24929a4 --- /dev/null +++ b/prepare/r-dyebias/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-marray +update_on: +- regex: dyebias_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/dyebias diff --git a/prepare/r-dynamictreecut/PKGBUILD b/prepare/r-dynamictreecut/PKGBUILD new file mode 100644 index 0000000000..81e2a269bd --- /dev/null +++ b/prepare/r-dynamictreecut/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=dynamicTreeCut +_pkgver=1.63-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methods for Detection of Clusters in Hierarchical Clustering Dendrograms' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dynamictreecut/lilac.py b/prepare/r-dynamictreecut/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dynamictreecut/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dynamictreecut/lilac.yaml b/prepare/r-dynamictreecut/lilac.yaml new file mode 100644 index 0000000000..c246cbc6ec --- /dev/null +++ b/prepare/r-dynamictreecut/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: dynamicTreeCut_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=dynamicTreeCut diff --git a/prepare/r-dyndoc/PKGBUILD b/prepare/r-dyndoc/PKGBUILD new file mode 100644 index 0000000000..e067ca0132 --- /dev/null +++ b/prepare/r-dyndoc/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=DynDoc +_pkgver=1.72.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dynamic document tools' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-dyndoc/lilac.py b/prepare/r-dyndoc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-dyndoc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-dyndoc/lilac.yaml b/prepare/r-dyndoc/lilac.yaml new file mode 100644 index 0000000000..cb4ee76db5 --- /dev/null +++ b/prepare/r-dyndoc/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: DynDoc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/DynDoc diff --git a/prepare/r-e1071/PKGBUILD b/prepare/r-e1071/PKGBUILD new file mode 100644 index 0000000000..3fd1384855 --- /dev/null +++ b/prepare/r-e1071/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=e1071 +_pkgver=1.7-9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-proxy +) +optdepends=( + r-cluster + r-mass + r-matrix + r-mlbench + r-nnet + r-randomforest + r-rpart + r-slam + r-sparsem + r-xtable +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-e1071/lilac.py b/prepare/r-e1071/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-e1071/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-e1071/lilac.yaml b/prepare/r-e1071/lilac.yaml new file mode 100644 index 0000000000..179266fc10 --- /dev/null +++ b/prepare/r-e1071/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-proxy +update_on: +- regex: e1071_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=e1071 diff --git a/prepare/r-earth/PKGBUILD b/prepare/r-earth/PKGBUILD new file mode 100644 index 0000000000..913a19a3f1 --- /dev/null +++ b/prepare/r-earth/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=earth +_pkgver=5.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multivariate Adaptive Regression Splines' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-formula + r-plotmo + r-teachingdemos +) +optdepends=( + r-gam + r-mass + r-mda + r-mgcv +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-earth/lilac.py b/prepare/r-earth/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-earth/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-earth/lilac.yaml b/prepare/r-earth/lilac.yaml new file mode 100644 index 0000000000..7d380e19c6 --- /dev/null +++ b/prepare/r-earth/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-formula +- r-plotmo +- r-teachingdemos +update_on: +- regex: earth_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=earth diff --git a/prepare/r-easier/PKGBUILD b/prepare/r-easier/PKGBUILD new file mode 100644 index 0000000000..2448075996 --- /dev/null +++ b/prepare/r-easier/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=easier +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimate Systems Immune Response from RNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-arules + r-biocparallel + r-coin + r-deseq2 + r-dorothea + r-dplyr + r-easierdata + r-ggplot2 + r-ggrepel + r-matrixstats + r-progeny + r-quantiseqr + r-reshape2 + r-rlang + r-rocr + r-rstatix +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-summarizedexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-easier/lilac.py b/prepare/r-easier/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-easier/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-easier/lilac.yaml b/prepare/r-easier/lilac.yaml new file mode 100644 index 0000000000..139eb1b5a4 --- /dev/null +++ b/prepare/r-easier/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-arules +- r-biocparallel +- r-coin +- r-deseq2 +- r-dorothea +- r-dplyr +- r-easierdata +- r-ggplot2 +- r-ggrepel +- r-matrixstats +- r-progeny +- r-quantiseqr +- r-reshape2 +- r-rlang +- r-rocr +- r-rstatix +update_on: +- regex: easier_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/easier diff --git a/prepare/r-easierdata/PKGBUILD b/prepare/r-easierdata/PKGBUILD new file mode 100644 index 0000000000..ad8db63b94 --- /dev/null +++ b/prepare/r-easierdata/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=easierData +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='easier internal data and exemplary dataset from IMvigor210CoreBiologies package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationhub + r-experimenthub + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-easierdata/lilac.py b/prepare/r-easierdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-easierdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-easierdata/lilac.yaml b/prepare/r-easierdata/lilac.yaml new file mode 100644 index 0000000000..9c1660095f --- /dev/null +++ b/prepare/r-easierdata/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-experimenthub +- r-summarizedexperiment +update_on: +- regex: easierData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/easierData diff --git a/prepare/r-easypubmed/PKGBUILD b/prepare/r-easypubmed/PKGBUILD new file mode 100644 index 0000000000..995648d198 --- /dev/null +++ b/prepare/r-easypubmed/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=easyPubMed +_pkgver=2.13 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Search and Retrieve Scientific Publication Records from PubMed' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-easypubmed/lilac.py b/prepare/r-easypubmed/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-easypubmed/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-easypubmed/lilac.yaml b/prepare/r-easypubmed/lilac.yaml new file mode 100644 index 0000000000..b49412c7c6 --- /dev/null +++ b/prepare/r-easypubmed/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: easyPubMed_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=easyPubMed diff --git a/prepare/r-easyreporting/PKGBUILD b/prepare/r-easyreporting/PKGBUILD new file mode 100644 index 0000000000..d129aa9ae8 --- /dev/null +++ b/prepare/r-easyreporting/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=easyreporting +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Helps creating report for improving Reproducible Computational Research' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-rlang + r-rmarkdown + r-shiny +) +optdepends=( + r-biocstyle + r-distill + r-edaseq + r-edger + r-knitr + r-limma + r-readxl + r-statmod +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-easyreporting/lilac.py b/prepare/r-easyreporting/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-easyreporting/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-easyreporting/lilac.yaml b/prepare/r-easyreporting/lilac.yaml new file mode 100644 index 0000000000..a33c21f18a --- /dev/null +++ b/prepare/r-easyreporting/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rlang +- r-rmarkdown +- r-shiny +update_on: +- regex: easyreporting_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/easyreporting diff --git a/prepare/r-easyrnaseq/PKGBUILD b/prepare/r-easyrnaseq/PKGBUILD new file mode 100644 index 0000000000..76e318987a --- /dev/null +++ b/prepare/r-easyrnaseq/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=easyRNASeq +_pkgver=2.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Count summarization and normalization for RNA-Seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocfilecache + r-biocgenerics + r-biocparallel + r-biomart + r-biostrings + r-edger + r-genomeinfodb + r-genomeintervals + r-genomicalignments + r-genomicranges + r-iranges + r-locfit + r-lsd + r-rappdirs + r-rsamtools + r-s4vectors + r-shortread + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-bsgenome + r-bsgenome.dmelanogaster.ucsc.dm3 + r-curl + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-easyrnaseq/lilac.py b/prepare/r-easyrnaseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-easyrnaseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-easyrnaseq/lilac.yaml b/prepare/r-easyrnaseq/lilac.yaml new file mode 100644 index 0000000000..37099b73e8 --- /dev/null +++ b/prepare/r-easyrnaseq/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocfilecache +- r-biocgenerics +- r-biocparallel +- r-biomart +- r-biostrings +- r-edger +- r-genomeinfodb +- r-genomeintervals +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-locfit +- r-lsd +- r-rappdirs +- r-rsamtools +- r-s4vectors +- r-shortread +- r-summarizedexperiment +update_on: +- regex: easyRNASeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/easyRNASeq diff --git a/prepare/r-ebarrays/PKGBUILD b/prepare/r-ebarrays/PKGBUILD new file mode 100644 index 0000000000..e7bc3b35ec --- /dev/null +++ b/prepare/r-ebarrays/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EBarrays +_pkgver=2.58.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ebarrays/lilac.py b/prepare/r-ebarrays/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ebarrays/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ebarrays/lilac.yaml b/prepare/r-ebarrays/lilac.yaml new file mode 100644 index 0000000000..b4be1ed821 --- /dev/null +++ b/prepare/r-ebarrays/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: EBarrays_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EBarrays diff --git a/prepare/r-ebcoexpress/PKGBUILD b/prepare/r-ebcoexpress/PKGBUILD new file mode 100644 index 0000000000..0a2b1191ac --- /dev/null +++ b/prepare/r-ebcoexpress/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EBcoexpress +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='EBcoexpress for Differential Co-Expression Analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ebarrays + r-mclust + r-minqa +) +optdepends=( + r-colorspace + r-graph + r-igraph +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ebcoexpress/lilac.py b/prepare/r-ebcoexpress/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ebcoexpress/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ebcoexpress/lilac.yaml b/prepare/r-ebcoexpress/lilac.yaml new file mode 100644 index 0000000000..6b44256c30 --- /dev/null +++ b/prepare/r-ebcoexpress/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ebarrays +- r-mclust +- r-minqa +update_on: +- regex: EBcoexpress_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EBcoexpress diff --git a/prepare/r-ebimage/PKGBUILD b/prepare/r-ebimage/PKGBUILD new file mode 100644 index 0000000000..10c41ba307 --- /dev/null +++ b/prepare/r-ebimage/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EBImage +_pkgver=4.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Image processing and analysis toolbox for R' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-abind + r-biocgenerics + r-fftwtools + r-htmltools + r-htmlwidgets + r-jpeg + r-locfit + r-png + r-rcurl + r-tiff +) +optdepends=( + r-biocstyle + r-digest + r-knitr + r-rmarkdown + r-shiny +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ebimage/lilac.py b/prepare/r-ebimage/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ebimage/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ebimage/lilac.yaml b/prepare/r-ebimage/lilac.yaml new file mode 100644 index 0000000000..5837e04f08 --- /dev/null +++ b/prepare/r-ebimage/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-biocgenerics +- r-fftwtools +- r-htmltools +- r-htmlwidgets +- r-jpeg +- r-locfit +- r-png +- r-rcurl +- r-tiff +update_on: +- regex: EBImage_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EBImage diff --git a/prepare/r-ebsea/PKGBUILD b/prepare/r-ebsea/PKGBUILD new file mode 100644 index 0000000000..7b2eb916bc --- /dev/null +++ b/prepare/r-ebsea/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EBSEA +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Exon Based Strategy for Expression Analysis of genes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-deseq2 + r-empiricalbrownsmethod +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ebsea/lilac.py b/prepare/r-ebsea/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ebsea/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ebsea/lilac.yaml b/prepare/r-ebsea/lilac.yaml new file mode 100644 index 0000000000..e5ef99f438 --- /dev/null +++ b/prepare/r-ebsea/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-deseq2 +- r-empiricalbrownsmethod +update_on: +- regex: EBSEA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EBSEA diff --git a/prepare/r-ebseq/PKGBUILD b/prepare/r-ebseq/PKGBUILD new file mode 100644 index 0000000000..206c7f7016 --- /dev/null +++ b/prepare/r-ebseq/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EBSeq +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package for gene and isoform differential expression analysis of RNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-blockmodeling + r-gplots + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ebseq/lilac.py b/prepare/r-ebseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ebseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ebseq/lilac.yaml b/prepare/r-ebseq/lilac.yaml new file mode 100644 index 0000000000..3e2f03a68c --- /dev/null +++ b/prepare/r-ebseq/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-blockmodeling +- r-gplots +- r-testthat +update_on: +- regex: EBSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EBSeq diff --git a/prepare/r-ebseqhmm/PKGBUILD b/prepare/r-ebseqhmm/PKGBUILD new file mode 100644 index 0000000000..899b330dcd --- /dev/null +++ b/prepare/r-ebseqhmm/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EBSeqHMM +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ebseq +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ebseqhmm/lilac.py b/prepare/r-ebseqhmm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ebseqhmm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ebseqhmm/lilac.yaml b/prepare/r-ebseqhmm/lilac.yaml new file mode 100644 index 0000000000..12f42852e1 --- /dev/null +++ b/prepare/r-ebseqhmm/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ebseq +update_on: +- regex: EBSeqHMM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EBSeqHMM diff --git a/prepare/r-echarts4r/PKGBUILD b/prepare/r-echarts4r/PKGBUILD new file mode 100644 index 0000000000..8196dcc881 --- /dev/null +++ b/prepare/r-echarts4r/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=echarts4r +_pkgver=0.4.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Create Interactive Graphs with 'Echarts JavaScript' Version 5" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-broom + r-corrplot + r-countrycode + r-dplyr + r-htmltools + r-htmlwidgets + r-jsonlite + r-purrr + r-rstudioapi + r-scales + r-shiny +) +optdepends=( + r-covr + r-data.tree + r-knitr + r-leaflet + r-rmarkdown + r-testthat + r-tibble + r-tidyr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-echarts4r/lilac.py b/prepare/r-echarts4r/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-echarts4r/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-echarts4r/lilac.yaml b/prepare/r-echarts4r/lilac.yaml new file mode 100644 index 0000000000..8f64449731 --- /dev/null +++ b/prepare/r-echarts4r/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-broom +- r-corrplot +- r-countrycode +- r-dplyr +- r-htmltools +- r-htmlwidgets +- r-jsonlite +- r-purrr +- r-rstudioapi +- r-scales +- r-shiny +update_on: +- regex: echarts4r_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=echarts4r diff --git a/prepare/r-ecolitk/PKGBUILD b/prepare/r-ecolitk/PKGBUILD new file mode 100644 index 0000000000..8dfaa80a22 --- /dev/null +++ b/prepare/r-ecolitk/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ecolitk +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Meta-data and tools for E. coli' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +optdepends=( + r-affy + r-ecolicdf + r-ecolileucine + r-graph + r-multtest +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ecolitk/lilac.py b/prepare/r-ecolitk/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ecolitk/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ecolitk/lilac.yaml b/prepare/r-ecolitk/lilac.yaml new file mode 100644 index 0000000000..2a23c86d2b --- /dev/null +++ b/prepare/r-ecolitk/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: ecolitk_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ecolitk diff --git a/prepare/r-ecp/PKGBUILD b/prepare/r-ecp/PKGBUILD new file mode 100644 index 0000000000..18a4a47ecc --- /dev/null +++ b/prepare/r-ecp/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ecp +_pkgver=3.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Non-Parametric Multiple Change-Point Analysis of Multivariate Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-combinat + r-mass + r-mvtnorm + r-r.rsp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ecp/lilac.py b/prepare/r-ecp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ecp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ecp/lilac.yaml b/prepare/r-ecp/lilac.yaml new file mode 100644 index 0000000000..8933d830fa --- /dev/null +++ b/prepare/r-ecp/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: ecp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ecp diff --git a/prepare/r-ecume/PKGBUILD b/prepare/r-ecume/PKGBUILD new file mode 100644 index 0000000000..d4c33045eb --- /dev/null +++ b/prepare/r-ecume/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Ecume +_pkgver=0.9.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Equality of 2 (or k) Continuous Univariate and Multivariate Distributions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-caret + r-dplyr + r-e1071 + r-kernlab + r-magrittr + r-pbapply + r-spatstat + r-spatstat.geom + r-transport +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ecume/lilac.py b/prepare/r-ecume/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ecume/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ecume/lilac.yaml b/prepare/r-ecume/lilac.yaml new file mode 100644 index 0000000000..3acd2e2c87 --- /dev/null +++ b/prepare/r-ecume/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-caret +- r-dplyr +- r-e1071 +- r-kernlab +- r-magrittr +- r-pbapply +- r-spatstat +- r-spatstat.geom +- r-transport +update_on: +- regex: Ecume_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Ecume diff --git a/prepare/r-edaseq/PKGBUILD b/prepare/r-edaseq/PKGBUILD new file mode 100644 index 0000000000..306a649d77 --- /dev/null +++ b/prepare/r-edaseq/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EDASeq +_pkgver=2.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Exploratory Data Analysis and Normalization for RNA-Seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-aroma.light + r-biobase + r-biocgenerics + r-biocmanager + r-biomart + r-biostrings + r-genomicfeatures + r-genomicranges + r-iranges + r-rsamtools + r-shortread +) +optdepends=( + r-biocstyle + r-deseq2 + r-edger + r-kernsmooth + r-knitr + r-leebamviews + r-rmarkdown + r-testthat + r-yeastrnaseq +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-edaseq/lilac.py b/prepare/r-edaseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-edaseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-edaseq/lilac.yaml b/prepare/r-edaseq/lilac.yaml new file mode 100644 index 0000000000..f1aa0c0125 --- /dev/null +++ b/prepare/r-edaseq/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-aroma.light +- r-biobase +- r-biocgenerics +- r-biocmanager +- r-biomart +- r-biostrings +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-rsamtools +- r-shortread +update_on: +- regex: EDASeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EDASeq diff --git a/prepare/r-edge/PKGBUILD b/prepare/r-edge/PKGBUILD new file mode 100644 index 0000000000..c9a95fd403 --- /dev/null +++ b/prepare/r-edge/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=edge +_pkgver=2.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Extraction of Differential Gene Expression' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-jackstraw + r-qvalue + r-snm + r-sva +) +optdepends=( + r-ggplot2 + r-knitr + r-reshape2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-edge/lilac.py b/prepare/r-edge/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-edge/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-edge/lilac.yaml b/prepare/r-edge/lilac.yaml new file mode 100644 index 0000000000..5e9bbb96c0 --- /dev/null +++ b/prepare/r-edge/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-jackstraw +- r-qvalue +- r-snm +- r-sva +update_on: +- regex: edge_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/edge diff --git a/prepare/r-edger/PKGBUILD b/prepare/r-edger/PKGBUILD new file mode 100644 index 0000000000..2ec135d975 --- /dev/null +++ b/prepare/r-edger/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=edgeR +_pkgver=3.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Empirical Analysis of Digital Gene Expression Data in R' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-limma + r-locfit + r-rcpp +) +optdepends=( + r-annotationdbi + r-biobase + r-jsonlite + r-org.hs.eg.db + r-readr + r-rhdf5 + r-splines + r-summarizedexperiment +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-edger/lilac.py b/prepare/r-edger/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-edger/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-edger/lilac.yaml b/prepare/r-edger/lilac.yaml new file mode 100644 index 0000000000..5fbdeb5eb4 --- /dev/null +++ b/prepare/r-edger/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-limma +- r-locfit +- r-rcpp +update_on: +- regex: edgeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/edgeR diff --git a/prepare/r-eegc/PKGBUILD b/prepare/r-eegc/PKGBUILD new file mode 100644 index 0000000000..fa9c4663de --- /dev/null +++ b/prepare/r-eegc/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=eegc +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Engineering Evaluation by Gene Categorization (eegc)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-clusterprofiler + r-deseq2 + r-dose + r-edger + r-ggplot2 + r-gplots + r-igraph + r-limma + r-org.hs.eg.db + r-org.mm.eg.db + r-pheatmap + r-r.utils + r-s4vectors + r-sna + r-wordcloud +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-eegc/lilac.py b/prepare/r-eegc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-eegc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-eegc/lilac.yaml b/prepare/r-eegc/lilac.yaml new file mode 100644 index 0000000000..bf6cc84537 --- /dev/null +++ b/prepare/r-eegc/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-clusterprofiler +- r-deseq2 +- r-dose +- r-edger +- r-ggplot2 +- r-gplots +- r-igraph +- r-limma +- r-org.hs.eg.db +- r-org.mm.eg.db +- r-pheatmap +- r-r.utils +- r-s4vectors +- r-sna +- r-wordcloud +update_on: +- regex: eegc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/eegc diff --git a/prepare/r-effsize/PKGBUILD b/prepare/r-effsize/PKGBUILD new file mode 100644 index 0000000000..fabc4e460f --- /dev/null +++ b/prepare/r-effsize/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=effsize +_pkgver=0.8.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Efficient Effect Size Computation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-effsize/lilac.py b/prepare/r-effsize/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-effsize/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-effsize/lilac.yaml b/prepare/r-effsize/lilac.yaml new file mode 100644 index 0000000000..d4988d18c0 --- /dev/null +++ b/prepare/r-effsize/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: effsize_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=effsize diff --git a/prepare/r-egad/PKGBUILD b/prepare/r-egad/PKGBUILD new file mode 100644 index 0000000000..d0c5784f1c --- /dev/null +++ b/prepare/r-egad/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EGAD +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Extending guilt by association by degree' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-geoquery + r-gplots + r-igraph + r-impute + r-limma + r-plyr + r-rcolorbrewer + r-rcurl + r-zoo +) +optdepends=( + r-knitr + r-markdown + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-egad/lilac.py b/prepare/r-egad/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-egad/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-egad/lilac.yaml b/prepare/r-egad/lilac.yaml new file mode 100644 index 0000000000..f38cc72784 --- /dev/null +++ b/prepare/r-egad/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-geoquery +- r-gplots +- r-igraph +- r-impute +- r-limma +- r-plyr +- r-rcolorbrewer +- r-rcurl +- r-zoo +update_on: +- regex: EGAD_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EGAD diff --git a/prepare/r-egg/PKGBUILD b/prepare/r-egg/PKGBUILD new file mode 100644 index 0000000000..a9ce325da3 --- /dev/null +++ b/prepare/r-egg/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=egg +_pkgver=0.4.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Extensions for 'ggplot2': Custom Geom, Custom Themes, Plot Alignment, Labelled Panels, Symmetric Scales, and Fixed Panel Size" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-gridextra + r-gtable +) +optdepends=( + r-knitr + r-png +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-egg/lilac.py b/prepare/r-egg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-egg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-egg/lilac.yaml b/prepare/r-egg/lilac.yaml new file mode 100644 index 0000000000..dc1990dc4c --- /dev/null +++ b/prepare/r-egg/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gridextra +- r-gtable +update_on: +- regex: egg_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=egg diff --git a/prepare/r-egsea/PKGBUILD b/prepare/r-egsea/PKGBUILD new file mode 100644 index 0000000000..375dc302fd --- /dev/null +++ b/prepare/r-egsea/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EGSEA +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Ensemble of Gene Set Enrichment Analyses' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biobase + r-dt + r-edger + r-egseadata + r-gage + r-ggplot2 + r-globaltest + r-gplots + r-gsva + r-htmlutils + r-htmlwidgets + r-hwriter + r-limma + r-metap + r-org.hs.eg.db + r-org.mm.eg.db + r-org.rn.eg.db + r-padog + r-pathview + r-plotly + r-rcolorbrewer + r-safe + r-stringi + r-topgo +) +optdepends=( + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-egsea/lilac.py b/prepare/r-egsea/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-egsea/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-egsea/lilac.yaml b/prepare/r-egsea/lilac.yaml new file mode 100644 index 0000000000..3a254b4831 --- /dev/null +++ b/prepare/r-egsea/lilac.yaml @@ -0,0 +1,34 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-dt +- r-edger +- r-egseadata +- r-gage +- r-ggplot2 +- r-globaltest +- r-gplots +- r-gsva +- r-htmlutils +- r-htmlwidgets +- r-hwriter +- r-limma +- r-metap +- r-org.hs.eg.db +- r-org.mm.eg.db +- r-org.rn.eg.db +- r-padog +- r-pathview +- r-plotly +- r-rcolorbrewer +- r-safe +- r-stringi +- r-topgo +update_on: +- regex: EGSEA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EGSEA diff --git a/prepare/r-egseadata/PKGBUILD b/prepare/r-egseadata/PKGBUILD new file mode 100644 index 0000000000..5a966a2fb1 --- /dev/null +++ b/prepare/r-egseadata/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EGSEAdata +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene set collections for the EGSEA package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r +) +optdepends=( + r-egsea +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-egseadata/lilac.py b/prepare/r-egseadata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-egseadata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-egseadata/lilac.yaml b/prepare/r-egseadata/lilac.yaml new file mode 100644 index 0000000000..1dbc0a9a25 --- /dev/null +++ b/prepare/r-egseadata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: EGSEAdata_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EGSEAdata diff --git a/prepare/r-einsum/PKGBUILD b/prepare/r-einsum/PKGBUILD new file mode 100644 index 0000000000..ecb2dc730b --- /dev/null +++ b/prepare/r-einsum/PKGBUILD @@ -0,0 +1,35 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=einsum +_pkgver=0.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Einstein Summation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-glue + r-mathjaxr + r-rcpp +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-einsum/lilac.py b/prepare/r-einsum/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-einsum/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-einsum/lilac.yaml b/prepare/r-einsum/lilac.yaml new file mode 100644 index 0000000000..59eb7a1be4 --- /dev/null +++ b/prepare/r-einsum/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-glue +- r-mathjaxr +- r-rcpp +update_on: +- regex: einsum_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=einsum diff --git a/prepare/r-eir/PKGBUILD b/prepare/r-eir/PKGBUILD new file mode 100644 index 0000000000..47cce2895a --- /dev/null +++ b/prepare/r-eir/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=eiR +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Accelerated similarity searching of small molecules' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-chemminer + r-dbi + r-digest + r-rcppannoy + r-rcurl + r-runit + r-snow + r-snowfall +) +optdepends=( + r-biocstyle + r-knitcitations + r-knitr + r-knitrbootstrap + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-eir/lilac.py b/prepare/r-eir/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-eir/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-eir/lilac.yaml b/prepare/r-eir/lilac.yaml new file mode 100644 index 0000000000..84d65e31f6 --- /dev/null +++ b/prepare/r-eir/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-chemminer +- r-dbi +- r-digest +- r-rcppannoy +- r-rcurl +- r-runit +- r-snow +- r-snowfall +update_on: +- regex: eiR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/eiR diff --git a/prepare/r-eisar/PKGBUILD b/prepare/r-eisar/PKGBUILD new file mode 100644 index 0000000000..e6cd9bf584 --- /dev/null +++ b/prepare/r-eisar/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=eisaR +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Exon-Intron Split Analysis (EISA) in R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-edger + r-genomicranges + r-iranges + r-limma + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-annotationdbi + r-biocstyle + r-biostrings + r-bsgenome + r-bsgenome.hsapiens.ucsc.hg38 + r-ensembldb + r-genomicfeatures + r-knitr + r-quasr + r-rbowtie + r-rhisat2 + r-rmarkdown + r-rtracklayer + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-eisar/lilac.py b/prepare/r-eisar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-eisar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-eisar/lilac.yaml b/prepare/r-eisar/lilac.yaml new file mode 100644 index 0000000000..6e971a91d9 --- /dev/null +++ b/prepare/r-eisar/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-edger +- r-genomicranges +- r-iranges +- r-limma +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: eisaR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/eisaR diff --git a/prepare/r-elasticnet/PKGBUILD b/prepare/r-elasticnet/PKGBUILD new file mode 100644 index 0000000000..b23029f054 --- /dev/null +++ b/prepare/r-elasticnet/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=elasticnet +_pkgver=1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Elastic-Net for Sparse Estimation and Sparse PCA' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-lars +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-elasticnet/lilac.py b/prepare/r-elasticnet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-elasticnet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-elasticnet/lilac.yaml b/prepare/r-elasticnet/lilac.yaml new file mode 100644 index 0000000000..4ca2cf2348 --- /dev/null +++ b/prepare/r-elasticnet/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lars +update_on: +- regex: elasticnet_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=elasticnet diff --git a/prepare/r-elitism/PKGBUILD b/prepare/r-elitism/PKGBUILD new file mode 100644 index 0000000000..8dfb838ddf --- /dev/null +++ b/prepare/r-elitism/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=elitism +_pkgver=1.0.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Equipment for Logarithmic and Linear Time Stepwise Multiple Hypothesis Testing' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-elitism/lilac.py b/prepare/r-elitism/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-elitism/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-elitism/lilac.yaml b/prepare/r-elitism/lilac.yaml new file mode 100644 index 0000000000..4bd22faf7f --- /dev/null +++ b/prepare/r-elitism/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: elitism_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=elitism diff --git a/prepare/r-ellipse/PKGBUILD b/prepare/r-ellipse/PKGBUILD new file mode 100644 index 0000000000..b05c6de9f6 --- /dev/null +++ b/prepare/r-ellipse/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ellipse +_pkgver=0.4.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for Drawing Ellipses and Ellipse-Like Confidence Regions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-mass +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ellipse/lilac.py b/prepare/r-ellipse/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ellipse/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ellipse/lilac.yaml b/prepare/r-ellipse/lilac.yaml new file mode 100644 index 0000000000..6ce0de0b47 --- /dev/null +++ b/prepare/r-ellipse/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ellipse_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ellipse diff --git a/prepare/r-elmer.data/PKGBUILD b/prepare/r-elmer.data/PKGBUILD new file mode 100644 index 0000000000..f2ec67cffc --- /dev/null +++ b/prepare/r-elmer.data/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ELMER.data +_pkgver=2.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data for the ELMER package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicranges +) +optdepends=( + r-biocstyle + r-devtools + r-dplyr + r-dt + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-elmer.data/lilac.py b/prepare/r-elmer.data/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-elmer.data/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-elmer.data/lilac.yaml b/prepare/r-elmer.data/lilac.yaml new file mode 100644 index 0000000000..41e050eaaa --- /dev/null +++ b/prepare/r-elmer.data/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +update_on: +- regex: ELMER.data_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ELMER.data diff --git a/prepare/r-elmer/PKGBUILD b/prepare/r-elmer/PKGBUILD new file mode 100644 index 0000000000..13ecc7648e --- /dev/null +++ b/prepare/r-elmer/PKGBUILD @@ -0,0 +1,75 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ELMER +_pkgver=2.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-circlize + r-complexheatmap + r-delayedarray + r-doparallel + r-downloader + r-dplyr + r-elmer.data + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggpubr + r-ggrepel + r-gridextra + r-gviz + r-iranges + r-magrittr + r-multiassayexperiment + r-plotly + r-plyr + r-progress + r-purrr + r-readr + r-reshape + r-reshape2 + r-rmarkdown + r-rtracklayer + r-rvest + r-s4vectors + r-scales + r-stringr + r-summarizedexperiment + r-tcgabiolinks + r-tibble + r-tidyr + r-xml2 +) +optdepends=( + r-biocstyle + r-covr + r-data.table + r-dt + r-genomicinteractions + r-knitr + r-r.utils + r-sesamedata + r-testthat + r-webshot +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-elmer/lilac.py b/prepare/r-elmer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-elmer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-elmer/lilac.yaml b/prepare/r-elmer/lilac.yaml new file mode 100644 index 0000000000..502b96f814 --- /dev/null +++ b/prepare/r-elmer/lilac.yaml @@ -0,0 +1,46 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-circlize +- r-complexheatmap +- r-delayedarray +- r-doparallel +- r-downloader +- r-dplyr +- r-elmer.data +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-ggpubr +- r-ggrepel +- r-gridextra +- r-gviz +- r-iranges +- r-magrittr +- r-multiassayexperiment +- r-plotly +- r-plyr +- r-progress +- r-purrr +- r-readr +- r-reshape +- r-reshape2 +- r-rmarkdown +- r-rtracklayer +- r-rvest +- r-s4vectors +- r-scales +- r-stringr +- r-summarizedexperiment +- r-tcgabiolinks +- r-tibble +- r-tidyr +- r-xml2 +update_on: +- regex: ELMER_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ELMER diff --git a/prepare/r-emdbook/PKGBUILD b/prepare/r-emdbook/PKGBUILD new file mode 100644 index 0000000000..667fa3ba78 --- /dev/null +++ b/prepare/r-emdbook/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=emdbook +_pkgver=1.3.12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Support Functions and Data for "Ecological Models and Data"' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bbmle + r-coda + r-plyr +) +optdepends=( + r-ellipse + r-numderiv + r-r2jags + r-rgl + r-suppdists + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-emdbook/lilac.py b/prepare/r-emdbook/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-emdbook/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-emdbook/lilac.yaml b/prepare/r-emdbook/lilac.yaml new file mode 100644 index 0000000000..fd5306c942 --- /dev/null +++ b/prepare/r-emdbook/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bbmle +- r-coda +- r-plyr +update_on: +- regex: emdbook_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=emdbook diff --git a/prepare/r-emdist/PKGBUILD b/prepare/r-emdist/PKGBUILD new file mode 100644 index 0000000000..34af8effd0 --- /dev/null +++ b/prepare/r-emdist/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=emdist +_pkgver=0.3-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Earth Mover's Distance" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-emdist/lilac.py b/prepare/r-emdist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-emdist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-emdist/lilac.yaml b/prepare/r-emdist/lilac.yaml new file mode 100644 index 0000000000..a18904b282 --- /dev/null +++ b/prepare/r-emdist/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: emdist_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=emdist diff --git a/prepare/r-emdomics/PKGBUILD b/prepare/r-emdomics/PKGBUILD new file mode 100644 index 0000000000..a68163a7d8 --- /dev/null +++ b/prepare/r-emdomics/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EMDomics +_pkgver=2.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Earth Mover's Distance for Differential Analysis of Genomics Data" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocparallel + r-cdft + r-emdist + r-ggplot2 + r-matrixstats + r-preprocesscore +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-emdomics/lilac.py b/prepare/r-emdomics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-emdomics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-emdomics/lilac.yaml b/prepare/r-emdomics/lilac.yaml new file mode 100644 index 0000000000..f8bffda8da --- /dev/null +++ b/prepare/r-emdomics/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-cdft +- r-emdist +- r-ggplot2 +- r-matrixstats +- r-preprocesscore +update_on: +- regex: EMDomics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EMDomics diff --git a/prepare/r-emmeans/PKGBUILD b/prepare/r-emmeans/PKGBUILD new file mode 100644 index 0000000000..79f1ecb785 --- /dev/null +++ b/prepare/r-emmeans/PKGBUILD @@ -0,0 +1,70 @@ +# Maintainer: Guoyi Zhang + +_pkgname=emmeans +_pkgver=1.7.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimated Marginal Means, aka Least-Squares Means' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-estimability + r-mvtnorm + r-numderiv + r-xtable +) +optdepends=( + r-bayesplot + r-bayestestr + r-biglm + r-brms + r-car + r-carbayes + r-coda + r-coxme + r-gee + r-geepack + r-ggplot2 + r-knitr + r-lattice + r-lme4 + r-lmertest + r-logspline + r-mass + r-mcmcglmm + r-mcmcpack + r-mediation + r-mgcv + r-mice + r-multcomp + r-multcompview + r-mumin + r-nlme + r-nnet + r-ordinal + r-pbkrtest + r-pscl + r-rmarkdown + r-rsm + r-rstanarm + r-scales + r-sommer + r-splines + r-survival + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-emmeans/lilac.py b/prepare/r-emmeans/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-emmeans/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-emmeans/lilac.yaml b/prepare/r-emmeans/lilac.yaml new file mode 100644 index 0000000000..e076f8c395 --- /dev/null +++ b/prepare/r-emmeans/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-estimability +- r-mvtnorm +- r-numderiv +- r-xtable +update_on: +- regex: emmeans_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=emmeans diff --git a/prepare/r-empiricalbrownsmethod/PKGBUILD b/prepare/r-empiricalbrownsmethod/PKGBUILD new file mode 100644 index 0000000000..0322fb62a5 --- /dev/null +++ b/prepare/r-empiricalbrownsmethod/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EmpiricalBrownsMethod +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Uses Brown's method to combine p-values from dependent tests" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-empiricalbrownsmethod/lilac.py b/prepare/r-empiricalbrownsmethod/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-empiricalbrownsmethod/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-empiricalbrownsmethod/lilac.yaml b/prepare/r-empiricalbrownsmethod/lilac.yaml new file mode 100644 index 0000000000..8117a224ed --- /dev/null +++ b/prepare/r-empiricalbrownsmethod/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: EmpiricalBrownsMethod_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EmpiricalBrownsMethod diff --git a/prepare/r-emt/PKGBUILD b/prepare/r-emt/PKGBUILD new file mode 100644 index 0000000000..8a74f18524 --- /dev/null +++ b/prepare/r-emt/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EMT +_pkgver=1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Exact Multinomial Test: Goodness-of-Fit Test for Discrete Multivariate Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-emt/lilac.py b/prepare/r-emt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-emt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-emt/lilac.yaml b/prepare/r-emt/lilac.yaml new file mode 100644 index 0000000000..53ebe0a768 --- /dev/null +++ b/prepare/r-emt/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: EMT_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=EMT diff --git a/prepare/r-encodeexplorer/PKGBUILD b/prepare/r-encodeexplorer/PKGBUILD new file mode 100644 index 0000000000..92176dd9c1 --- /dev/null +++ b/prepare/r-encodeexplorer/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ENCODExplorer +_pkgver=2.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A compilation of ENCODE metadata' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-jsonlite + r-rcurl + r-tidyr + r-data.table + r-dplyr + r-stringr + r-stringi + r-annotationhub + r-genomicranges + r-rtracklayer + r-s4vectors + r-genomeinfodb + r-encodeexplordata +) +makedepends=( + git + tar +) +optdepends=( + r-runit + r-biocgenerics + r-knitr + r-curl + r-httr + r-shiny + r-shinythemes + r-dt +) +source=("git+https://git.bioconductor.org/packages/${_pkgname}.git") +sha256sums=('SKIP') + +build() { + tar -zcvf ${_pkgname}.tar.gz ${_pkgname} + R CMD INSTALL ${_pkgname}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: + diff --git a/prepare/r-encodeexplorer/lilac.py b/prepare/r-encodeexplorer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-encodeexplorer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-encodeexplorer/lilac.yaml b/prepare/r-encodeexplorer/lilac.yaml new file mode 100644 index 0000000000..df41917b0e --- /dev/null +++ b/prepare/r-encodeexplorer/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-jsonlite +- r-rcurl +- r-tidyr +- r-data.table +- r-dplyr +- r-stringr +- r-stringi +- r-annotationhub +- r-genomicranges +- r-rtracklayer +- r-s4vectors +- r-genomeinfodb +- r-encodeexplordata +update_on: +- regex: Version(\d+.\d+.\d+) + source: regex + url: https://bioconductor.org/packages/ENCODExplorer diff --git a/prepare/r-encodexplorerdata/PKGBUILD b/prepare/r-encodexplorerdata/PKGBUILD new file mode 100644 index 0000000000..b66b3cbe1e --- /dev/null +++ b/prepare/r-encodexplorerdata/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ENCODExplorerData +_pkgver=0.99.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A compilation of ENCODE metadata' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-data.table + r-jsonlite + r-rcurl +) +optdepends=( + r-annotationhub + r-biocgenerics + r-curl + r-httr + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-encodexplorerdata/lilac.py b/prepare/r-encodexplorerdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-encodexplorerdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-encodexplorerdata/lilac.yaml b/prepare/r-encodexplorerdata/lilac.yaml new file mode 100644 index 0000000000..7739c0f2f1 --- /dev/null +++ b/prepare/r-encodexplorerdata/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-jsonlite +- r-rcurl +update_on: +- regex: ENCODExplorerData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ENCODExplorerData diff --git a/prepare/r-energy/PKGBUILD b/prepare/r-energy/PKGBUILD new file mode 100644 index 0000000000..b7cc707c3d --- /dev/null +++ b/prepare/r-energy/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=energy +_pkgver=1.7-8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='E-Statistics: Multivariate Inference via the Energy of Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-gsl + r-rcpp +) +optdepends=( + r-compquadform + r-mass +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-energy/lilac.py b/prepare/r-energy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-energy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-energy/lilac.yaml b/prepare/r-energy/lilac.yaml new file mode 100644 index 0000000000..8210ad176b --- /dev/null +++ b/prepare/r-energy/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gsl +- r-rcpp +update_on: +- regex: energy_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=energy diff --git a/prepare/r-english/PKGBUILD b/prepare/r-english/PKGBUILD new file mode 100644 index 0000000000..0b6d1f4db8 --- /dev/null +++ b/prepare/r-english/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=english +_pkgver=1.2-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Translate Integers into English' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown + r-utils +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-english/lilac.py b/prepare/r-english/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-english/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-english/lilac.yaml b/prepare/r-english/lilac.yaml new file mode 100644 index 0000000000..aeb52b20bc --- /dev/null +++ b/prepare/r-english/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: english_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=english diff --git a/prepare/r-enhancedvolcano/PKGBUILD b/prepare/r-enhancedvolcano/PKGBUILD new file mode 100644 index 0000000000..093a90084d --- /dev/null +++ b/prepare/r-enhancedvolcano/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EnhancedVolcano +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Publication-ready volcano plots with enhanced colouring and labeling' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggalt + r-ggplot2 + r-ggrastr + r-ggrepel +) +optdepends=( + r-airway + r-biocgenerics + r-deseq2 + r-gridextra + r-knitr + r-magrittr + r-org.hs.eg.db + r-pasilla + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-enhancedvolcano/lilac.py b/prepare/r-enhancedvolcano/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-enhancedvolcano/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-enhancedvolcano/lilac.yaml b/prepare/r-enhancedvolcano/lilac.yaml new file mode 100644 index 0000000000..d117aa7b57 --- /dev/null +++ b/prepare/r-enhancedvolcano/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggalt +- r-ggplot2 +- r-ggrastr +- r-ggrepel +update_on: +- regex: EnhancedVolcano_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EnhancedVolcano diff --git a/prepare/r-enhancerhomologsearch/PKGBUILD b/prepare/r-enhancerhomologsearch/PKGBUILD new file mode 100644 index 0000000000..20aeca3696 --- /dev/null +++ b/prepare/r-enhancerhomologsearch/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=enhancerHomologSearch +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identification of putative mammalian orthologs to given enhancer' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocfilecache + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-httr + r-iranges + r-jsonlite + r-motifmatchr + r-rcpp + r-rtracklayer + r-s4vectors +) +optdepends=( + r-bsgenome.drerio.ucsc.danrer10 + r-bsgenome.hsapiens.ucsc.hg38 + r-bsgenome.mmusculus.ucsc.mm10 + r-knitr + r-motifdb + r-org.hs.eg.db + r-org.mm.eg.db + r-rmarkdown + r-testthat + r-tfbstools + r-txdb.hsapiens.ucsc.hg38.knowngene + r-txdb.mmusculus.ucsc.mm10.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-enhancerhomologsearch/lilac.py b/prepare/r-enhancerhomologsearch/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-enhancerhomologsearch/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-enhancerhomologsearch/lilac.yaml b/prepare/r-enhancerhomologsearch/lilac.yaml new file mode 100644 index 0000000000..dbdfa70a78 --- /dev/null +++ b/prepare/r-enhancerhomologsearch/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-genomeinfodb +- r-genomicranges +- r-httr +- r-iranges +- r-jsonlite +- r-motifmatchr +- r-rcpp +- r-rtracklayer +- r-s4vectors +update_on: +- regex: enhancerHomologSearch_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/enhancerHomologSearch diff --git a/prepare/r-enmcb/PKGBUILD b/prepare/r-enmcb/PKGBUILD new file mode 100644 index 0000000000..4536ea010f --- /dev/null +++ b/prepare/r-enmcb/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EnMCB +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-doparallel + r-foreach + r-ggplot2 + r-glmnet + r-illuminahumanmethylation450kanno.ilmn12.hg19 + r-mboost + r-minfi + r-rms + r-survivalroc + r-survivalsvm +) +optdepends=( + r-affycoretools + r-biobase + r-knitr + r-plotroc + r-prognosticroc + r-rmarkdown + r-summarizedexperiment + r-survminer + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-enmcb/lilac.py b/prepare/r-enmcb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-enmcb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-enmcb/lilac.yaml b/prepare/r-enmcb/lilac.yaml new file mode 100644 index 0000000000..e926234cdf --- /dev/null +++ b/prepare/r-enmcb/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-foreach +- r-ggplot2 +- r-glmnet +- r-illuminahumanmethylation450kanno.ilmn12.hg19 +- r-mboost +- r-minfi +- r-rms +- r-survivalroc +- r-survivalsvm +update_on: +- regex: EnMCB_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EnMCB diff --git a/prepare/r-enmix/PKGBUILD b/prepare/r-enmix/PKGBUILD new file mode 100644 index 0000000000..1fb2505986 --- /dev/null +++ b/prepare/r-enmix/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ENmix +_pkgver=1.30.01 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quality control and analysis tools for Illumina DNA methylation BeadChip' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationhub + r-biobase + r-doparallel + r-dynamictreecut + r-experimenthub + r-foreach + r-genefilter + r-geneplotter + r-gplots + r-gtools + r-illuminaio + r-impute + r-iranges + r-matrixstats + r-minfi + r-preprocesscore + r-quadprog + r-rpmm + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocgenerics + r-minfidata + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-enmix/lilac.py b/prepare/r-enmix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-enmix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-enmix/lilac.yaml b/prepare/r-enmix/lilac.yaml new file mode 100644 index 0000000000..09a7e6508b --- /dev/null +++ b/prepare/r-enmix/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-biobase +- r-doparallel +- r-dynamictreecut +- r-experimenthub +- r-foreach +- r-genefilter +- r-geneplotter +- r-gplots +- r-gtools +- r-illuminaio +- r-impute +- r-iranges +- r-matrixstats +- r-minfi +- r-preprocesscore +- r-quadprog +- r-rpmm +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: ENmix_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ENmix diff --git a/prepare/r-enrichedheatmap/PKGBUILD b/prepare/r-enrichedheatmap/PKGBUILD new file mode 100644 index 0000000000..e0b6b79caf --- /dev/null +++ b/prepare/r-enrichedheatmap/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EnrichedHeatmap +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Making Enriched Heatmaps' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-circlize + r-complexheatmap + r-genomicranges + r-getoptlong + r-iranges + r-locfit + r-matrixstats + r-rcpp +) +optdepends=( + r-genefilter + r-knitr + r-markdown + r-rcolorbrewer + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-enrichedheatmap/lilac.py b/prepare/r-enrichedheatmap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-enrichedheatmap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-enrichedheatmap/lilac.yaml b/prepare/r-enrichedheatmap/lilac.yaml new file mode 100644 index 0000000000..d22caeb8ff --- /dev/null +++ b/prepare/r-enrichedheatmap/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circlize +- r-complexheatmap +- r-genomicranges +- r-getoptlong +- r-iranges +- r-locfit +- r-matrixstats +- r-rcpp +update_on: +- regex: EnrichedHeatmap_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EnrichedHeatmap diff --git a/prepare/r-enrichmentbrowser/PKGBUILD b/prepare/r-enrichmentbrowser/PKGBUILD new file mode 100644 index 0000000000..b12b0b96b3 --- /dev/null +++ b/prepare/r-enrichmentbrowser/PKGBUILD @@ -0,0 +1,58 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EnrichmentBrowser +_pkgver=2.24.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Seamless navigation through combined results of set-based and network-based enrichment analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biocfilecache + r-biocmanager + r-edger + r-go.db + r-graph + r-graphite + r-gseabase + r-hwriter + r-kegggraph + r-keggrest + r-limma + r-pathview + r-rgraphviz + r-s4vectors + r-safe + r-spia + r-summarizedexperiment +) +optdepends=( + r-airway + r-all + r-biocgraph + r-biocstyle + r-complexheatmap + r-deseq2 + r-geneplotter + r-hgu95av2.db + r-knitr + r-msigdbr + r-reportingtools + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-enrichmentbrowser/lilac.py b/prepare/r-enrichmentbrowser/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-enrichmentbrowser/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-enrichmentbrowser/lilac.yaml b/prepare/r-enrichmentbrowser/lilac.yaml new file mode 100644 index 0000000000..4cde2518af --- /dev/null +++ b/prepare/r-enrichmentbrowser/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocfilecache +- r-biocmanager +- r-edger +- r-go.db +- r-graph +- r-graphite +- r-gseabase +- r-hwriter +- r-kegggraph +- r-keggrest +- r-limma +- r-pathview +- r-rgraphviz +- r-s4vectors +- r-safe +- r-spia +- r-summarizedexperiment +update_on: +- regex: EnrichmentBrowser_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EnrichmentBrowser diff --git a/prepare/r-enrichplot/PKGBUILD b/prepare/r-enrichplot/PKGBUILD new file mode 100644 index 0000000000..4eaa50176e --- /dev/null +++ b/prepare/r-enrichplot/PKGBUILD @@ -0,0 +1,66 @@ +# Maintainer: Guoyi Zhang + +_pkgname=enrichplot +_pkgver=1.14.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization of Functional Enrichment Result' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-aplot + r-dose + r-ggplot2 + r-ggraph + r-ggtree + r-gosemsim + r-igraph + r-magrittr + r-plyr + r-purrr + r-rcolorbrewer + r-reshape2 + r-scatterpie + r-shadowtext + r-yulab.utils +) +optdepends=( + r-annotationdbi + r-clusterprofiler + r-dplyr + r-europepmc + r-ggforce + r-ggnewscale + r-ggplotify + r-ggrepel + r-ggridges + r-ggstar + r-ggtreeextra + r-ggupset + r-grdevices + r-gridextra + r-knitr + r-org.hs.eg.db + r-prettydoc + r-rmarkdown + r-scales + r-tibble + r-tidyr + r-tidytree + r-treeio +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-enrichplot/lilac.py b/prepare/r-enrichplot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-enrichplot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-enrichplot/lilac.yaml b/prepare/r-enrichplot/lilac.yaml new file mode 100644 index 0000000000..e89b7dd44c --- /dev/null +++ b/prepare/r-enrichplot/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aplot +- r-dose +- r-ggplot2 +- r-ggraph +- r-ggtree +- r-gosemsim +- r-igraph +- r-magrittr +- r-plyr +- r-purrr +- r-rcolorbrewer +- r-reshape2 +- r-scatterpie +- r-shadowtext +- r-yulab.utils +update_on: +- regex: enrichplot_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/enrichplot diff --git a/prepare/r-enrichr/PKGBUILD b/prepare/r-enrichr/PKGBUILD new file mode 100644 index 0000000000..cb0eeefd42 --- /dev/null +++ b/prepare/r-enrichr/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=enrichR +_pkgver=3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Provides an R Interface to 'Enrichr'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-httr + r-rjson +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-enrichr/lilac.py b/prepare/r-enrichr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-enrichr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-enrichr/lilac.yaml b/prepare/r-enrichr/lilac.yaml new file mode 100644 index 0000000000..9b9e9715a3 --- /dev/null +++ b/prepare/r-enrichr/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-httr +- r-rjson +update_on: +- regex: enrichR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=enrichR diff --git a/prepare/r-enrichtf/PKGBUILD b/prepare/r-enrichtf/PKGBUILD new file mode 100644 index 0000000000..c231a86d61 --- /dev/null +++ b/prepare/r-enrichtf/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=enrichTF +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Transcription Factors Enrichment Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-bsgenome + r-clusterprofiler + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-ggpubr + r-heatmap3 + r-iranges + r-jaspar2018 + r-magrittr + r-motifmatchr + r-pipeframe + r-r.utils + r-rmarkdown + r-rtracklayer + r-s4vectors + r-tfbstools +) +optdepends=( + r-knitr + r-testthat + r-webshot +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-enrichtf/lilac.py b/prepare/r-enrichtf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-enrichtf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-enrichtf/lilac.yaml b/prepare/r-enrichtf/lilac.yaml new file mode 100644 index 0000000000..9ec557185c --- /dev/null +++ b/prepare/r-enrichtf/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-bsgenome +- r-clusterprofiler +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-ggpubr +- r-heatmap3 +- r-iranges +- r-jaspar2018 +- r-magrittr +- r-motifmatchr +- r-pipeframe +- r-r.utils +- r-rmarkdown +- r-rtracklayer +- r-s4vectors +- r-tfbstools +update_on: +- regex: enrichTF_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/enrichTF diff --git a/prepare/r-ensdb.hsapiens.v75/PKGBUILD b/prepare/r-ensdb.hsapiens.v75/PKGBUILD new file mode 100644 index 0000000000..6250ba2342 --- /dev/null +++ b/prepare/r-ensdb.hsapiens.v75/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EnsDb.Hsapiens.v75 +_pkgver=2.99.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Ensembl based annotation package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ensembldb +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ensdb.hsapiens.v75/lilac.py b/prepare/r-ensdb.hsapiens.v75/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ensdb.hsapiens.v75/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ensdb.hsapiens.v75/lilac.yaml b/prepare/r-ensdb.hsapiens.v75/lilac.yaml new file mode 100644 index 0000000000..d8ef1504fa --- /dev/null +++ b/prepare/r-ensdb.hsapiens.v75/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ensembldb +update_on: +- regex: EnsDb.Hsapiens.v75_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EnsDb.Hsapiens.v75 diff --git a/prepare/r-ensdb.hsapiens.v86/PKGBUILD b/prepare/r-ensdb.hsapiens.v86/PKGBUILD new file mode 100644 index 0000000000..8aeb24ce0d --- /dev/null +++ b/prepare/r-ensdb.hsapiens.v86/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EnsDb.Hsapiens.v86 +_pkgver=2.99.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Ensembl based annotation package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ensembldb +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ensdb.hsapiens.v86/lilac.py b/prepare/r-ensdb.hsapiens.v86/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ensdb.hsapiens.v86/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ensdb.hsapiens.v86/lilac.yaml b/prepare/r-ensdb.hsapiens.v86/lilac.yaml new file mode 100644 index 0000000000..b99e82132c --- /dev/null +++ b/prepare/r-ensdb.hsapiens.v86/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ensembldb +update_on: +- regex: EnsDb.Hsapiens.v86_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EnsDb.Hsapiens.v86 diff --git a/prepare/r-ensembldb/PKGBUILD b/prepare/r-ensembldb/PKGBUILD new file mode 100644 index 0000000000..5a6bd67347 --- /dev/null +++ b/prepare/r-ensembldb/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ensembldb +_pkgver=2.18.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities to create and use Ensembl-based annotation databases' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-annotationdbi + r-annotationfilter + r-biobase + r-biocgenerics + r-biostrings + r-curl + r-dbi + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-protgenerics + r-rsamtools + r-rsqlite + r-rtracklayer + r-s4vectors +) +optdepends=( + r-annotationhub + r-biocstyle + r-bsgenome.hsapiens.ncbi.grch38 + r-ensdb.hsapiens.v86 + r-ggbio + r-gviz + r-knitr + r-magrittr + r-rmariadb + r-rmarkdown + r-shiny + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ensembldb/lilac.py b/prepare/r-ensembldb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ensembldb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ensembldb/lilac.yaml b/prepare/r-ensembldb/lilac.yaml new file mode 100644 index 0000000000..f0bfad7848 --- /dev/null +++ b/prepare/r-ensembldb/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationfilter +- r-biobase +- r-biocgenerics +- r-biostrings +- r-curl +- r-dbi +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-protgenerics +- r-rsamtools +- r-rsqlite +- r-rtracklayer +- r-s4vectors +update_on: +- regex: ensembldb_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ensembldb diff --git a/prepare/r-ensemblvep/PKGBUILD b/prepare/r-ensemblvep/PKGBUILD new file mode 100644 index 0000000000..11ced9149a --- /dev/null +++ b/prepare/r-ensemblvep/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: Ensembl VEP (API version 104) and the Perl modulesDBI and DBD::mysql must be installed. See the package READMEand Ensembl installation instructions:http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer +# Maintainer: Guoyi Zhang + +_pkgname=ensemblVEP +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Interface to Ensembl Variant Effect Predictor' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biostrings + r-genomeinfodb + r-genomicranges + r-s4vectors + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ensemblvep/lilac.py b/prepare/r-ensemblvep/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ensemblvep/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ensemblvep/lilac.yaml b/prepare/r-ensemblvep/lilac.yaml new file mode 100644 index 0000000000..26cc601752 --- /dev/null +++ b/prepare/r-ensemblvep/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-genomeinfodb +- r-genomicranges +- r-s4vectors +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: ensemblVEP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ensemblVEP diff --git a/prepare/r-ensurer/PKGBUILD b/prepare/r-ensurer/PKGBUILD new file mode 100644 index 0000000000..2ddb68de7c --- /dev/null +++ b/prepare/r-ensurer/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ensurer +_pkgver=1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Ensure Values at Runtime' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-knitr + r-magrittr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ensurer/lilac.py b/prepare/r-ensurer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ensurer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ensurer/lilac.yaml b/prepare/r-ensurer/lilac.yaml new file mode 100644 index 0000000000..1250b39d93 --- /dev/null +++ b/prepare/r-ensurer/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ensurer_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ensurer diff --git a/prepare/r-entropy/PKGBUILD b/prepare/r-entropy/PKGBUILD new file mode 100644 index 0000000000..1c2faf4272 --- /dev/null +++ b/prepare/r-entropy/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=entropy +_pkgver=1.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimation of Entropy, Mutual Information and Related Quantities' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-entropy/lilac.py b/prepare/r-entropy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-entropy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-entropy/lilac.yaml b/prepare/r-entropy/lilac.yaml new file mode 100644 index 0000000000..9cdf600ce8 --- /dev/null +++ b/prepare/r-entropy/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: entropy_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=entropy diff --git a/prepare/r-entropyexplorer/PKGBUILD b/prepare/r-entropyexplorer/PKGBUILD new file mode 100644 index 0000000000..573b654960 --- /dev/null +++ b/prepare/r-entropyexplorer/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EntropyExplorer +_pkgver=1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Exploring Differential Shannon Entropy, Differential Coefficient of Variation and Differential Expression' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-entropyexplorer/lilac.py b/prepare/r-entropyexplorer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-entropyexplorer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-entropyexplorer/lilac.yaml b/prepare/r-entropyexplorer/lilac.yaml new file mode 100644 index 0000000000..dc499281bb --- /dev/null +++ b/prepare/r-entropyexplorer/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: EntropyExplorer_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=EntropyExplorer diff --git a/prepare/r-envipat/PKGBUILD b/prepare/r-envipat/PKGBUILD new file mode 100644 index 0000000000..263c40f308 --- /dev/null +++ b/prepare/r-envipat/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=enviPat +_pkgver=2.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Isotope Pattern, Profile and Centroid Calculation for Mass Spectrometry' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-envipat/lilac.py b/prepare/r-envipat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-envipat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-envipat/lilac.yaml b/prepare/r-envipat/lilac.yaml new file mode 100644 index 0000000000..9ea9f06bd8 --- /dev/null +++ b/prepare/r-envipat/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: enviPat_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=enviPat diff --git a/prepare/r-envisionquery/PKGBUILD b/prepare/r-envisionquery/PKGBUILD new file mode 100644 index 0000000000..6dc2afd294 --- /dev/null +++ b/prepare/r-envisionquery/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ENVISIONQuery +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Retrieval from the ENVISION bioinformatics data portal into R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rjava + r-xml +) +makedepends=( + git + tar +) +source=("git+https://git.bioconductor.org/packages/${_pkgname}.git") +sha256sums=('SKIP') + +build() { + tar -zcvf ${_pkgname}.tar.gz ${_pkgname} + R CMD INSTALL ${_pkgname}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: + diff --git a/prepare/r-envisionquery/lilac.py b/prepare/r-envisionquery/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-envisionquery/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-envisionquery/lilac.yaml b/prepare/r-envisionquery/lilac.yaml new file mode 100644 index 0000000000..2b8ea593ea --- /dev/null +++ b/prepare/r-envisionquery/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-xml +- r-rjava +update_on: +- regex: Version(\d+.\d+.\d+) + source: regex + url: https://bioconductor.org/packages/ENVISIONQuery diff --git a/prepare/r-envstats/PKGBUILD b/prepare/r-envstats/PKGBUILD new file mode 100644 index 0000000000..5068a4a4b5 --- /dev/null +++ b/prepare/r-envstats/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EnvStats +_pkgver=2.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Package for Environmental Statistics, Including US EPA Guidance' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-nortest +) +optdepends=( + r-boot + r-lattice + r-qcc + r-sp + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-envstats/lilac.py b/prepare/r-envstats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-envstats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-envstats/lilac.yaml b/prepare/r-envstats/lilac.yaml new file mode 100644 index 0000000000..684b6f64f4 --- /dev/null +++ b/prepare/r-envstats/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-nortest +update_on: +- regex: EnvStats_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=EnvStats diff --git a/prepare/r-epialleler/PKGBUILD b/prepare/r-epialleler/PKGBUILD new file mode 100644 index 0000000000..07fd82e36e --- /dev/null +++ b/prepare/r-epialleler/PKGBUILD @@ -0,0 +1,43 @@ +# system requirements: C++17, GNU make +# Maintainer: Guoyi Zhang + +_pkgname=epialleleR +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast, Epiallele-Aware Methylation Reporter' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bh + r-biocgenerics + r-data.table + r-genomeinfodb + r-genomicranges + r-rcpp + r-rhtslib + r-stringi + r-summarizedexperiment + r-variantannotation + r-zlibbioc +) +optdepends=( + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-epialleler/lilac.py b/prepare/r-epialleler/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-epialleler/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-epialleler/lilac.yaml b/prepare/r-epialleler/lilac.yaml new file mode 100644 index 0000000000..8466f9a12b --- /dev/null +++ b/prepare/r-epialleler/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-biocgenerics +- r-data.table +- r-genomeinfodb +- r-genomicranges +- r-rcpp +- r-rhtslib +- r-stringi +- r-summarizedexperiment +- r-variantannotation +- r-zlibbioc +update_on: +- regex: epialleleR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/epialleleR diff --git a/prepare/r-epidecoder/PKGBUILD b/prepare/r-epidecoder/PKGBUILD new file mode 100644 index 0000000000..c5c39bc49f --- /dev/null +++ b/prepare/r-epidecoder/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=epidecodeR +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-envstats + r-genomicranges + r-ggplot2 + r-ggpubr + r-iranges + r-rstatix + r-rtracklayer +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-epidecoder/lilac.py b/prepare/r-epidecoder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-epidecoder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-epidecoder/lilac.yaml b/prepare/r-epidecoder/lilac.yaml new file mode 100644 index 0000000000..da50bb1ba8 --- /dev/null +++ b/prepare/r-epidecoder/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-envstats +- r-genomicranges +- r-ggplot2 +- r-ggpubr +- r-iranges +- r-rstatix +- r-rtracklayer +update_on: +- regex: epidecodeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/epidecodeR diff --git a/prepare/r-epidish/PKGBUILD b/prepare/r-epidish/PKGBUILD new file mode 100644 index 0000000000..08b16b7b80 --- /dev/null +++ b/prepare/r-epidish/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EpiDISH +_pkgver=2.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Epigenetic Dissection of Intra-Sample-Heterogeneity' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-e1071 + r-locfdr + r-matrixstats + r-quadprog + r-stringr +) +optdepends=( + r-biobase + r-biocstyle + r-geoquery + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-epidish/lilac.py b/prepare/r-epidish/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-epidish/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-epidish/lilac.yaml b/prepare/r-epidish/lilac.yaml new file mode 100644 index 0000000000..d208b4821c --- /dev/null +++ b/prepare/r-epidish/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-e1071 +- r-locfdr +- r-matrixstats +- r-quadprog +- r-stringr +update_on: +- regex: EpiDISH_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EpiDISH diff --git a/prepare/r-epigenomix/PKGBUILD b/prepare/r-epigenomix/PKGBUILD new file mode 100644 index 0000000000..3e5b3ea241 --- /dev/null +++ b/prepare/r-epigenomix/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=epigenomix +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Epigenetic and gene transcription data normalization and integration with mixture models' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-beadarray + r-biobase + r-biocgenerics + r-genomeinfodb + r-genomicranges + r-iranges + r-mcmcpack + r-rsamtools + r-s4vectors + r-summarizedexperiment +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-epigenomix/lilac.py b/prepare/r-epigenomix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-epigenomix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-epigenomix/lilac.yaml b/prepare/r-epigenomix/lilac.yaml new file mode 100644 index 0000000000..64c66461ea --- /dev/null +++ b/prepare/r-epigenomix/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beadarray +- r-biobase +- r-biocgenerics +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-mcmcpack +- r-rsamtools +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: epigenomix_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/epigenomix diff --git a/prepare/r-epigrahmm/PKGBUILD b/prepare/r-epigrahmm/PKGBUILD new file mode 100644 index 0000000000..87fef25c17 --- /dev/null +++ b/prepare/r-epigrahmm/PKGBUILD @@ -0,0 +1,58 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=epigraHMM +_pkgver=1.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Epigenomic R-based analysis with hidden Markov models' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-bamsignals + r-csaw + r-data.table + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-ggpubr + r-greylistchip + r-iranges + r-limma + r-magrittr + r-pheatmap + r-rcpp + r-rcpparmadillo + r-rhdf5 + r-rhdf5lib + r-rsamtools + r-rtracklayer + r-s4vectors + r-scales + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-bsgenome.rnorvegicus.ucsc.rn4 + r-chromstardata + r-gcapc + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-epigrahmm/lilac.py b/prepare/r-epigrahmm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-epigrahmm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-epigrahmm/lilac.yaml b/prepare/r-epigrahmm/lilac.yaml new file mode 100644 index 0000000000..dc2953c53c --- /dev/null +++ b/prepare/r-epigrahmm/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bamsignals +- r-csaw +- r-data.table +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-ggpubr +- r-greylistchip +- r-iranges +- r-limma +- r-magrittr +- r-pheatmap +- r-rcpp +- r-rcpparmadillo +- r-rhdf5 +- r-rhdf5lib +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-scales +- r-summarizedexperiment +update_on: +- regex: epigraHMM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/epigraHMM diff --git a/prepare/r-epihet/PKGBUILD b/prepare/r-epihet/PKGBUILD new file mode 100644 index 0000000000..86baf1a5a4 --- /dev/null +++ b/prepare/r-epihet/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=epihet +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-data.table + r-doparallel + r-entropyexplorer + r-foreach + r-genomicranges + r-ggplot2 + r-igraph + r-iranges + r-pheatmap + r-qvalue + r-reactomepa + r-rtsne + r-s4vectors + r-wgcna +) +optdepends=( + r-clusterprofiler + r-ggfortify + r-knitr + r-org.hs.eg.db + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-epihet/lilac.py b/prepare/r-epihet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-epihet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-epihet/lilac.yaml b/prepare/r-epihet/lilac.yaml new file mode 100644 index 0000000000..de36453c5c --- /dev/null +++ b/prepare/r-epihet/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-doparallel +- r-entropyexplorer +- r-foreach +- r-genomicranges +- r-ggplot2 +- r-igraph +- r-iranges +- r-pheatmap +- r-qvalue +- r-reactomepa +- r-rtsne +- r-s4vectors +- r-wgcna +update_on: +- regex: epihet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/epihet diff --git a/prepare/r-epinem/PKGBUILD b/prepare/r-epinem/PKGBUILD new file mode 100644 index 0000000000..03c75d650a --- /dev/null +++ b/prepare/r-epinem/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=epiNEM +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='epiNEM' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-boolnet + r-e1071 + r-graph + r-gtools + r-igraph + r-latex2exp + r-latticeextra + r-minet + r-mnem + r-pcalg + r-rcolorbrewer +) +optdepends=( + r-annotationhub + r-biocgenerics + r-devtools + r-gosemsim + r-knitr + r-org.sc.sgd.db + r-rmarkdown + r-runit + r-stringdb +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-epinem/lilac.py b/prepare/r-epinem/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-epinem/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-epinem/lilac.yaml b/prepare/r-epinem/lilac.yaml new file mode 100644 index 0000000000..433a62150a --- /dev/null +++ b/prepare/r-epinem/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-boolnet +- r-e1071 +- r-graph +- r-gtools +- r-igraph +- r-latex2exp +- r-latticeextra +- r-minet +- r-mnem +- r-pcalg +- r-rcolorbrewer +update_on: +- regex: epiNEM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/epiNEM diff --git a/prepare/r-epir/PKGBUILD b/prepare/r-epir/PKGBUILD new file mode 100644 index 0000000000..694bd27878 --- /dev/null +++ b/prepare/r-epir/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=epiR +_pkgver=2.0.41 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for the Analysis of Epidemiological Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-biasedurn + r-lubridate + r-pander + r-sf +) +optdepends=( + r-foreign + r-ggplot2 + r-kableextra + r-knitr + r-mapproj + r-maptools + r-mass + r-plyr + r-rcolorbrewer + r-rgdal + r-rgeos + r-rmarkdown + r-scales + r-spatstat + r-spdata + r-tidyverse +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-epir/lilac.py b/prepare/r-epir/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-epir/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-epir/lilac.yaml b/prepare/r-epir/lilac.yaml new file mode 100644 index 0000000000..8c9819d81d --- /dev/null +++ b/prepare/r-epir/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biasedurn +- r-lubridate +- r-pander +- r-sf +update_on: +- regex: epiR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=epiR diff --git a/prepare/r-epistack/PKGBUILD b/prepare/r-epistack/PKGBUILD new file mode 100644 index 0000000000..ad510f8730 --- /dev/null +++ b/prepare/r-epistack/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=epistack +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Heatmaps of Stack Profiles from Epigenetic Signals' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-genomicranges + r-iranges + r-plotrix + r-s4vectors + r-viridislite +) +optdepends=( + r-biocstyle + r-biomart + r-covr + r-enrichedheatmap + r-knitr + r-magick + r-rmarkdown + r-rtracklayer + r-testthat + r-vdiffr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-epistack/lilac.py b/prepare/r-epistack/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-epistack/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-epistack/lilac.yaml b/prepare/r-epistack/lilac.yaml new file mode 100644 index 0000000000..1a4f0b5030 --- /dev/null +++ b/prepare/r-epistack/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomicranges +- r-iranges +- r-plotrix +- r-s4vectors +- r-viridislite +update_on: +- regex: epistack_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/epistack diff --git a/prepare/r-epitxdb/PKGBUILD b/prepare/r-epitxdb/PKGBUILD new file mode 100644 index 0000000000..66c6ba765b --- /dev/null +++ b/prepare/r-epitxdb/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EpiTxDb +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Storing and accessing epitranscriptomic information using the AnnotationDbi interface' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biocfilecache + r-biocgenerics + r-biostrings + r-curl + r-dbi + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-httr + r-iranges + r-modstrings + r-rsqlite + r-s4vectors + r-trnadbimport + r-xml2 +) +optdepends=( + r-annotationhub + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg38 + r-bsgenome.scerevisiae.ucsc.saccer3 + r-ensembldb + r-epitxdb.hs.hg38 + r-ggplot2 + r-httptest + r-knitr + r-rmarkdown + r-testthat + r-txdb.hsapiens.ucsc.hg38.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-epitxdb/lilac.py b/prepare/r-epitxdb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-epitxdb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-epitxdb/lilac.yaml b/prepare/r-epitxdb/lilac.yaml new file mode 100644 index 0000000000..4c38d5ccce --- /dev/null +++ b/prepare/r-epitxdb/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocfilecache +- r-biocgenerics +- r-biostrings +- r-curl +- r-dbi +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-httr +- r-iranges +- r-modstrings +- r-rsqlite +- r-s4vectors +- r-trnadbimport +- r-xml2 +update_on: +- regex: EpiTxDb_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EpiTxDb diff --git a/prepare/r-epivizr/PKGBUILD b/prepare/r-epivizr/PKGBUILD new file mode 100644 index 0000000000..2062791ec9 --- /dev/null +++ b/prepare/r-epivizr/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=epivizr +_pkgver=2.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Interface to epiviz web app' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bumphunter + r-epivizrdata + r-epivizrserver + r-genomeinfodb + r-genomicranges + r-iranges + r-s4vectors +) +optdepends=( + r-antiprofilesdata + r-biobase + r-biocstyle + r-hgu133plus2.db + r-knitr + r-minfi + r-mus.musculus + r-rmarkdown + r-roxygen2 + r-summarizedexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-epivizr/lilac.py b/prepare/r-epivizr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-epivizr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-epivizr/lilac.yaml b/prepare/r-epivizr/lilac.yaml new file mode 100644 index 0000000000..bfc17facd8 --- /dev/null +++ b/prepare/r-epivizr/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bumphunter +- r-epivizrdata +- r-epivizrserver +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-s4vectors +update_on: +- regex: epivizr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/epivizr diff --git a/prepare/r-epivizrchart/PKGBUILD b/prepare/r-epivizrchart/PKGBUILD new file mode 100644 index 0000000000..853042cdcc --- /dev/null +++ b/prepare/r-epivizrchart/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=epivizrChart +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R interface to epiviz web components' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-epivizrdata + r-epivizrserver + r-htmltools + r-rjson +) +optdepends=( + r-annotationhub + r-antiprofilesdata + r-biobase + r-biocstyle + r-genomicranges + r-hgu133plus2.db + r-homo.sapiens + r-iranges + r-knitr + r-magrittr + r-minfi + r-mus.musculus + r-rcolorbrewer + r-roxygen2 + r-rsamtools + r-rtracklayer + r-s4vectors + r-shiny + r-summarizedexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-epivizrchart/lilac.py b/prepare/r-epivizrchart/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-epivizrchart/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-epivizrchart/lilac.yaml b/prepare/r-epivizrchart/lilac.yaml new file mode 100644 index 0000000000..743a59029e --- /dev/null +++ b/prepare/r-epivizrchart/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-epivizrdata +- r-epivizrserver +- r-htmltools +- r-rjson +update_on: +- regex: epivizrChart_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/epivizrChart diff --git a/prepare/r-epivizrdata/PKGBUILD b/prepare/r-epivizrdata/PKGBUILD new file mode 100644 index 0000000000..bb5e807826 --- /dev/null +++ b/prepare/r-epivizrdata/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=epivizrData +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data Management API for epiviz interactive visualization app' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-ensembldb + r-epivizrserver + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-organismdbi + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-annotationhub + r-biocstyle + r-bumphunter + r-dbi + r-ensdb.mmusculus.v79 + r-hgu133plus2.db + r-knitr + r-matrixstats + r-mus.musculus + r-rjson + r-rmarkdown + r-rmysql + r-roxygen2 + r-rtracklayer + r-testthat + r-txdb.mmusculus.ucsc.mm10.knowngene + r-utils +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-epivizrdata/lilac.py b/prepare/r-epivizrdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-epivizrdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-epivizrdata/lilac.yaml b/prepare/r-epivizrdata/lilac.yaml new file mode 100644 index 0000000000..ecfa00050e --- /dev/null +++ b/prepare/r-epivizrdata/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-ensembldb +- r-epivizrserver +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-organismdbi +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: epivizrData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/epivizrData diff --git a/prepare/r-epivizrserver/PKGBUILD b/prepare/r-epivizrserver/PKGBUILD new file mode 100644 index 0000000000..c59d7ade73 --- /dev/null +++ b/prepare/r-epivizrserver/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=epivizrServer +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='WebSocket server infrastructure for epivizr apps and packages' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-httpuv + r-mime + r-r6 + r-rjson +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-epivizrserver/lilac.py b/prepare/r-epivizrserver/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-epivizrserver/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-epivizrserver/lilac.yaml b/prepare/r-epivizrserver/lilac.yaml new file mode 100644 index 0000000000..ba870278ef --- /dev/null +++ b/prepare/r-epivizrserver/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-httpuv +- r-mime +- r-r6 +- r-rjson +update_on: +- regex: epivizrServer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/epivizrServer diff --git a/prepare/r-epivizrstandalone/PKGBUILD b/prepare/r-epivizrstandalone/PKGBUILD new file mode 100644 index 0000000000..87b15c1d58 --- /dev/null +++ b/prepare/r-epivizrstandalone/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=epivizrStandalone +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Run Epiviz Interactive Genomic Data Visualization App within R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-epivizr + r-epivizrserver + r-genomeinfodb + r-genomicfeatures + r-git2r + r-s4vectors +) +optdepends=( + r-biobase + r-biocstyle + r-knitr + r-mus.musculus + r-organismdbi + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-epivizrstandalone/lilac.py b/prepare/r-epivizrstandalone/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-epivizrstandalone/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-epivizrstandalone/lilac.yaml b/prepare/r-epivizrstandalone/lilac.yaml new file mode 100644 index 0000000000..16d5b3a75d --- /dev/null +++ b/prepare/r-epivizrstandalone/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-epivizr +- r-epivizrserver +- r-genomeinfodb +- r-genomicfeatures +- r-git2r +- r-s4vectors +update_on: +- regex: epivizrStandalone_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/epivizrStandalone diff --git a/prepare/r-erccdashboard/PKGBUILD b/prepare/r-erccdashboard/PKGBUILD new file mode 100644 index 0000000000..1e01d90786 --- /dev/null +++ b/prepare/r-erccdashboard/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=erccdashboard +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assess Differential Gene Expression Experiments with ERCC Controls' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-edger + r-ggplot2 + r-gplots + r-gridextra + r-gtools + r-limma + r-locfit + r-plyr + r-qvalue + r-reshape2 + r-rocr + r-scales + r-stringr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-erccdashboard/lilac.py b/prepare/r-erccdashboard/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-erccdashboard/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-erccdashboard/lilac.yaml b/prepare/r-erccdashboard/lilac.yaml new file mode 100644 index 0000000000..bdbad5320f --- /dev/null +++ b/prepare/r-erccdashboard/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-edger +- r-ggplot2 +- r-gplots +- r-gridextra +- r-gtools +- r-limma +- r-locfit +- r-plyr +- r-qvalue +- r-reshape2 +- r-rocr +- r-scales +- r-stringr +update_on: +- regex: erccdashboard_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/erccdashboard diff --git a/prepare/r-erma/PKGBUILD b/prepare/r-erma/PKGBUILD new file mode 100644 index 0000000000..590a53c619 --- /dev/null +++ b/prepare/r-erma/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=erma +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='epigenomic road map adventures' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicfiles + r-genomicranges + r-ggplot2 + r-homo.sapiens + r-iranges + r-rtracklayer + r-s4vectors + r-shiny + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-doparallel + r-dt + r-go.db + r-knitr + r-png + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-erma/lilac.py b/prepare/r-erma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-erma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-erma/lilac.yaml b/prepare/r-erma/lilac.yaml new file mode 100644 index 0000000000..4707119df0 --- /dev/null +++ b/prepare/r-erma/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-genomeinfodb +- r-genomicfiles +- r-genomicranges +- r-ggplot2 +- r-homo.sapiens +- r-iranges +- r-rtracklayer +- r-s4vectors +- r-shiny +- r-summarizedexperiment +update_on: +- regex: erma_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/erma diff --git a/prepare/r-erssa/PKGBUILD b/prepare/r-erssa/PKGBUILD new file mode 100644 index 0000000000..3df984feb3 --- /dev/null +++ b/prepare/r-erssa/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ERSSA +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Empirical RNA-seq Sample Size Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-deseq2 + r-edger + r-ggplot2 + r-plyr + r-rcolorbrewer +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-erssa/lilac.py b/prepare/r-erssa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-erssa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-erssa/lilac.yaml b/prepare/r-erssa/lilac.yaml new file mode 100644 index 0000000000..2fe2295f23 --- /dev/null +++ b/prepare/r-erssa/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-deseq2 +- r-edger +- r-ggplot2 +- r-plyr +- r-rcolorbrewer +update_on: +- regex: ERSSA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ERSSA diff --git a/prepare/r-esatac/PKGBUILD b/prepare/r-esatac/PKGBUILD new file mode 100644 index 0000000000..0372158746 --- /dev/null +++ b/prepare/r-esatac/PKGBUILD @@ -0,0 +1,65 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=esATAC +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Easy-to-use Systematic pipeline for ATACseq data analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocgenerics + r-biocmanager + r-biostrings + r-bsgenome + r-chipseeker + r-clusterprofiler + r-corrplot + r-digest + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-igraph + r-iranges + r-jaspar2018 + r-knitr + r-magrittr + r-motifmatchr + r-pipeframe + r-r.utils + r-rbowtie2 + r-rcpp + r-rjava + r-rmarkdown + r-rsamtools + r-rtracklayer + r-s4vectors + r-shortread + r-tfbstools + r-venndiagram +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg19 + r-org.hs.eg.db + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene + r-webshot +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-esatac/lilac.py b/prepare/r-esatac/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-esatac/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-esatac/lilac.yaml b/prepare/r-esatac/lilac.yaml new file mode 100644 index 0000000000..9a45dad558 --- /dev/null +++ b/prepare/r-esatac/lilac.yaml @@ -0,0 +1,40 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-biocmanager +- r-biostrings +- r-bsgenome +- r-chipseeker +- r-clusterprofiler +- r-corrplot +- r-digest +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-igraph +- r-iranges +- r-jaspar2018 +- r-knitr +- r-magrittr +- r-motifmatchr +- r-pipeframe +- r-r.utils +- r-rbowtie2 +- r-rcpp +- r-rjava +- r-rmarkdown +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-shortread +- r-tfbstools +- r-venndiagram +update_on: +- regex: esATAC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/esATAC diff --git a/prepare/r-escape/PKGBUILD b/prepare/r-escape/PKGBUILD new file mode 100644 index 0000000000..0d5a50efd0 --- /dev/null +++ b/prepare/r-escape/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=escape +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Easy single cell analysis platform for enrichment' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Apache') +depends=( + r + r-biocparallel + r-dplyr + r-ggplot2 + r-ggridges + r-gseabase + r-gsva + r-limma + r-msigdbr + r-singlecellexperiment +) +optdepends=( + r-biocstyle + r-dittoseq + r-knitr + r-rmarkdown + r-seurat + r-seuratobject + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-escape/lilac.py b/prepare/r-escape/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-escape/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-escape/lilac.yaml b/prepare/r-escape/lilac.yaml new file mode 100644 index 0000000000..8ffceb775b --- /dev/null +++ b/prepare/r-escape/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-dplyr +- r-ggplot2 +- r-ggridges +- r-gseabase +- r-gsva +- r-limma +- r-msigdbr +- r-singlecellexperiment +update_on: +- regex: escape_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/escape diff --git a/prepare/r-esetvis/PKGBUILD b/prepare/r-esetvis/PKGBUILD new file mode 100644 index 0000000000..4bfa888aa3 --- /dev/null +++ b/prepare/r-esetvis/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=esetVis +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualizations of expressionSet Bioconductor object' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-hexbin + r-mlp + r-mpm + r-rtsne +) +optdepends=( + r-all + r-annotationdbi + r-ggplot2 + r-ggrepel + r-ggvis + r-hgu95av2.db + r-knitr + r-pander + r-rbokeh + r-rmarkdown + r-summarizedexperiment +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-esetvis/lilac.py b/prepare/r-esetvis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-esetvis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-esetvis/lilac.yaml b/prepare/r-esetvis/lilac.yaml new file mode 100644 index 0000000000..ba8e4d7930 --- /dev/null +++ b/prepare/r-esetvis/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-hexbin +- r-mlp +- r-mpm +- r-rtsne +update_on: +- regex: esetVis_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/esetVis diff --git a/prepare/r-estimability/PKGBUILD b/prepare/r-estimability/PKGBUILD new file mode 100644 index 0000000000..430f939bef --- /dev/null +++ b/prepare/r-estimability/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=estimability +_pkgver=1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Assessing Estimability of Linear Predictions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-estimability/lilac.py b/prepare/r-estimability/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-estimability/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-estimability/lilac.yaml b/prepare/r-estimability/lilac.yaml new file mode 100644 index 0000000000..ae12700181 --- /dev/null +++ b/prepare/r-estimability/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: estimability_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=estimability diff --git a/prepare/r-etrunct/PKGBUILD b/prepare/r-etrunct/PKGBUILD new file mode 100644 index 0000000000..a1d6a37d25 --- /dev/null +++ b/prepare/r-etrunct/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=etrunct +_pkgver=0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Computes Moments of Univariate Truncated t Distribution' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-etrunct/lilac.py b/prepare/r-etrunct/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-etrunct/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-etrunct/lilac.yaml b/prepare/r-etrunct/lilac.yaml new file mode 100644 index 0000000000..9329f639ef --- /dev/null +++ b/prepare/r-etrunct/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: etrunct_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=etrunct diff --git a/prepare/r-eudysbiome/PKGBUILD b/prepare/r-eudysbiome/PKGBUILD new file mode 100644 index 0000000000..12292f21ff --- /dev/null +++ b/prepare/r-eudysbiome/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=eudysbiome +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cartesian plot and contingency test on 16S Microbial data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-plyr + r-r.utils + r-rsamtools +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-eudysbiome/lilac.py b/prepare/r-eudysbiome/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-eudysbiome/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-eudysbiome/lilac.yaml b/prepare/r-eudysbiome/lilac.yaml new file mode 100644 index 0000000000..54c39a8156 --- /dev/null +++ b/prepare/r-eudysbiome/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-plyr +- r-r.utils +- r-rsamtools +update_on: +- regex: eudysbiome_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/eudysbiome diff --git a/prepare/r-eulerr/PKGBUILD b/prepare/r-eulerr/PKGBUILD new file mode 100644 index 0000000000..bfe902d69d --- /dev/null +++ b/prepare/r-eulerr/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=eulerr +_pkgver=6.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Area-Proportional Euler and Venn Diagrams with Ellipses' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-gensa + r-polyclip + r-polylabelr + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-covr + r-knitr + r-lattice + r-pbrackets + r-rconics + r-rmarkdown + r-spelling + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-eulerr/lilac.py b/prepare/r-eulerr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-eulerr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-eulerr/lilac.yaml b/prepare/r-eulerr/lilac.yaml new file mode 100644 index 0000000000..f0c5fe13ff --- /dev/null +++ b/prepare/r-eulerr/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gensa +- r-polyclip +- r-polylabelr +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: eulerr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=eulerr diff --git a/prepare/r-eva/PKGBUILD b/prepare/r-eva/PKGBUILD new file mode 100644 index 0000000000..d235588081 --- /dev/null +++ b/prepare/r-eva/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=eva +_pkgver=0.2.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Extreme Value Analysis with Goodness-of-Fit Testing' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-envstats +) +optdepends=( + r-knitr + r-rmarkdown + r-spatialextremes +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-eva/lilac.py b/prepare/r-eva/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-eva/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-eva/lilac.yaml b/prepare/r-eva/lilac.yaml new file mode 100644 index 0000000000..0ce093591a --- /dev/null +++ b/prepare/r-eva/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-envstats +update_on: +- regex: eva_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=eva diff --git a/prepare/r-evaluate/PKGBUILD b/prepare/r-evaluate/PKGBUILD new file mode 100644 index 0000000000..4fd35161d6 --- /dev/null +++ b/prepare/r-evaluate/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=evaluate +_pkgver=0.14 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Parsing and Evaluation Tools that Provide More Details than the Default' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-ggplot2 + r-lattice + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-evaluate/lilac.py b/prepare/r-evaluate/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-evaluate/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-evaluate/lilac.yaml b/prepare/r-evaluate/lilac.yaml new file mode 100644 index 0000000000..c5982afeb2 --- /dev/null +++ b/prepare/r-evaluate/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: evaluate_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=evaluate diff --git a/prepare/r-evaluomer/PKGBUILD b/prepare/r-evaluomer/PKGBUILD new file mode 100644 index 0000000000..d175c18140 --- /dev/null +++ b/prepare/r-evaluomer/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=evaluomeR +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Evaluation of Bioinformatics Metrics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-corrplot + r-flexmix + r-fpc + r-ggdendro + r-ggplot2 + r-kableextra + r-matrixstats + r-mclust + r-multiassayexperiment + r-plotrix + r-prabclus + r-randomforest + r-rdpack + r-reshape2 + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-magrittr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-evaluomer/lilac.py b/prepare/r-evaluomer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-evaluomer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-evaluomer/lilac.yaml b/prepare/r-evaluomer/lilac.yaml new file mode 100644 index 0000000000..87a71a225e --- /dev/null +++ b/prepare/r-evaluomer/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-corrplot +- r-flexmix +- r-fpc +- r-ggdendro +- r-ggplot2 +- r-kableextra +- r-matrixstats +- r-mclust +- r-multiassayexperiment +- r-plotrix +- r-prabclus +- r-randomforest +- r-rdpack +- r-reshape2 +- r-summarizedexperiment +update_on: +- regex: evaluomeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/evaluomeR diff --git a/prepare/r-evd/PKGBUILD b/prepare/r-evd/PKGBUILD new file mode 100644 index 0000000000..39a5d63416 --- /dev/null +++ b/prepare/r-evd/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=evd +_pkgver=2.3-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for Extreme Value Distributions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-akima +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-evd/lilac.py b/prepare/r-evd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-evd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-evd/lilac.yaml b/prepare/r-evd/lilac.yaml new file mode 100644 index 0000000000..9de950628e --- /dev/null +++ b/prepare/r-evd/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: evd_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=evd diff --git a/prepare/r-eventpointer/PKGBUILD b/prepare/r-eventpointer/PKGBUILD new file mode 100644 index 0000000000..8ee1d4e0f9 --- /dev/null +++ b/prepare/r-eventpointer/PKGBUILD @@ -0,0 +1,65 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EventPointer +_pkgver=3.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An effective identification of alternative splicing events using junction arrays and RNA-Seq data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-abind + r-affxparser + r-biostrings + r-bsgenome + r-cobs + r-doparallel + r-foreach + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-glmnet + r-graph + r-igraph + r-iranges + r-iterators + r-limma + r-lpsolve + r-matrixstats + r-nnls + r-poibin + r-prodlim + r-qvalue + r-rbgl + r-rhdf5 + r-s4vectors + r-sgseq + r-speedglm + r-stringr + r-summarizedexperiment + r-tximport +) +optdepends=( + r-biocgenerics + r-biocstyle + r-dplyr + r-kableextra + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-eventpointer/lilac.py b/prepare/r-eventpointer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-eventpointer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-eventpointer/lilac.yaml b/prepare/r-eventpointer/lilac.yaml new file mode 100644 index 0000000000..d68f9f676f --- /dev/null +++ b/prepare/r-eventpointer/lilac.yaml @@ -0,0 +1,39 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-affxparser +- r-biostrings +- r-bsgenome +- r-cobs +- r-doparallel +- r-foreach +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-glmnet +- r-graph +- r-igraph +- r-iranges +- r-iterators +- r-limma +- r-lpsolve +- r-matrixstats +- r-nnls +- r-poibin +- r-prodlim +- r-qvalue +- r-rbgl +- r-rhdf5 +- r-s4vectors +- r-sgseq +- r-speedglm +- r-stringr +- r-summarizedexperiment +- r-tximport +update_on: +- regex: EventPointer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EventPointer diff --git a/prepare/r-evmix/PKGBUILD b/prepare/r-evmix/PKGBUILD new file mode 100644 index 0000000000..b189ccc8ef --- /dev/null +++ b/prepare/r-evmix/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=evmix +_pkgver=2.12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Extreme Value Mixture Modelling, Threshold Estimation and Boundary Corrected Kernel Density Estimation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-gsl + r-sparsem +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-evmix/lilac.py b/prepare/r-evmix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-evmix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-evmix/lilac.yaml b/prepare/r-evmix/lilac.yaml new file mode 100644 index 0000000000..73ffe47f91 --- /dev/null +++ b/prepare/r-evmix/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gsl +- r-sparsem +update_on: +- regex: evmix_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=evmix diff --git a/prepare/r-ewce/PKGBUILD b/prepare/r-ewce/PKGBUILD new file mode 100644 index 0000000000..ccd2be8727 --- /dev/null +++ b/prepare/r-ewce/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=EWCE +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Expression Weighted Celltype Enrichment' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationhub + r-biomart + r-cowplot + r-ewcedata + r-experimenthub + r-future + r-ggdendro + r-ggplot2 + r-gridextra + r-hgnchelper + r-limma + r-reshape2 + r-rnomni + r-scales + r-stringr + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-data.table + r-devtools + r-knitr + r-markdown + r-memoise + r-readxl + r-rmarkdown + r-sctransform + r-singlecellexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ewce/lilac.py b/prepare/r-ewce/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ewce/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ewce/lilac.yaml b/prepare/r-ewce/lilac.yaml new file mode 100644 index 0000000000..cb7700fc76 --- /dev/null +++ b/prepare/r-ewce/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-biomart +- r-cowplot +- r-ewcedata +- r-experimenthub +- r-future +- r-ggdendro +- r-ggplot2 +- r-gridextra +- r-hgnchelper +- r-limma +- r-reshape2 +- r-rnomni +- r-scales +- r-stringr +- r-summarizedexperiment +update_on: +- regex: EWCE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/EWCE diff --git a/prepare/r-ewcedata/PKGBUILD b/prepare/r-ewcedata/PKGBUILD new file mode 100644 index 0000000000..07ab642ab9 --- /dev/null +++ b/prepare/r-ewcedata/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ewceData +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The ewceData package provides reference data required for ewce' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-experimenthub +) +optdepends=( + r-biocstyle + r-cowplot + r-ggplot2 + r-knitr + r-markdown + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ewcedata/lilac.py b/prepare/r-ewcedata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ewcedata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ewcedata/lilac.yaml b/prepare/r-ewcedata/lilac.yaml new file mode 100644 index 0000000000..e9cb6a312e --- /dev/null +++ b/prepare/r-ewcedata/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-experimenthub +update_on: +- regex: ewceData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ewceData diff --git a/prepare/r-exact/PKGBUILD b/prepare/r-exact/PKGBUILD new file mode 100644 index 0000000000..507e085635 --- /dev/null +++ b/prepare/r-exact/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Exact +_pkgver=3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Unconditional Exact Test' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rootsolve +) +optdepends=( + r-exactdata +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-exact/lilac.py b/prepare/r-exact/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-exact/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-exact/lilac.yaml b/prepare/r-exact/lilac.yaml new file mode 100644 index 0000000000..07e6c6b933 --- /dev/null +++ b/prepare/r-exact/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rootsolve +update_on: +- regex: Exact_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Exact diff --git a/prepare/r-exactranktests/PKGBUILD b/prepare/r-exactranktests/PKGBUILD new file mode 100644 index 0000000000..764d7ff36e --- /dev/null +++ b/prepare/r-exactranktests/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=exactRankTests +_pkgver=0.8-34 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Exact Distributions for Rank and Permutation Tests' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-survival +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-exactranktests/lilac.py b/prepare/r-exactranktests/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-exactranktests/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-exactranktests/lilac.yaml b/prepare/r-exactranktests/lilac.yaml new file mode 100644 index 0000000000..d4e21471b8 --- /dev/null +++ b/prepare/r-exactranktests/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: exactRankTests_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=exactRankTests diff --git a/prepare/r-excelr/PKGBUILD b/prepare/r-excelr/PKGBUILD new file mode 100644 index 0000000000..a5d6edcdd8 --- /dev/null +++ b/prepare/r-excelr/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=excelR +_pkgver=0.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="A Wrapper of the 'JavaScript' Library 'jExcel'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmlwidgets + r-jsonlite +) +optdepends=( + r-covr + r-shiny + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-excelr/lilac.py b/prepare/r-excelr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-excelr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-excelr/lilac.yaml b/prepare/r-excelr/lilac.yaml new file mode 100644 index 0000000000..49e008a14f --- /dev/null +++ b/prepare/r-excelr/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmlwidgets +- r-jsonlite +update_on: +- regex: excelR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=excelR diff --git a/prepare/r-excluster/PKGBUILD b/prepare/r-excluster/PKGBUILD new file mode 100644 index 0000000000..4763fb006d --- /dev/null +++ b/prepare/r-excluster/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ExCluster +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicranges + r-iranges + r-matrixstats + r-rsubread + r-rtracklayer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-excluster/lilac.py b/prepare/r-excluster/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-excluster/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-excluster/lilac.yaml b/prepare/r-excluster/lilac.yaml new file mode 100644 index 0000000000..f7a6b86571 --- /dev/null +++ b/prepare/r-excluster/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-iranges +- r-matrixstats +- r-rsubread +- r-rtracklayer +update_on: +- regex: ExCluster_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ExCluster diff --git a/prepare/r-eximir/PKGBUILD b/prepare/r-eximir/PKGBUILD new file mode 100644 index 0000000000..64965f9bf0 --- /dev/null +++ b/prepare/r-eximir/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ExiMiR +_pkgver=2.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R functions for the normalization of Exiqon miRNA array data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-affyio + r-biobase + r-limma + r-preprocesscore +) +optdepends=( + r-mirna10cdf +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-eximir/lilac.py b/prepare/r-eximir/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-eximir/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-eximir/lilac.yaml b/prepare/r-eximir/lilac.yaml new file mode 100644 index 0000000000..33b42fb795 --- /dev/null +++ b/prepare/r-eximir/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-affyio +- r-biobase +- r-limma +- r-preprocesscore +update_on: +- regex: ExiMiR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ExiMiR diff --git a/prepare/r-exomecopy/PKGBUILD b/prepare/r-exomecopy/PKGBUILD new file mode 100644 index 0000000000..123ac3e327 --- /dev/null +++ b/prepare/r-exomecopy/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=exomeCopy +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Copy number variant detection from exome sequencing read depth' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomeinfodb + r-genomicranges + r-iranges + r-rsamtools +) +optdepends=( + r-biostrings +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-exomecopy/lilac.py b/prepare/r-exomecopy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-exomecopy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-exomecopy/lilac.yaml b/prepare/r-exomecopy/lilac.yaml new file mode 100644 index 0000000000..db3f9d503f --- /dev/null +++ b/prepare/r-exomecopy/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rsamtools +update_on: +- regex: exomeCopy_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/exomeCopy diff --git a/prepare/r-exomepeak2/PKGBUILD b/prepare/r-exomepeak2/PKGBUILD new file mode 100644 index 0000000000..75958f05c2 --- /dev/null +++ b/prepare/r-exomepeak2/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=exomePeak2 +_pkgver=1.6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bias-aware Peak Calling and Quantification for MeRIP-Seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-apeglm + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-cqn + r-deseq2 + r-genefilter + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-mclust + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-knitr + r-rmariadb + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-exomepeak2/lilac.py b/prepare/r-exomepeak2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-exomepeak2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-exomepeak2/lilac.yaml b/prepare/r-exomepeak2/lilac.yaml new file mode 100644 index 0000000000..09b19021aa --- /dev/null +++ b/prepare/r-exomepeak2/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-apeglm +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-cqn +- r-deseq2 +- r-genefilter +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-mclust +- r-reshape2 +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: exomePeak2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/exomePeak2 diff --git a/prepare/r-experimenthub/PKGBUILD b/prepare/r-experimenthub/PKGBUILD new file mode 100644 index 0000000000..d23e90dfcb --- /dev/null +++ b/prepare/r-experimenthub/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ExperimentHub +_pkgver=2.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Client to access ExperimentHub resources' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationhub + r-biocfilecache + r-biocgenerics + r-biocmanager + r-curl + r-rappdirs + r-s4vectors +) +optdepends=( + r-biocstyle + r-experimenthubdata + r-hubpub + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-experimenthub/lilac.py b/prepare/r-experimenthub/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-experimenthub/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-experimenthub/lilac.yaml b/prepare/r-experimenthub/lilac.yaml new file mode 100644 index 0000000000..e01a9cc3f1 --- /dev/null +++ b/prepare/r-experimenthub/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-biocfilecache +- r-biocgenerics +- r-biocmanager +- r-curl +- r-rappdirs +- r-s4vectors +update_on: +- regex: ExperimentHub_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ExperimentHub diff --git a/prepare/r-experimenthubdata/PKGBUILD b/prepare/r-experimenthubdata/PKGBUILD new file mode 100644 index 0000000000..63d6643627 --- /dev/null +++ b/prepare/r-experimenthubdata/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ExperimentHubData +_pkgver=1.20.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Add resources to ExperimentHub' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationhubdata + r-biocgenerics + r-biocmanager + r-curl + r-dbi + r-experimenthub + r-httr + r-s4vectors +) +optdepends=( + r-biocstyle + r-genomeinfodb + r-hubpub + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-experimenthubdata/lilac.py b/prepare/r-experimenthubdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-experimenthubdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-experimenthubdata/lilac.yaml b/prepare/r-experimenthubdata/lilac.yaml new file mode 100644 index 0000000000..dcb2ccfe5b --- /dev/null +++ b/prepare/r-experimenthubdata/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhubdata +- r-biocgenerics +- r-biocmanager +- r-curl +- r-dbi +- r-experimenthub +- r-httr +- r-s4vectors +update_on: +- regex: ExperimentHubData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ExperimentHubData diff --git a/prepare/r-experimentsubset/PKGBUILD b/prepare/r-experimentsubset/PKGBUILD new file mode 100644 index 0000000000..ea4c6fee1d --- /dev/null +++ b/prepare/r-experimentsubset/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ExperimentSubset +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Manages subsets of data with Bioconductor Experiment objects' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-s4vectors + r-singlecellexperiment + r-spatialexperiment + r-summarizedexperiment + r-treesummarizedexperiment +) +optdepends=( + r-airway + r-biocstyle + r-covr + r-knitr + r-rmarkdown + r-scater + r-scds + r-scran + r-stats + r-tenxpbmcdata + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-experimentsubset/lilac.py b/prepare/r-experimentsubset/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-experimentsubset/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-experimentsubset/lilac.yaml b/prepare/r-experimentsubset/lilac.yaml new file mode 100644 index 0000000000..15d93fc318 --- /dev/null +++ b/prepare/r-experimentsubset/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-s4vectors +- r-singlecellexperiment +- r-spatialexperiment +- r-summarizedexperiment +- r-treesummarizedexperiment +update_on: +- regex: ExperimentSubset_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ExperimentSubset diff --git a/prepare/r-exploremodelmatrix/PKGBUILD b/prepare/r-exploremodelmatrix/PKGBUILD new file mode 100644 index 0000000000..23299f02c4 --- /dev/null +++ b/prepare/r-exploremodelmatrix/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ExploreModelMatrix +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Graphical Exploration of Design Matrices' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-cowplot + r-dplyr + r-dt + r-ggplot2 + r-limma + r-magrittr + r-rintrojs + r-s4vectors + r-scales + r-shiny + r-shinydashboard + r-shinyjs + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-htmltools + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-exploremodelmatrix/lilac.py b/prepare/r-exploremodelmatrix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-exploremodelmatrix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-exploremodelmatrix/lilac.yaml b/prepare/r-exploremodelmatrix/lilac.yaml new file mode 100644 index 0000000000..9a73ed22fe --- /dev/null +++ b/prepare/r-exploremodelmatrix/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cowplot +- r-dplyr +- r-dt +- r-ggplot2 +- r-limma +- r-magrittr +- r-rintrojs +- r-s4vectors +- r-scales +- r-shiny +- r-shinydashboard +- r-shinyjs +- r-tibble +- r-tidyr +update_on: +- regex: ExploreModelMatrix_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ExploreModelMatrix diff --git a/prepare/r-expm/PKGBUILD b/prepare/r-expm/PKGBUILD new file mode 100644 index 0000000000..ec88ff534f --- /dev/null +++ b/prepare/r-expm/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=expm +_pkgver=0.999-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Matrix Exponential, Log, 'etc'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-rcolorbrewer + r-rmpfr + r-sfsmisc +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-expm/lilac.py b/prepare/r-expm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-expm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-expm/lilac.yaml b/prepare/r-expm/lilac.yaml new file mode 100644 index 0000000000..633f4d6962 --- /dev/null +++ b/prepare/r-expm/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: expm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=expm diff --git a/prepare/r-expressionatlas/PKGBUILD b/prepare/r-expressionatlas/PKGBUILD new file mode 100644 index 0000000000..795f632b2b --- /dev/null +++ b/prepare/r-expressionatlas/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ExpressionAtlas +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Download datasets from EMBL-EBI Expression Atlas' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-httr + r-limma + r-s4vectors + r-summarizedexperiment + r-xml + r-xml2 +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-expressionatlas/lilac.py b/prepare/r-expressionatlas/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-expressionatlas/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-expressionatlas/lilac.yaml b/prepare/r-expressionatlas/lilac.yaml new file mode 100644 index 0000000000..6bc3aee06b --- /dev/null +++ b/prepare/r-expressionatlas/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-httr +- r-limma +- r-s4vectors +- r-summarizedexperiment +- r-xml +- r-xml2 +update_on: +- regex: ExpressionAtlas_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ExpressionAtlas diff --git a/prepare/r-extdist/PKGBUILD b/prepare/r-extdist/PKGBUILD new file mode 100644 index 0000000000..540fc604a6 --- /dev/null +++ b/prepare/r-extdist/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ExtDist +_pkgver=0.6-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Extending the Range of Functions for Probability Distributions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-numderiv + r-optimx +) +optdepends=( + r-ggplot2 + r-graphics + r-knitr + r-performanceanalytics + r-rmarkdown + r-stats + r-suppdists + r-truncdist + r-utils + r-vgam + r-xtable +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-extdist/lilac.py b/prepare/r-extdist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-extdist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-extdist/lilac.yaml b/prepare/r-extdist/lilac.yaml new file mode 100644 index 0000000000..c6b3f1bff7 --- /dev/null +++ b/prepare/r-extdist/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-numderiv +- r-optimx +update_on: +- regex: ExtDist_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ExtDist diff --git a/prepare/r-extradistr/PKGBUILD b/prepare/r-extradistr/PKGBUILD new file mode 100644 index 0000000000..8b4d61c549 --- /dev/null +++ b/prepare/r-extradistr/PKGBUILD @@ -0,0 +1,38 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=extraDistr +_pkgver=1.9.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Additional Univariate and Multivariate Distributions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-actuar + r-evd + r-hoa + r-laplacesdemon + r-skellam + r-testthat + r-triangle + r-vgam +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-extradistr/lilac.py b/prepare/r-extradistr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-extradistr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-extradistr/lilac.yaml b/prepare/r-extradistr/lilac.yaml new file mode 100644 index 0000000000..b24a6d4d7f --- /dev/null +++ b/prepare/r-extradistr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: extraDistr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=extraDistr diff --git a/prepare/r-extrafont/PKGBUILD b/prepare/r-extrafont/PKGBUILD new file mode 100644 index 0000000000..e3206fc873 --- /dev/null +++ b/prepare/r-extrafont/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=extrafont +_pkgver=0.17 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for using fonts' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-extrafontdb + r-rttf2pt1 +) +optdepends=( + r-fontcm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-extrafont/lilac.py b/prepare/r-extrafont/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-extrafont/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-extrafont/lilac.yaml b/prepare/r-extrafont/lilac.yaml new file mode 100644 index 0000000000..16d5d9938e --- /dev/null +++ b/prepare/r-extrafont/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-extrafontdb +- r-rttf2pt1 +update_on: +- regex: extrafont_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=extrafont diff --git a/prepare/r-extrafontdb/PKGBUILD b/prepare/r-extrafontdb/PKGBUILD new file mode 100644 index 0000000000..81d5d631f7 --- /dev/null +++ b/prepare/r-extrafontdb/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=extrafontdb +_pkgver=1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Package for holding the database for the extrafont package' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-extrafontdb/lilac.py b/prepare/r-extrafontdb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-extrafontdb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-extrafontdb/lilac.yaml b/prepare/r-extrafontdb/lilac.yaml new file mode 100644 index 0000000000..f335edd2a8 --- /dev/null +++ b/prepare/r-extrafontdb/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: extrafontdb_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=extrafontdb diff --git a/prepare/r-extremes/PKGBUILD b/prepare/r-extremes/PKGBUILD new file mode 100644 index 0000000000..cbd411c468 --- /dev/null +++ b/prepare/r-extremes/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=extRemes +_pkgver=2.1-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Extreme Value Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-distillery + r-lmoments +) +optdepends=( + r-fields +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-extremes/lilac.py b/prepare/r-extremes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-extremes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-extremes/lilac.yaml b/prepare/r-extremes/lilac.yaml new file mode 100644 index 0000000000..d5e4977ee8 --- /dev/null +++ b/prepare/r-extremes/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-distillery +- r-lmoments +update_on: +- regex: extRemes_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=extRemes diff --git a/prepare/r-faahko/PKGBUILD b/prepare/r-faahko/PKGBUILD new file mode 100644 index 0000000000..63ac3c127f --- /dev/null +++ b/prepare/r-faahko/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=faahKO +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Saghatelian et al. (2004) FAAH knockout LC/MS data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-xcms +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-faahko/lilac.py b/prepare/r-faahko/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-faahko/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-faahko/lilac.yaml b/prepare/r-faahko/lilac.yaml new file mode 100644 index 0000000000..de96e5269a --- /dev/null +++ b/prepare/r-faahko/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-xcms +update_on: +- regex: faahKO_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/faahKO diff --git a/prepare/r-fabia/PKGBUILD b/prepare/r-fabia/PKGBUILD new file mode 100644 index 0000000000..43af60dd26 --- /dev/null +++ b/prepare/r-fabia/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fabia +_pkgver=2.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='FABIA: Factor Analysis for Bicluster Acquisition' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fabia/lilac.py b/prepare/r-fabia/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fabia/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fabia/lilac.yaml b/prepare/r-fabia/lilac.yaml new file mode 100644 index 0000000000..9ccea0fc8a --- /dev/null +++ b/prepare/r-fabia/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: fabia_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/fabia diff --git a/prepare/r-factdesign/PKGBUILD b/prepare/r-factdesign/PKGBUILD new file mode 100644 index 0000000000..95f906cbf8 --- /dev/null +++ b/prepare/r-factdesign/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=factDesign +_pkgver=1.70.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Factorial designed microarray experiment analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase +) +optdepends=( + r-affy + r-genefilter + r-multtest +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-factdesign/lilac.py b/prepare/r-factdesign/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-factdesign/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-factdesign/lilac.yaml b/prepare/r-factdesign/lilac.yaml new file mode 100644 index 0000000000..9912267f76 --- /dev/null +++ b/prepare/r-factdesign/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: factDesign_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/factDesign diff --git a/prepare/r-factoextra/PKGBUILD b/prepare/r-factoextra/PKGBUILD new file mode 100644 index 0000000000..51b0621052 --- /dev/null +++ b/prepare/r-factoextra/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=factoextra +_pkgver=1.0.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Extract and Visualize the Results of Multivariate Data Analyses' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-dendextend + r-factominer + r-ggplot2 + r-ggpubr + r-ggrepel + r-reshape2 + r-tidyr +) +optdepends=( + r-ade4 + r-ca + r-igraph + r-knitr + r-mass + r-mclust +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-factoextra/lilac.py b/prepare/r-factoextra/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-factoextra/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-factoextra/lilac.yaml b/prepare/r-factoextra/lilac.yaml new file mode 100644 index 0000000000..4105b4fe5f --- /dev/null +++ b/prepare/r-factoextra/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-dendextend +- r-factominer +- r-ggplot2 +- r-ggpubr +- r-ggrepel +- r-reshape2 +- r-tidyr +update_on: +- regex: factoextra_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=factoextra diff --git a/prepare/r-factominer/PKGBUILD b/prepare/r-factominer/PKGBUILD new file mode 100644 index 0000000000..58027c8b6a --- /dev/null +++ b/prepare/r-factominer/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FactoMineR +_pkgver=2.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multivariate Exploratory Data Analysis and Data Mining' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-car + r-dt + r-ellipse + r-flashclust + r-ggplot2 + r-ggrepel + r-leaps + r-scatterplot3d +) +optdepends=( + r-factoshiny + r-knitr + r-markdown + r-missmda +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-factominer/lilac.py b/prepare/r-factominer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-factominer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-factominer/lilac.yaml b/prepare/r-factominer/lilac.yaml new file mode 100644 index 0000000000..3e0427ad45 --- /dev/null +++ b/prepare/r-factominer/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-car +- r-dt +- r-ellipse +- r-flashclust +- r-ggplot2 +- r-ggrepel +- r-leaps +- r-scatterplot3d +update_on: +- regex: FactoMineR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=FactoMineR diff --git a/prepare/r-famagg/PKGBUILD b/prepare/r-famagg/PKGBUILD new file mode 100644 index 0000000000..71a52744b4 --- /dev/null +++ b/prepare/r-famagg/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FamAgg +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pedigree Analysis and Familial Aggregation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-gap + r-igraph + r-kinship2 + r-survey +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-famagg/lilac.py b/prepare/r-famagg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-famagg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-famagg/lilac.yaml b/prepare/r-famagg/lilac.yaml new file mode 100644 index 0000000000..9008b6f53e --- /dev/null +++ b/prepare/r-famagg/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-gap +- r-igraph +- r-kinship2 +- r-survey +update_on: +- regex: FamAgg_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FamAgg diff --git a/prepare/r-famat/PKGBUILD b/prepare/r-famat/PKGBUILD new file mode 100644 index 0000000000..ea252baa5b --- /dev/null +++ b/prepare/r-famat/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=famat +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functional analysis of metabolic and transcriptomic data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-clusterprofiler + r-dplyr + r-dt + r-go.db + r-gprofiler2 + r-keggrest + r-magrittr + r-mpinet + r-ontologyindex + r-org.hs.eg.db + r-plotly + r-reactome.db + r-rwikipathways + r-shiny + r-shinybs + r-shinydashboard + r-stringr + r-tidyr +) +optdepends=( + r-biocmanager + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-famat/lilac.py b/prepare/r-famat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-famat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-famat/lilac.yaml b/prepare/r-famat/lilac.yaml new file mode 100644 index 0000000000..4263ee3884 --- /dev/null +++ b/prepare/r-famat/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clusterprofiler +- r-dplyr +- r-dt +- r-go.db +- r-gprofiler2 +- r-keggrest +- r-magrittr +- r-mpinet +- r-ontologyindex +- r-org.hs.eg.db +- r-plotly +- r-reactome.db +- r-rwikipathways +- r-shiny +- r-shinybs +- r-shinydashboard +- r-stringr +- r-tidyr +update_on: +- regex: famat_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/famat diff --git a/prepare/r-farms/PKGBUILD b/prepare/r-farms/PKGBUILD new file mode 100644 index 0000000000..91ba0c35f8 --- /dev/null +++ b/prepare/r-farms/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=farms +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='FARMS - Factor Analysis for Robust Microarray Summarization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-affy + r-biobase +) +optdepends=( + r-affydata + r-biobase + r-utils +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-farms/lilac.py b/prepare/r-farms/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-farms/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-farms/lilac.yaml b/prepare/r-farms/lilac.yaml new file mode 100644 index 0000000000..3d47a33ab3 --- /dev/null +++ b/prepare/r-farms/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +update_on: +- regex: farms_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/farms diff --git a/prepare/r-farver/PKGBUILD b/prepare/r-farver/PKGBUILD new file mode 100644 index 0000000000..3c7c124721 --- /dev/null +++ b/prepare/r-farver/PKGBUILD @@ -0,0 +1,32 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=farver +_pkgver=2.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='High Performance Colour Space Manipulation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-farver/lilac.py b/prepare/r-farver/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-farver/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-farver/lilac.yaml b/prepare/r-farver/lilac.yaml new file mode 100644 index 0000000000..ed10d86766 --- /dev/null +++ b/prepare/r-farver/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: farver_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=farver diff --git a/prepare/r-fastcluster/PKGBUILD b/prepare/r-fastcluster/PKGBUILD new file mode 100644 index 0000000000..e2206b015c --- /dev/null +++ b/prepare/r-fastcluster/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fastcluster +_pkgver=1.2.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Fast Hierarchical Clustering Routines for R and 'Python'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-flashclust + r-stats +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fastcluster/lilac.py b/prepare/r-fastcluster/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fastcluster/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fastcluster/lilac.yaml b/prepare/r-fastcluster/lilac.yaml new file mode 100644 index 0000000000..7c425d1c19 --- /dev/null +++ b/prepare/r-fastcluster/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: fastcluster_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fastcluster diff --git a/prepare/r-fastdummies/PKGBUILD b/prepare/r-fastdummies/PKGBUILD new file mode 100644 index 0000000000..ae6564750f --- /dev/null +++ b/prepare/r-fastdummies/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fastDummies +_pkgver=1.6.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast Creation of Dummy (Binary) Columns and Rows from Categorical Variables' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-data.table + r-stringr + r-tibble +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-spelling + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fastdummies/lilac.py b/prepare/r-fastdummies/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fastdummies/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fastdummies/lilac.yaml b/prepare/r-fastdummies/lilac.yaml new file mode 100644 index 0000000000..47dee45dc8 --- /dev/null +++ b/prepare/r-fastdummies/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-stringr +- r-tibble +update_on: +- regex: fastDummies_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fastDummies diff --git a/prepare/r-fastica/PKGBUILD b/prepare/r-fastica/PKGBUILD new file mode 100644 index 0000000000..0d6f3786b6 --- /dev/null +++ b/prepare/r-fastica/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fastICA +_pkgver=1.2-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='FastICA Algorithms to Perform ICA and Projection Pursuit' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-mass +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fastica/lilac.py b/prepare/r-fastica/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fastica/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fastica/lilac.yaml b/prepare/r-fastica/lilac.yaml new file mode 100644 index 0000000000..99e15be385 --- /dev/null +++ b/prepare/r-fastica/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: fastICA_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fastICA diff --git a/prepare/r-fastliquidassociation/PKGBUILD b/prepare/r-fastliquidassociation/PKGBUILD new file mode 100644 index 0000000000..1bb20b84ec --- /dev/null +++ b/prepare/r-fastliquidassociation/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fastLiquidAssociation +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='functions for genome-wide application of Liquid Association' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-doparallel + r-hmisc + r-impute + r-liquidassociation + r-preprocesscore + r-wgcna +) +optdepends=( + r-gostats + r-org.sc.sgd.db + r-yeastcc +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fastliquidassociation/lilac.py b/prepare/r-fastliquidassociation/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fastliquidassociation/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fastliquidassociation/lilac.yaml b/prepare/r-fastliquidassociation/lilac.yaml new file mode 100644 index 0000000000..e9c744f610 --- /dev/null +++ b/prepare/r-fastliquidassociation/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-hmisc +- r-impute +- r-liquidassociation +- r-preprocesscore +- r-wgcna +update_on: +- regex: fastLiquidAssociation_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/fastLiquidAssociation diff --git a/prepare/r-fastmatch/PKGBUILD b/prepare/r-fastmatch/PKGBUILD new file mode 100644 index 0000000000..79ecd5053e --- /dev/null +++ b/prepare/r-fastmatch/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fastmatch +_pkgver=1.1-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Fast 'match()' Function" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fastmatch/lilac.py b/prepare/r-fastmatch/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fastmatch/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fastmatch/lilac.yaml b/prepare/r-fastmatch/lilac.yaml new file mode 100644 index 0000000000..0288eebc6b --- /dev/null +++ b/prepare/r-fastmatch/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: fastmatch_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fastmatch diff --git a/prepare/r-fastqcleaner/PKGBUILD b/prepare/r-fastqcleaner/PKGBUILD new file mode 100644 index 0000000000..ccb8b9a63b --- /dev/null +++ b/prepare/r-fastqcleaner/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FastqCleaner +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biostrings + r-dt + r-htmltools + r-iranges + r-rcpp + r-s4vectors + r-shiny + r-shinybs + r-shortread +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fastqcleaner/lilac.py b/prepare/r-fastqcleaner/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fastqcleaner/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fastqcleaner/lilac.yaml b/prepare/r-fastqcleaner/lilac.yaml new file mode 100644 index 0000000000..d405c1986d --- /dev/null +++ b/prepare/r-fastqcleaner/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-dt +- r-htmltools +- r-iranges +- r-rcpp +- r-s4vectors +- r-shiny +- r-shinybs +- r-shortread +update_on: +- regex: FastqCleaner_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FastqCleaner diff --git a/prepare/r-fastseg/PKGBUILD b/prepare/r-fastseg/PKGBUILD new file mode 100644 index 0000000000..91c658a24a --- /dev/null +++ b/prepare/r-fastseg/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fastseg +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='fastseg - a fast segmentation algorithm' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-biocgenerics + r-genomicranges + r-iranges + r-s4vectors +) +optdepends=( + r-dnacopy + r-oligo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fastseg/lilac.py b/prepare/r-fastseg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fastseg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fastseg/lilac.yaml b/prepare/r-fastseg/lilac.yaml new file mode 100644 index 0000000000..4cfbb2c7d8 --- /dev/null +++ b/prepare/r-fastseg/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-genomicranges +- r-iranges +- r-s4vectors +update_on: +- regex: fastseg_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/fastseg diff --git a/prepare/r-fbasics/PKGBUILD b/prepare/r-fbasics/PKGBUILD new file mode 100644 index 0000000000..1c59e8e5d3 --- /dev/null +++ b/prepare/r-fbasics/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fBasics +_pkgver=3042.89.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Rmetrics - Markets and Basic Statistics' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-gss + r-stabledist + r-timedate + r-timeseries +) +optdepends=( + r-akima + r-runit + r-tcltk +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fbasics/lilac.py b/prepare/r-fbasics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fbasics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fbasics/lilac.yaml b/prepare/r-fbasics/lilac.yaml new file mode 100644 index 0000000000..5c342cbf92 --- /dev/null +++ b/prepare/r-fbasics/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gss +- r-stabledist +- r-timedate +- r-timeseries +update_on: +- regex: fBasics_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fBasics diff --git a/prepare/r-fcbf/PKGBUILD b/prepare/r-fcbf/PKGBUILD new file mode 100644 index 0000000000..2e54eab973 --- /dev/null +++ b/prepare/r-fcbf/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FCBF +_pkgver=2.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast Correlation Based Filter for Feature Selection' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-ggplot2 + r-gridextra + r-mclust + r-pbapply + r-summarizedexperiment +) +optdepends=( + r-biocmanager + r-caret + r-knitr + r-mlbench + r-rmarkdown + r-singlecellexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fcbf/lilac.py b/prepare/r-fcbf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fcbf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fcbf/lilac.yaml b/prepare/r-fcbf/lilac.yaml new file mode 100644 index 0000000000..be95a2b44e --- /dev/null +++ b/prepare/r-fcbf/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gridextra +- r-mclust +- r-pbapply +- r-summarizedexperiment +update_on: +- regex: FCBF_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FCBF diff --git a/prepare/r-fccac/PKGBUILD b/prepare/r-fccac/PKGBUILD new file mode 100644 index 0000000000..1cb7ca5504 --- /dev/null +++ b/prepare/r-fccac/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fCCAC +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-complexheatmap + r-fda + r-genomation + r-genomicranges + r-ggplot2 + r-iranges + r-rcolorbrewer + r-s4vectors +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fccac/lilac.py b/prepare/r-fccac/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fccac/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fccac/lilac.yaml b/prepare/r-fccac/lilac.yaml new file mode 100644 index 0000000000..636a4111e0 --- /dev/null +++ b/prepare/r-fccac/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-complexheatmap +- r-fda +- r-genomation +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-rcolorbrewer +- r-s4vectors +update_on: +- regex: fCCAC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/fCCAC diff --git a/prepare/r-fci/PKGBUILD b/prepare/r-fci/PKGBUILD new file mode 100644 index 0000000000..b9ce282d8d --- /dev/null +++ b/prepare/r-fci/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fCI +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-fnn + r-gtools + r-psych + r-rgl + r-venndiagram + r-zoo +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fci/lilac.py b/prepare/r-fci/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fci/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fci/lilac.yaml b/prepare/r-fci/lilac.yaml new file mode 100644 index 0000000000..262165673d --- /dev/null +++ b/prepare/r-fci/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fnn +- r-gtools +- r-psych +- r-rgl +- r-venndiagram +- r-zoo +update_on: +- regex: fCI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/fCI diff --git a/prepare/r-fcoex/PKGBUILD b/prepare/r-fcoex/PKGBUILD new file mode 100644 index 0000000000..09dbce6817 --- /dev/null +++ b/prepare/r-fcoex/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fcoex +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='FCBF-based Co-Expression Networks for Single Cells' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-clusterprofiler + r-data.table + r-dplyr + r-fcbf + r-ggplot2 + r-ggrepel + r-igraph + r-intergraph + r-network + r-pathwaypca + r-progress + r-scales + r-singlecellexperiment + r-sna + r-stringr +) +optdepends=( + r-biocmanager + r-devtools + r-gridextra + r-knitr + r-rmarkdown + r-scater + r-schex + r-scran + r-seurat + r-tenxpbmcdata + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fcoex/lilac.py b/prepare/r-fcoex/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fcoex/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fcoex/lilac.yaml b/prepare/r-fcoex/lilac.yaml new file mode 100644 index 0000000000..05e0d316f2 --- /dev/null +++ b/prepare/r-fcoex/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clusterprofiler +- r-data.table +- r-dplyr +- r-fcbf +- r-ggplot2 +- r-ggrepel +- r-igraph +- r-intergraph +- r-network +- r-pathwaypca +- r-progress +- r-scales +- r-singlecellexperiment +- r-sna +- r-stringr +update_on: +- regex: fcoex_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/fcoex diff --git a/prepare/r-fcscan/PKGBUILD b/prepare/r-fcscan/PKGBUILD new file mode 100644 index 0000000000..d12b7b47bf --- /dev/null +++ b/prepare/r-fcscan/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fcScan +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='fcScan for detecting clusters of coordinates with user defined options' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-doparallel + r-foreach + r-genomicranges + r-iranges + r-plyr + r-rtracklayer + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fcscan/lilac.py b/prepare/r-fcscan/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fcscan/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fcscan/lilac.yaml b/prepare/r-fcscan/lilac.yaml new file mode 100644 index 0000000000..f0cad57142 --- /dev/null +++ b/prepare/r-fcscan/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-foreach +- r-genomicranges +- r-iranges +- r-plyr +- r-rtracklayer +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: fcScan_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/fcScan diff --git a/prepare/r-fda/PKGBUILD b/prepare/r-fda/PKGBUILD new file mode 100644 index 0000000000..5d632ebb3b --- /dev/null +++ b/prepare/r-fda/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fda +_pkgver=5.5.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functional Data Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-desolve + r-fds +) +optdepends=( + r-lattice +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fda/lilac.py b/prepare/r-fda/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fda/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fda/lilac.yaml b/prepare/r-fda/lilac.yaml new file mode 100644 index 0000000000..6ca7da68f3 --- /dev/null +++ b/prepare/r-fda/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-desolve +- r-fds +update_on: +- regex: fda_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fda diff --git a/prepare/r-fdb.infiniummethylation.hg19/PKGBUILD b/prepare/r-fdb.infiniummethylation.hg19/PKGBUILD new file mode 100644 index 0000000000..66b2de8f28 --- /dev/null +++ b/prepare/r-fdb.infiniummethylation.hg19/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FDb.InfiniumMethylation.hg19 +_pkgver=2.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation package for Illumina Infinium DNA methylation probes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biostrings + r-genomicfeatures + r-org.hs.eg.db + r-txdb.hsapiens.ucsc.hg19.knowngene +) +optdepends=( + r-fdb.ucsc.snp135common.hg19 +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fdb.infiniummethylation.hg19/lilac.py b/prepare/r-fdb.infiniummethylation.hg19/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fdb.infiniummethylation.hg19/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fdb.infiniummethylation.hg19/lilac.yaml b/prepare/r-fdb.infiniummethylation.hg19/lilac.yaml new file mode 100644 index 0000000000..b198b75478 --- /dev/null +++ b/prepare/r-fdb.infiniummethylation.hg19/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biostrings +- r-genomicfeatures +- r-org.hs.eg.db +- r-txdb.hsapiens.ucsc.hg19.knowngene +update_on: +- regex: FDb.InfiniumMethylation.hg19_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19 diff --git a/prepare/r-fdrame/PKGBUILD b/prepare/r-fdrame/PKGBUILD new file mode 100644 index 0000000000..afd9d72441 --- /dev/null +++ b/prepare/r-fdrame/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fdrame +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='FDR adjustments of Microarray Experiments (FDR-AME)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fdrame/lilac.py b/prepare/r-fdrame/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fdrame/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fdrame/lilac.yaml b/prepare/r-fdrame/lilac.yaml new file mode 100644 index 0000000000..b8738c49f7 --- /dev/null +++ b/prepare/r-fdrame/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: fdrame_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/fdrame diff --git a/prepare/r-fdrtool/PKGBUILD b/prepare/r-fdrtool/PKGBUILD new file mode 100644 index 0000000000..9cfecd9d7c --- /dev/null +++ b/prepare/r-fdrtool/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fdrtool +_pkgver=1.2.17 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimation of (Local) False Discovery Rates and Higher Criticism' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fdrtool/lilac.py b/prepare/r-fdrtool/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fdrtool/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fdrtool/lilac.yaml b/prepare/r-fdrtool/lilac.yaml new file mode 100644 index 0000000000..a83104725a --- /dev/null +++ b/prepare/r-fdrtool/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: fdrtool_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fdrtool diff --git a/prepare/r-fds/PKGBUILD b/prepare/r-fds/PKGBUILD new file mode 100644 index 0000000000..30d51cd3d3 --- /dev/null +++ b/prepare/r-fds/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fds +_pkgver=1.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functional Data Sets' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rainbow + r-rcurl +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fds/lilac.py b/prepare/r-fds/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fds/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fds/lilac.yaml b/prepare/r-fds/lilac.yaml new file mode 100644 index 0000000000..a621960bcf --- /dev/null +++ b/prepare/r-fds/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rainbow +- r-rcurl +update_on: +- regex: fds_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fds diff --git a/prepare/r-feast/PKGBUILD b/prepare/r-feast/PKGBUILD new file mode 100644 index 0000000000..12a837c7e9 --- /dev/null +++ b/prepare/r-feast/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FEAST +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='FEAture SelcTion (FEAST) for Single-cell clustering' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-irlba + r-matrixstats + r-mclust + r-sc3 + r-singlecellexperiment + r-summarizedexperiment + r-tscan +) +optdepends=( + r-biocstyle + r-ggpubr + r-knitr + r-rmarkdown + r-seurat + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-feast/lilac.py b/prepare/r-feast/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-feast/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-feast/lilac.yaml b/prepare/r-feast/lilac.yaml new file mode 100644 index 0000000000..58821ea837 --- /dev/null +++ b/prepare/r-feast/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-irlba +- r-matrixstats +- r-mclust +- r-sc3 +- r-singlecellexperiment +- r-summarizedexperiment +- r-tscan +update_on: +- regex: FEAST_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FEAST diff --git a/prepare/r-feather/PKGBUILD b/prepare/r-feather/PKGBUILD new file mode 100644 index 0000000000..fea2326eb6 --- /dev/null +++ b/prepare/r-feather/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: little-endian platform +# Maintainer: Guoyi Zhang + +_pkgname=feather +_pkgver=0.3.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="R Bindings to the Feather 'API'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-hms + r-rcpp + r-tibble +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-feather/lilac.py b/prepare/r-feather/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-feather/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-feather/lilac.yaml b/prepare/r-feather/lilac.yaml new file mode 100644 index 0000000000..cebf6b3cfe --- /dev/null +++ b/prepare/r-feather/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-hms +- r-rcpp +- r-tibble +update_on: +- regex: feather_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=feather diff --git a/prepare/r-feature/PKGBUILD b/prepare/r-feature/PKGBUILD new file mode 100644 index 0000000000..03bdc80ab3 --- /dev/null +++ b/prepare/r-feature/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=feature +_pkgver=1.2.15 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Local Inferential Feature Significance for Multivariate Kernel Density Estimation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ks + r-plot3d +) +optdepends=( + r-knitr + r-mass + r-misc3d + r-rgl + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-feature/lilac.py b/prepare/r-feature/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-feature/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-feature/lilac.yaml b/prepare/r-feature/lilac.yaml new file mode 100644 index 0000000000..08108fd8bb --- /dev/null +++ b/prepare/r-feature/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ks +- r-plot3d +update_on: +- regex: feature_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=feature diff --git a/prepare/r-fedup/PKGBUILD b/prepare/r-fedup/PKGBUILD new file mode 100644 index 0000000000..a33960dac4 --- /dev/null +++ b/prepare/r-fedup/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fedup +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Fisher's Test for Enrichment and Depletion of User-Defined Pathways" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-data.table + r-dplyr + r-forcats + r-ggplot2 + r-ggthemes + r-openxlsx + r-rcolorbrewer + r-rcy3 + r-tibble +) +optdepends=( + r-biomart + r-covr + r-devtools + r-knitr + r-rmarkdown + r-testthat + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fedup/lilac.py b/prepare/r-fedup/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fedup/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fedup/lilac.yaml b/prepare/r-fedup/lilac.yaml new file mode 100644 index 0000000000..a687ed7c3d --- /dev/null +++ b/prepare/r-fedup/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-dplyr +- r-forcats +- r-ggplot2 +- r-ggthemes +- r-openxlsx +- r-rcolorbrewer +- r-rcy3 +- r-tibble +update_on: +- regex: fedup_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/fedup diff --git a/prepare/r-fella/PKGBUILD b/prepare/r-fella/PKGBUILD new file mode 100644 index 0000000000..9588e693c9 --- /dev/null +++ b/prepare/r-fella/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FELLA +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interpretation and enrichment for metabolomics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-igraph + r-keggrest + r-plyr +) +optdepends=( + r-annotationdbi + r-biocstyle + r-biomart + r-dt + r-gosemsim + r-knitr + r-magrittr + r-org.hs.eg.db + r-org.mm.eg.db + r-rmarkdown + r-shiny + r-testthat + r-visnetwork +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fella/lilac.py b/prepare/r-fella/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fella/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fella/lilac.yaml b/prepare/r-fella/lilac.yaml new file mode 100644 index 0000000000..f155b1c3fa --- /dev/null +++ b/prepare/r-fella/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +- r-keggrest +- r-plyr +update_on: +- regex: FELLA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FELLA diff --git a/prepare/r-ff/PKGBUILD b/prepare/r-ff/PKGBUILD new file mode 100644 index 0000000000..7f1d4e40d6 --- /dev/null +++ b/prepare/r-ff/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ff +_pkgver=4.0.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Memory-Efficient Storage of Large Data on Disk and Fast Access Functions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bit +) +optdepends=( + r-biglm + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ff/lilac.py b/prepare/r-ff/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ff/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ff/lilac.yaml b/prepare/r-ff/lilac.yaml new file mode 100644 index 0000000000..3bf7a3d861 --- /dev/null +++ b/prepare/r-ff/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bit +update_on: +- regex: ff_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ff diff --git a/prepare/r-ffbase/PKGBUILD b/prepare/r-ffbase/PKGBUILD new file mode 100644 index 0000000000..ec5e1fa274 --- /dev/null +++ b/prepare/r-ffbase/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ffbase +_pkgver=0.13.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Basic Statistical Functions for Package 'ff'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bit + r-fastmatch + r-ff +) +optdepends=( + r-biglm + r-laf + r-parallel + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ffbase/lilac.py b/prepare/r-ffbase/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ffbase/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ffbase/lilac.yaml b/prepare/r-ffbase/lilac.yaml new file mode 100644 index 0000000000..49857f6194 --- /dev/null +++ b/prepare/r-ffbase/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bit +- r-fastmatch +- r-ff +update_on: +- regex: ffbase_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ffbase diff --git a/prepare/r-ffield/PKGBUILD b/prepare/r-ffield/PKGBUILD new file mode 100644 index 0000000000..cd0eb71898 --- /dev/null +++ b/prepare/r-ffield/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FField +_pkgver=0.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Force field simulation for a set of points' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-ggplot2 + r-gridextra +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ffield/lilac.py b/prepare/r-ffield/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ffield/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ffield/lilac.yaml b/prepare/r-ffield/lilac.yaml new file mode 100644 index 0000000000..89b470fada --- /dev/null +++ b/prepare/r-ffield/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: FField_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=FField diff --git a/prepare/r-ffpe/PKGBUILD b/prepare/r-ffpe/PKGBUILD new file mode 100644 index 0000000000..8bfabef944 --- /dev/null +++ b/prepare/r-ffpe/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ffpe +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quality assessment and control for FFPE microarray expression data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-biobase + r-biocgenerics + r-lumi + r-methylumi + r-sfsmisc + r-ttr +) +optdepends=( + r-ffpeexampledata + r-genefilter +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ffpe/lilac.py b/prepare/r-ffpe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ffpe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ffpe/lilac.yaml b/prepare/r-ffpe/lilac.yaml new file mode 100644 index 0000000000..483cad0ccd --- /dev/null +++ b/prepare/r-ffpe/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +- r-biocgenerics +- r-lumi +- r-methylumi +- r-sfsmisc +- r-ttr +update_on: +- regex: ffpe_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ffpe diff --git a/prepare/r-fftw/PKGBUILD b/prepare/r-fftw/PKGBUILD new file mode 100644 index 0000000000..5062385616 --- /dev/null +++ b/prepare/r-fftw/PKGBUILD @@ -0,0 +1,27 @@ +# system requirements: fftw3 (>= 3.1.2) +# Maintainer: Guoyi Zhang + +_pkgname=fftw +_pkgver=1.0-6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast FFT and DCT Based on the FFTW Library' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fftw/lilac.py b/prepare/r-fftw/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fftw/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fftw/lilac.yaml b/prepare/r-fftw/lilac.yaml new file mode 100644 index 0000000000..979be57a9f --- /dev/null +++ b/prepare/r-fftw/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: fftw_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fftw diff --git a/prepare/r-fftwtools/PKGBUILD b/prepare/r-fftwtools/PKGBUILD new file mode 100644 index 0000000000..097a17fbb7 --- /dev/null +++ b/prepare/r-fftwtools/PKGBUILD @@ -0,0 +1,30 @@ +# system requirements: fftw3 (libfftw3-dev (deb), or fftw-devel (rpm)) +# Maintainer: Guoyi Zhang + +_pkgname=fftwtools +_pkgver=0.9-11 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Wrapper for 'FFTW3' Includes: One-Dimensional, Two-Dimensional, Three-Dimensional, and Multivariate Transforms" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-fftw +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fftwtools/lilac.py b/prepare/r-fftwtools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fftwtools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fftwtools/lilac.yaml b/prepare/r-fftwtools/lilac.yaml new file mode 100644 index 0000000000..62736125cf --- /dev/null +++ b/prepare/r-fftwtools/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: fftwtools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fftwtools diff --git a/prepare/r-fgarch/PKGBUILD b/prepare/r-fgarch/PKGBUILD new file mode 100644 index 0000000000..6ea2495149 --- /dev/null +++ b/prepare/r-fgarch/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fGarch +_pkgver=3042.83.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Rmetrics - Autoregressive Conditional Heteroskedastic Modelling' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-fastica + r-fbasics + r-timedate + r-timeseries +) +optdepends=( + r-runit + r-tcltk +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fgarch/lilac.py b/prepare/r-fgarch/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fgarch/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fgarch/lilac.yaml b/prepare/r-fgarch/lilac.yaml new file mode 100644 index 0000000000..fcf9fa4ba0 --- /dev/null +++ b/prepare/r-fgarch/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fastica +- r-fbasics +- r-timedate +- r-timeseries +update_on: +- regex: fGarch_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fGarch diff --git a/prepare/r-fgga/PKGBUILD b/prepare/r-fgga/PKGBUILD new file mode 100644 index 0000000000..b371bcdf3e --- /dev/null +++ b/prepare/r-fgga/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fgga +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Hierarchical ensemble method based on factor graph' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocfilecache + r-curl + r-e1071 + r-graph + r-grbase + r-jsonlite + r-rbgl +) +optdepends=( + r-biocgenerics + r-go.db + r-gostats + r-knitr + r-perfmeas + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fgga/lilac.py b/prepare/r-fgga/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fgga/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fgga/lilac.yaml b/prepare/r-fgga/lilac.yaml new file mode 100644 index 0000000000..f4e789e0ad --- /dev/null +++ b/prepare/r-fgga/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-curl +- r-e1071 +- r-graph +- r-grbase +- r-jsonlite +- r-rbgl +update_on: +- regex: fgga_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/fgga diff --git a/prepare/r-fgnet/PKGBUILD b/prepare/r-fgnet/PKGBUILD new file mode 100644 index 0000000000..e5b9ec550f --- /dev/null +++ b/prepare/r-fgnet/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FGNet +_pkgver=3.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functional Gene Networks derived from biological enrichment analyses' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-hwriter + r-igraph + r-plotrix + r-png + r-r.utils + r-rcolorbrewer + r-reshape2 + r-xml +) +optdepends=( + r-annotationdbi + r-biocgenerics + r-biocmanager + r-gage + r-go.db + r-knitr + r-org.sc.sgd.db + r-rcurl + r-reactome.db + r-rgtk2 + r-rmarkdown + r-runit + r-topgo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fgnet/lilac.py b/prepare/r-fgnet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fgnet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fgnet/lilac.yaml b/prepare/r-fgnet/lilac.yaml new file mode 100644 index 0000000000..f5dfa71f3d --- /dev/null +++ b/prepare/r-fgnet/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-hwriter +- r-igraph +- r-plotrix +- r-png +- r-r.utils +- r-rcolorbrewer +- r-reshape2 +- r-xml +update_on: +- regex: FGNet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FGNet diff --git a/prepare/r-fgsea/PKGBUILD b/prepare/r-fgsea/PKGBUILD new file mode 100644 index 0000000000..ca03dfbcd5 --- /dev/null +++ b/prepare/r-fgsea/PKGBUILD @@ -0,0 +1,46 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=fgsea +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast Gene Set Enrichment Analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-bh + r-biocparallel + r-data.table + r-fastmatch + r-ggplot2 + r-gridextra + r-rcpp +) +optdepends=( + r-annotationdbi + r-geoquery + r-knitr + r-limma + r-org.mm.eg.db + r-parallel + r-reactome.db + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENCE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fgsea/lilac.py b/prepare/r-fgsea/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fgsea/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fgsea/lilac.yaml b/prepare/r-fgsea/lilac.yaml new file mode 100644 index 0000000000..50378a5b99 --- /dev/null +++ b/prepare/r-fgsea/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-biocparallel +- r-data.table +- r-fastmatch +- r-ggplot2 +- r-gridextra +- r-rcpp +update_on: +- regex: fgsea_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/fgsea diff --git a/prepare/r-fields/PKGBUILD b/prepare/r-fields/PKGBUILD new file mode 100644 index 0000000000..9e024a8c5a --- /dev/null +++ b/prepare/r-fields/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fields +_pkgver=13.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Spatial Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-maps + r-spam + r-viridis +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fields/lilac.py b/prepare/r-fields/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fields/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fields/lilac.yaml b/prepare/r-fields/lilac.yaml new file mode 100644 index 0000000000..9dda6c7a53 --- /dev/null +++ b/prepare/r-fields/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-maps +- r-spam +- r-viridis +update_on: +- regex: fields_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fields diff --git a/prepare/r-filehash/PKGBUILD b/prepare/r-filehash/PKGBUILD new file mode 100644 index 0000000000..d429efcbda --- /dev/null +++ b/prepare/r-filehash/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=filehash +_pkgver=2.4-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Simple Key-Value Database' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-filehash/lilac.py b/prepare/r-filehash/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-filehash/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-filehash/lilac.yaml b/prepare/r-filehash/lilac.yaml new file mode 100644 index 0000000000..9e00bd8fbb --- /dev/null +++ b/prepare/r-filehash/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: filehash_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=filehash diff --git a/prepare/r-filematrix/PKGBUILD b/prepare/r-filematrix/PKGBUILD new file mode 100644 index 0000000000..523824430d --- /dev/null +++ b/prepare/r-filematrix/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=filematrix +_pkgver=1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='File-Backed Matrix Class with Convenient Read and Write Access' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown + r-rsqlite +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-filematrix/lilac.py b/prepare/r-filematrix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-filematrix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-filematrix/lilac.yaml b/prepare/r-filematrix/lilac.yaml new file mode 100644 index 0000000000..cc39a0a6b2 --- /dev/null +++ b/prepare/r-filematrix/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: filematrix_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=filematrix diff --git a/prepare/r-filterffpe/PKGBUILD b/prepare/r-filterffpe/PKGBUILD new file mode 100644 index 0000000000..3eb0c0c7e9 --- /dev/null +++ b/prepare/r-filterffpe/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FilterFFPE +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='FFPE Artificial Chimeric Read Filter for NGS data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-doparallel + r-foreach + r-genomicranges + r-iranges + r-rsamtools + r-s4vectors +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-filterffpe/lilac.py b/prepare/r-filterffpe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-filterffpe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-filterffpe/lilac.yaml b/prepare/r-filterffpe/lilac.yaml new file mode 100644 index 0000000000..9abd185a29 --- /dev/null +++ b/prepare/r-filterffpe/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-foreach +- r-genomicranges +- r-iranges +- r-rsamtools +- r-s4vectors +update_on: +- regex: FilterFFPE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FilterFFPE diff --git a/prepare/r-findit2/PKGBUILD b/prepare/r-findit2/PKGBUILD new file mode 100644 index 0000000000..e6840dbaeb --- /dev/null +++ b/prepare/r-findit2/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FindIT2 +_pkgver=1.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='find influential TF and Target based on multi-omics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biocparallel + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggrepel + r-glmnet + r-iranges + r-multiassayexperiment + r-patchwork + r-progress + r-purrr + r-qvalue + r-rlang + r-rtracklayer + r-s4vectors + r-stringr + r-summarizedexperiment + r-tibble + r-tidyr + r-withr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-sessioninfo + r-testthat + r-txdb.athaliana.biomart.plantsmart28 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-findit2/lilac.py b/prepare/r-findit2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-findit2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-findit2/lilac.yaml b/prepare/r-findit2/lilac.yaml new file mode 100644 index 0000000000..43aaf7167f --- /dev/null +++ b/prepare/r-findit2/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-dplyr +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-ggrepel +- r-glmnet +- r-iranges +- r-multiassayexperiment +- r-patchwork +- r-progress +- r-purrr +- r-qvalue +- r-rlang +- r-rtracklayer +- r-s4vectors +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-tidyr +- r-withr +update_on: +- regex: FindIT2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FindIT2 diff --git a/prepare/r-findmyfriends/PKGBUILD b/prepare/r-findmyfriends/PKGBUILD new file mode 100644 index 0000000000..70cd074a7b --- /dev/null +++ b/prepare/r-findmyfriends/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FindMyFriends +_pkgver=1.23.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Microbial Comparative Genomics in R' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-digest + r-dplyr + r-filehash + r-ggdendro + r-ggplot2 + r-gtable + r-igraph + r-iranges + r-kebabs + r-rcpp + r-reshape2 + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-reutils + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-findmyfriends/lilac.py b/prepare/r-findmyfriends/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-findmyfriends/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-findmyfriends/lilac.yaml b/prepare/r-findmyfriends/lilac.yaml new file mode 100644 index 0000000000..e655ce7a6d --- /dev/null +++ b/prepare/r-findmyfriends/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-digest +- r-dplyr +- r-filehash +- r-ggdendro +- r-ggplot2 +- r-gtable +- r-igraph +- r-iranges +- r-kebabs +- r-rcpp +- r-reshape2 +- r-s4vectors +update_on: +- regex: FindMyFriends_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FindMyFriends diff --git a/prepare/r-findpython/PKGBUILD b/prepare/r-findpython/PKGBUILD new file mode 100644 index 0000000000..52305ceec7 --- /dev/null +++ b/prepare/r-findpython/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=findpython +_pkgver=1.0.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions to Find an Acceptable Python Binary' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-reticulate + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-findpython/lilac.py b/prepare/r-findpython/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-findpython/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-findpython/lilac.yaml b/prepare/r-findpython/lilac.yaml new file mode 100644 index 0000000000..792a8bd96b --- /dev/null +++ b/prepare/r-findpython/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: findpython_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=findpython diff --git a/prepare/r-fingerprint/PKGBUILD b/prepare/r-fingerprint/PKGBUILD new file mode 100644 index 0000000000..868e5e4b2f --- /dev/null +++ b/prepare/r-fingerprint/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fingerprint +_pkgver=3.5.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions to Operate on Binary Fingerprint Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-runit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fingerprint/lilac.py b/prepare/r-fingerprint/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fingerprint/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fingerprint/lilac.yaml b/prepare/r-fingerprint/lilac.yaml new file mode 100644 index 0000000000..5b92610e81 --- /dev/null +++ b/prepare/r-fingerprint/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: fingerprint_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fingerprint diff --git a/prepare/r-fis/PKGBUILD b/prepare/r-fis/PKGBUILD new file mode 100644 index 0000000000..d34d61d102 --- /dev/null +++ b/prepare/r-fis/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FIs +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Human Functional Interactions (FIs) for splineTimeR package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fis/lilac.py b/prepare/r-fis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fis/lilac.yaml b/prepare/r-fis/lilac.yaml new file mode 100644 index 0000000000..920d6b94f2 --- /dev/null +++ b/prepare/r-fis/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: FIs_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FIs diff --git a/prepare/r-fishalyser/PKGBUILD b/prepare/r-fishalyser/PKGBUILD new file mode 100644 index 0000000000..8ba25e7387 --- /dev/null +++ b/prepare/r-fishalyser/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FISHalyseR +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='FISHalyseR a package for automated FISH quantification' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-abind + r-ebimage +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fishalyser/lilac.py b/prepare/r-fishalyser/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fishalyser/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fishalyser/lilac.yaml b/prepare/r-fishalyser/lilac.yaml new file mode 100644 index 0000000000..0a60eda611 --- /dev/null +++ b/prepare/r-fishalyser/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-ebimage +update_on: +- regex: FISHalyseR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FISHalyseR diff --git a/prepare/r-fishpond/PKGBUILD b/prepare/r-fishpond/PKGBUILD new file mode 100644 index 0000000000..ea77864265 --- /dev/null +++ b/prepare/r-fishpond/PKGBUILD @@ -0,0 +1,50 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=fishpond +_pkgver=2.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fishpond: differential transcript and gene expression with inferential replicates' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-gtools + r-jsonlite + r-matrixstats + r-qvalue + r-rcpp + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-svmisc +) +optdepends=( + r-apeglm + r-deseq2 + r-knitr + r-limma + r-macrophage + r-org.hs.eg.db + r-rmarkdown + r-samr + r-testthat + r-tximeta + r-tximportdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fishpond/lilac.py b/prepare/r-fishpond/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fishpond/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fishpond/lilac.yaml b/prepare/r-fishpond/lilac.yaml new file mode 100644 index 0000000000..9329bff35e --- /dev/null +++ b/prepare/r-fishpond/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-gtools +- r-jsonlite +- r-matrixstats +- r-qvalue +- r-rcpp +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +- r-svmisc +update_on: +- regex: fishpond_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/fishpond diff --git a/prepare/r-fission/PKGBUILD b/prepare/r-fission/PKGBUILD new file mode 100644 index 0000000000..98e8b24657 --- /dev/null +++ b/prepare/r-fission/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fission +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RangedSummarizedExperiment for time course RNA-Seq of fission yeast in response to stress, by Leong et al., Nat Commun 2014.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-summarizedexperiment +) +optdepends=( + r-knitr + r-markdown +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fission/lilac.py b/prepare/r-fission/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fission/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fission/lilac.yaml b/prepare/r-fission/lilac.yaml new file mode 100644 index 0000000000..5df0bbd8d5 --- /dev/null +++ b/prepare/r-fission/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-summarizedexperiment +update_on: +- regex: fission_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/fission diff --git a/prepare/r-fit.models/PKGBUILD b/prepare/r-fit.models/PKGBUILD new file mode 100644 index 0000000000..5f1a3510dd --- /dev/null +++ b/prepare/r-fit.models/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fit.models +_pkgver=0.64 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Compare Fitted Models' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-mass +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fit.models/lilac.py b/prepare/r-fit.models/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fit.models/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fit.models/lilac.yaml b/prepare/r-fit.models/lilac.yaml new file mode 100644 index 0000000000..5a080ae58f --- /dev/null +++ b/prepare/r-fit.models/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: fit.models_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fit.models diff --git a/prepare/r-fitdistrplus/PKGBUILD b/prepare/r-fitdistrplus/PKGBUILD new file mode 100644 index 0000000000..7d863dd841 --- /dev/null +++ b/prepare/r-fitdistrplus/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fitdistrplus +_pkgver=1.1-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Help to Fit of a Parametric Distribution to Non-Censored or Censored Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-actuar + r-gamlss.dist + r-generalizedhyperbolic + r-ggplot2 + r-hmisc + r-knitr + r-mc2d + r-rgenoud + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fitdistrplus/lilac.py b/prepare/r-fitdistrplus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fitdistrplus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fitdistrplus/lilac.yaml b/prepare/r-fitdistrplus/lilac.yaml new file mode 100644 index 0000000000..faf78b5593 --- /dev/null +++ b/prepare/r-fitdistrplus/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: fitdistrplus_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fitdistrplus diff --git a/prepare/r-fithic/PKGBUILD b/prepare/r-fithic/PKGBUILD new file mode 100644 index 0000000000..76b25695a1 --- /dev/null +++ b/prepare/r-fithic/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FitHiC +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Confidence estimation for intra-chromosomal contact maps' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-fdrtool + r-rcpp +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fithic/lilac.py b/prepare/r-fithic/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fithic/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fithic/lilac.yaml b/prepare/r-fithic/lilac.yaml new file mode 100644 index 0000000000..58c48cef30 --- /dev/null +++ b/prepare/r-fithic/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-fdrtool +- r-rcpp +update_on: +- regex: FitHiC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FitHiC diff --git a/prepare/r-flagme/PKGBUILD b/prepare/r-flagme/PKGBUILD new file mode 100644 index 0000000000..aa9daf4dd2 --- /dev/null +++ b/prepare/r-flagme/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flagme +_pkgver=1.50.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Metabolomics GC/MS Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-camera + r-gcspikelite + r-gplots + r-sparsem + r-xcms +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flagme/lilac.py b/prepare/r-flagme/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flagme/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flagme/lilac.yaml b/prepare/r-flagme/lilac.yaml new file mode 100644 index 0000000000..7af1d4608b --- /dev/null +++ b/prepare/r-flagme/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-camera +- r-gcspikelite +- r-gplots +- r-sparsem +- r-xcms +update_on: +- regex: flagme_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flagme diff --git a/prepare/r-flames/PKGBUILD b/prepare/r-flames/PKGBUILD new file mode 100644 index 0000000000..e7f7d4860c --- /dev/null +++ b/prepare/r-flames/PKGBUILD @@ -0,0 +1,48 @@ +# system requirements: GNU make, C++11 +# Maintainer: Guoyi Zhang + +_pkgname=FLAMES +_pkgver=1.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-basilisk + r-dplyr + r-magrittr + r-rcpp + r-reticulate + r-rhtslib + r-rsamtools + r-s4vectors + r-scater + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-tidyr + r-zlibbioc +) +optdepends=( + r-biocfilecache + r-biocstyle + r-knitr + r-markdown + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flames/lilac.py b/prepare/r-flames/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flames/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flames/lilac.yaml b/prepare/r-flames/lilac.yaml new file mode 100644 index 0000000000..eec8a92d17 --- /dev/null +++ b/prepare/r-flames/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-basilisk +- r-dplyr +- r-magrittr +- r-rcpp +- r-reticulate +- r-rhtslib +- r-rsamtools +- r-s4vectors +- r-scater +- r-scuttle +- r-singlecellexperiment +- r-summarizedexperiment +- r-tidyr +- r-zlibbioc +update_on: +- regex: FLAMES_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FLAMES diff --git a/prepare/r-flashclust/PKGBUILD b/prepare/r-flashclust/PKGBUILD new file mode 100644 index 0000000000..1e94ef2ec1 --- /dev/null +++ b/prepare/r-flashclust/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flashClust +_pkgver=1.01-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Implementation of optimal hierarchical clustering' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flashclust/lilac.py b/prepare/r-flashclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flashclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flashclust/lilac.yaml b/prepare/r-flashclust/lilac.yaml new file mode 100644 index 0000000000..6519de5b72 --- /dev/null +++ b/prepare/r-flashclust/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: flashClust_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=flashClust diff --git a/prepare/r-flexclust/PKGBUILD b/prepare/r-flexclust/PKGBUILD new file mode 100644 index 0000000000..522f8afefc --- /dev/null +++ b/prepare/r-flexclust/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flexclust +_pkgver=1.4-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Flexible Cluster Algorithms' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-modeltools +) +optdepends=( + r-clue + r-cluster + r-ellipse + r-seriation + r-skmeans +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flexclust/lilac.py b/prepare/r-flexclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flexclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flexclust/lilac.yaml b/prepare/r-flexclust/lilac.yaml new file mode 100644 index 0000000000..05d708af66 --- /dev/null +++ b/prepare/r-flexclust/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-modeltools +update_on: +- regex: flexclust_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=flexclust diff --git a/prepare/r-flexdashboard/PKGBUILD b/prepare/r-flexdashboard/PKGBUILD new file mode 100644 index 0000000000..d24e35a02d --- /dev/null +++ b/prepare/r-flexdashboard/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flexdashboard +_pkgver=0.5.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Markdown Format for Flexible Dashboards' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmltools + r-htmlwidgets + r-jsonlite + r-knitr + r-rmarkdown + r-shiny +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flexdashboard/lilac.py b/prepare/r-flexdashboard/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flexdashboard/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flexdashboard/lilac.yaml b/prepare/r-flexdashboard/lilac.yaml new file mode 100644 index 0000000000..487ee1865c --- /dev/null +++ b/prepare/r-flexdashboard/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-htmlwidgets +- r-jsonlite +- r-knitr +- r-rmarkdown +- r-shiny +update_on: +- regex: flexdashboard_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=flexdashboard diff --git a/prepare/r-flexmix/PKGBUILD b/prepare/r-flexmix/PKGBUILD new file mode 100644 index 0000000000..29fba943e1 --- /dev/null +++ b/prepare/r-flexmix/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flexmix +_pkgver=2.3-17 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Flexible Mixture Modeling' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-modeltools +) +optdepends=( + r-actuar + r-codetools + r-diptest + r-ecdat + r-ellipse + r-gclus + r-glmnet + r-lme4 + r-mass + r-mgcv + r-mlbench + r-multcomp + r-mvtnorm + r-suppdists + r-survival +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flexmix/lilac.py b/prepare/r-flexmix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flexmix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flexmix/lilac.yaml b/prepare/r-flexmix/lilac.yaml new file mode 100644 index 0000000000..d01791efcc --- /dev/null +++ b/prepare/r-flexmix/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-modeltools +update_on: +- regex: flexmix_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=flexmix diff --git a/prepare/r-flextable/PKGBUILD b/prepare/r-flextable/PKGBUILD new file mode 100644 index 0000000000..ef270e3123 --- /dev/null +++ b/prepare/r-flextable/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flextable +_pkgver=0.6.10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for Tabular Reporting' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-base64enc + r-data.table + r-gdtools + r-htmltools + r-knitr + r-officer + r-rlang + r-rmarkdown + r-uuid + r-xml2 +) +optdepends=( + r-bookdown + r-broom + r-commonmark + r-equatags + r-ggplot2 + r-magick + r-mgcv + r-pdftools + r-scales + r-testthat + r-webshot + r-xtable +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flextable/lilac.py b/prepare/r-flextable/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flextable/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flextable/lilac.yaml b/prepare/r-flextable/lilac.yaml new file mode 100644 index 0000000000..dd8832504f --- /dev/null +++ b/prepare/r-flextable/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-data.table +- r-gdtools +- r-htmltools +- r-knitr +- r-officer +- r-rlang +- r-rmarkdown +- r-uuid +- r-xml2 +update_on: +- regex: flextable_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=flextable diff --git a/prepare/r-float/PKGBUILD b/prepare/r-float/PKGBUILD new file mode 100644 index 0000000000..2ae578a840 --- /dev/null +++ b/prepare/r-float/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=float +_pkgver=0.2-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='32-Bit Floats' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-float/lilac.py b/prepare/r-float/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-float/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-float/lilac.yaml b/prepare/r-float/lilac.yaml new file mode 100644 index 0000000000..f7fd938b4a --- /dev/null +++ b/prepare/r-float/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: float_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=float diff --git a/prepare/r-flock/PKGBUILD b/prepare/r-flock/PKGBUILD new file mode 100644 index 0000000000..f0fcf329a1 --- /dev/null +++ b/prepare/r-flock/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flock +_pkgver=0.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Process Synchronization Using File Locks' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-rcpp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flock/lilac.py b/prepare/r-flock/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flock/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flock/lilac.yaml b/prepare/r-flock/lilac.yaml new file mode 100644 index 0000000000..dab6719c36 --- /dev/null +++ b/prepare/r-flock/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: flock_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=flock diff --git a/prepare/r-flowai/PKGBUILD b/prepare/r-flowai/PKGBUILD new file mode 100644 index 0000000000..862044c50f --- /dev/null +++ b/prepare/r-flowai/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowAI +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automatic and interactive quality control for flow cytometry data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-changepoint + r-flowcore + r-ggplot2 + r-knitr + r-plyr + r-rcolorbrewer + r-reshape2 + r-rmarkdown + r-scales +) +optdepends=( + r-biocstyle + r-shiny + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowai/lilac.py b/prepare/r-flowai/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowai/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowai/lilac.yaml b/prepare/r-flowai/lilac.yaml new file mode 100644 index 0000000000..190cb9ccaf --- /dev/null +++ b/prepare/r-flowai/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-changepoint +- r-flowcore +- r-ggplot2 +- r-knitr +- r-plyr +- r-rcolorbrewer +- r-reshape2 +- r-rmarkdown +- r-scales +update_on: +- regex: flowAI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowAI diff --git a/prepare/r-flowbeads/PKGBUILD b/prepare/r-flowbeads/PKGBUILD new file mode 100644 index 0000000000..0c2ff30753 --- /dev/null +++ b/prepare/r-flowbeads/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowBeads +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='flowBeads: Analysis of flow bead data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-flowcore + r-knitr + r-rrcov + r-xtable +) +optdepends=( + r-flowviz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowbeads/lilac.py b/prepare/r-flowbeads/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowbeads/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowbeads/lilac.yaml b/prepare/r-flowbeads/lilac.yaml new file mode 100644 index 0000000000..18abb94902 --- /dev/null +++ b/prepare/r-flowbeads/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-flowcore +- r-knitr +- r-rrcov +- r-xtable +update_on: +- regex: flowBeads_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowBeads diff --git a/prepare/r-flowbin/PKGBUILD b/prepare/r-flowbin/PKGBUILD new file mode 100644 index 0000000000..1c12ff336b --- /dev/null +++ b/prepare/r-flowbin/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowBin +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Combining multitube flow cytometry data by binning' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-flowcore + r-flowfp + r-limma + r-snow +) +optdepends=( + r-parallel +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowbin/lilac.py b/prepare/r-flowbin/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowbin/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowbin/lilac.yaml b/prepare/r-flowbin/lilac.yaml new file mode 100644 index 0000000000..4226674d00 --- /dev/null +++ b/prepare/r-flowbin/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-flowcore +- r-flowfp +- r-limma +- r-snow +update_on: +- regex: flowBin_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowBin diff --git a/prepare/r-flowcatchr/PKGBUILD b/prepare/r-flowcatchr/PKGBUILD new file mode 100644 index 0000000000..9c7d0d5d66 --- /dev/null +++ b/prepare/r-flowcatchr/PKGBUILD @@ -0,0 +1,39 @@ +# system requirements: ImageMagick +# Maintainer: Guoyi Zhang + +_pkgname=flowcatchR +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-abind + r-biocparallel + r-colorramps + r-ebimage + r-plotly + r-shiny +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowcatchr/lilac.py b/prepare/r-flowcatchr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowcatchr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowcatchr/lilac.yaml b/prepare/r-flowcatchr/lilac.yaml new file mode 100644 index 0000000000..d9ed23a068 --- /dev/null +++ b/prepare/r-flowcatchr/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-biocparallel +- r-colorramps +- r-ebimage +- r-plotly +- r-shiny +update_on: +- regex: flowcatchR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowcatchR diff --git a/prepare/r-flowchic/PKGBUILD b/prepare/r-flowchic/PKGBUILD new file mode 100644 index 0000000000..9618bd2647 --- /dev/null +++ b/prepare/r-flowchic/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowCHIC +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analyze flow cytometric data using histogram information' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ebimage + r-flowcore + r-ggplot2 + r-hexbin + r-vegan +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowchic/lilac.py b/prepare/r-flowchic/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowchic/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowchic/lilac.yaml b/prepare/r-flowchic/lilac.yaml new file mode 100644 index 0000000000..9d1ff6aaa5 --- /dev/null +++ b/prepare/r-flowchic/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ebimage +- r-flowcore +- r-ggplot2 +- r-hexbin +- r-vegan +update_on: +- regex: flowCHIC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowCHIC diff --git a/prepare/r-flowcl/PKGBUILD b/prepare/r-flowcl/PKGBUILD new file mode 100644 index 0000000000..a0f9e79165 --- /dev/null +++ b/prepare/r-flowcl/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowCL +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Semantic labelling of flow cytometric cell populations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-graph + r-rgraphviz + r-sparql +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowcl/lilac.py b/prepare/r-flowcl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowcl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowcl/lilac.yaml b/prepare/r-flowcl/lilac.yaml new file mode 100644 index 0000000000..d018218456 --- /dev/null +++ b/prepare/r-flowcl/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +- r-rgraphviz +- r-sparql +update_on: +- regex: flowCL_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowCL diff --git a/prepare/r-flowclean/PKGBUILD b/prepare/r-flowclean/PKGBUILD new file mode 100644 index 0000000000..48d5be0682 --- /dev/null +++ b/prepare/r-flowclean/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowClean +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='flowClean' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bit + r-changepoint + r-flowcore + r-sfsmisc +) +optdepends=( + r-flowviz + r-grid + r-gridextra +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowclean/lilac.py b/prepare/r-flowclean/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowclean/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowclean/lilac.yaml b/prepare/r-flowclean/lilac.yaml new file mode 100644 index 0000000000..5817a2316b --- /dev/null +++ b/prepare/r-flowclean/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bit +- r-changepoint +- r-flowcore +- r-sfsmisc +update_on: +- regex: flowClean_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowClean diff --git a/prepare/r-flowclust/PKGBUILD b/prepare/r-flowclust/PKGBUILD new file mode 100644 index 0000000000..ec2398ed10 --- /dev/null +++ b/prepare/r-flowclust/PKGBUILD @@ -0,0 +1,44 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=flowClust +_pkgver=3.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clustering for Flow Cytometry' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-clue + r-corpcor + r-ellipse + r-flowcore + r-flowviz + r-graph + r-mnormt +) +optdepends=( + r-flowworkspace + r-flowworkspacedata + r-knitr + r-opencyto + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowclust/lilac.py b/prepare/r-flowclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowclust/lilac.yaml b/prepare/r-flowclust/lilac.yaml new file mode 100644 index 0000000000..662acc7d4c --- /dev/null +++ b/prepare/r-flowclust/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-clue +- r-corpcor +- r-ellipse +- r-flowcore +- r-flowviz +- r-graph +- r-mnormt +update_on: +- regex: flowClust_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowClust diff --git a/prepare/r-flowcore/PKGBUILD b/prepare/r-flowcore/PKGBUILD new file mode 100644 index 0000000000..8bbf276414 --- /dev/null +++ b/prepare/r-flowcore/PKGBUILD @@ -0,0 +1,48 @@ +# system requirements: GNU make, C++11 +# Maintainer: Guoyi Zhang + +_pkgname=flowCore +_pkgver=2.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='flowCore: Basic structures for flow cytometry data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bh + r-biobase + r-biocgenerics + r-cytolib + r-matrixstats + r-rcpp + r-rcpparmadillo + r-rprotobuflib + r-s4vectors +) +optdepends=( + r-flowstats + r-flowviz + r-flowworkspace + r-flowworkspacedata + r-ggcyto + r-gridextra + r-knitr + r-opencyto + r-rgraphviz + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowcore/lilac.py b/prepare/r-flowcore/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowcore/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowcore/lilac.yaml b/prepare/r-flowcore/lilac.yaml new file mode 100644 index 0000000000..fad825974b --- /dev/null +++ b/prepare/r-flowcore/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-biobase +- r-biocgenerics +- r-cytolib +- r-matrixstats +- r-rcpp +- r-rcpparmadillo +- r-rprotobuflib +- r-s4vectors +update_on: +- regex: flowCore_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowCore diff --git a/prepare/r-flowcut/PKGBUILD b/prepare/r-flowcut/PKGBUILD new file mode 100644 index 0000000000..e8229fdf00 --- /dev/null +++ b/prepare/r-flowcut/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowCut +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Precise and Accurate Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-cairo + r-e1071 + r-flowcore + r-flowdensity +) +optdepends=( + r-biocgenerics + r-knitr + r-markdown + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowcut/lilac.py b/prepare/r-flowcut/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowcut/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowcut/lilac.yaml b/prepare/r-flowcut/lilac.yaml new file mode 100644 index 0000000000..1ed854b51f --- /dev/null +++ b/prepare/r-flowcut/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cairo +- r-e1071 +- r-flowcore +- r-flowdensity +update_on: +- regex: flowCut_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowCut diff --git a/prepare/r-flowcybar/PKGBUILD b/prepare/r-flowcybar/PKGBUILD new file mode 100644 index 0000000000..d62fc6adf6 --- /dev/null +++ b/prepare/r-flowcybar/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowCyBar +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analyze flow cytometric data using gate information' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-gplots + r-vegan +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowcybar/lilac.py b/prepare/r-flowcybar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowcybar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowcybar/lilac.yaml b/prepare/r-flowcybar/lilac.yaml new file mode 100644 index 0000000000..fd29b791de --- /dev/null +++ b/prepare/r-flowcybar/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gplots +- r-vegan +update_on: +- regex: flowCyBar_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowCyBar diff --git a/prepare/r-flowdensity/PKGBUILD b/prepare/r-flowdensity/PKGBUILD new file mode 100644 index 0000000000..b2016621fa --- /dev/null +++ b/prepare/r-flowdensity/PKGBUILD @@ -0,0 +1,39 @@ +# system requirements: xml2, GNU make, C++11 +# Maintainer: Guoyi Zhang + +_pkgname=flowDensity +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sequential Flow Cytometry Data Gating' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-car + r-flowcore + r-flowviz + r-flowworkspace + r-gplots + r-rfoc + r-rgeos + r-sp +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowdensity/lilac.py b/prepare/r-flowdensity/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowdensity/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowdensity/lilac.yaml b/prepare/r-flowdensity/lilac.yaml new file mode 100644 index 0000000000..18190006ea --- /dev/null +++ b/prepare/r-flowdensity/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-car +- r-flowcore +- r-flowviz +- r-flowworkspace +- r-gplots +- r-rfoc +- r-rgeos +- r-sp +update_on: +- regex: flowDensity_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowDensity diff --git a/prepare/r-flowfp/PKGBUILD b/prepare/r-flowfp/PKGBUILD new file mode 100644 index 0000000000..a28218ecc6 --- /dev/null +++ b/prepare/r-flowfp/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowFP +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fingerprinting for Flow Cytometry' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-flowcore + r-flowviz +) +optdepends=( + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowfp/lilac.py b/prepare/r-flowfp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowfp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowfp/lilac.yaml b/prepare/r-flowfp/lilac.yaml new file mode 100644 index 0000000000..e7015ae349 --- /dev/null +++ b/prepare/r-flowfp/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-flowcore +- r-flowviz +update_on: +- regex: flowFP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowFP diff --git a/prepare/r-flowgraph/PKGBUILD b/prepare/r-flowgraph/PKGBUILD new file mode 100644 index 0000000000..ba2bfdbbdb --- /dev/null +++ b/prepare/r-flowgraph/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowGraph +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identifying differential cell populations in flow cytometry data accounting for marker frequency' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-data.table + r-effsize + r-furrr + r-future + r-ggiraph + r-ggplot2 + r-ggrepel + r-gridextra + r-htmlwidgets + r-igraph + r-matrixstats + r-purrr + r-rdpack + r-stringi + r-stringr + r-visnetwork +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowgraph/lilac.py b/prepare/r-flowgraph/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowgraph/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowgraph/lilac.yaml b/prepare/r-flowgraph/lilac.yaml new file mode 100644 index 0000000000..9af3aad849 --- /dev/null +++ b/prepare/r-flowgraph/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-effsize +- r-furrr +- r-future +- r-ggiraph +- r-ggplot2 +- r-ggrepel +- r-gridextra +- r-htmlwidgets +- r-igraph +- r-matrixstats +- r-purrr +- r-rdpack +- r-stringi +- r-stringr +- r-visnetwork +update_on: +- regex: flowGraph_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowGraph diff --git a/prepare/r-flowmap/PKGBUILD b/prepare/r-flowmap/PKGBUILD new file mode 100644 index 0000000000..3b6d1a720e --- /dev/null +++ b/prepare/r-flowmap/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowMap +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-Rafsky Test' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-ade4 + r-doparallel + r-reshape2 + r-scales +) +optdepends=( + r-biocstyle + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowmap/lilac.py b/prepare/r-flowmap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowmap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowmap/lilac.yaml b/prepare/r-flowmap/lilac.yaml new file mode 100644 index 0000000000..932b04944b --- /dev/null +++ b/prepare/r-flowmap/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-ade4 +- r-doparallel +- r-reshape2 +- r-scales +update_on: +- regex: flowMap_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowMap diff --git a/prepare/r-flowmatch/PKGBUILD b/prepare/r-flowmatch/PKGBUILD new file mode 100644 index 0000000000..409dd510d7 --- /dev/null +++ b/prepare/r-flowmatch/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowMatch +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Matching and meta-clustering in flow cytometry' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-flowcore + r-rcpp +) +optdepends=( + r-healthyflowdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowmatch/lilac.py b/prepare/r-flowmatch/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowmatch/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowmatch/lilac.yaml b/prepare/r-flowmatch/lilac.yaml new file mode 100644 index 0000000000..4ea47f3821 --- /dev/null +++ b/prepare/r-flowmatch/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-flowcore +- r-rcpp +update_on: +- regex: flowMatch_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowMatch diff --git a/prepare/r-flowmeans/PKGBUILD b/prepare/r-flowmeans/PKGBUILD new file mode 100644 index 0000000000..f600d4c177 --- /dev/null +++ b/prepare/r-flowmeans/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowMeans +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Non-parametric Flow Cytometry Data Gating' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-feature + r-flowcore + r-rrcov +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowmeans/lilac.py b/prepare/r-flowmeans/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowmeans/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowmeans/lilac.yaml b/prepare/r-flowmeans/lilac.yaml new file mode 100644 index 0000000000..56e6a661b2 --- /dev/null +++ b/prepare/r-flowmeans/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-feature +- r-flowcore +- r-rrcov +update_on: +- regex: flowMeans_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowMeans diff --git a/prepare/r-flowmerge/PKGBUILD b/prepare/r-flowmerge/PKGBUILD new file mode 100644 index 0000000000..7485236124 --- /dev/null +++ b/prepare/r-flowmerge/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowMerge +_pkgver=2.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cluster Merging for Flow Cytometry Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-feature + r-flowclust + r-flowcore + r-foreach + r-graph + r-rgraphviz + r-rrcov + r-snow +) +optdepends=( + r-domc + r-knitr + r-multicore + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowmerge/lilac.py b/prepare/r-flowmerge/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowmerge/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowmerge/lilac.yaml b/prepare/r-flowmerge/lilac.yaml new file mode 100644 index 0000000000..4205b9641b --- /dev/null +++ b/prepare/r-flowmerge/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-feature +- r-flowclust +- r-flowcore +- r-foreach +- r-graph +- r-rgraphviz +- r-rrcov +- r-snow +update_on: +- regex: flowMerge_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowMerge diff --git a/prepare/r-flowpeaks/PKGBUILD b/prepare/r-flowpeaks/PKGBUILD new file mode 100644 index 0000000000..a20a3c96d0 --- /dev/null +++ b/prepare/r-flowpeaks/PKGBUILD @@ -0,0 +1,30 @@ +# system requirements: gsl +# Maintainer: Guoyi Zhang + +_pkgname=flowPeaks +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package for flow data clustering' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-flowcore +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowpeaks/lilac.py b/prepare/r-flowpeaks/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowpeaks/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowpeaks/lilac.yaml b/prepare/r-flowpeaks/lilac.yaml new file mode 100644 index 0000000000..d11903c422 --- /dev/null +++ b/prepare/r-flowpeaks/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: flowPeaks_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowPeaks diff --git a/prepare/r-flowploidy/PKGBUILD b/prepare/r-flowploidy/PKGBUILD new file mode 100644 index 0000000000..dab97b408d --- /dev/null +++ b/prepare/r-flowploidy/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowPloidy +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analyze flow cytometer data to determine sample ploidy' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-car + r-catools + r-flowcore + r-knitr + r-minpack.lm + r-rmarkdown + r-shiny +) +optdepends=( + r-flowploidydata + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowploidy/lilac.py b/prepare/r-flowploidy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowploidy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowploidy/lilac.yaml b/prepare/r-flowploidy/lilac.yaml new file mode 100644 index 0000000000..a628335851 --- /dev/null +++ b/prepare/r-flowploidy/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-car +- r-catools +- r-flowcore +- r-knitr +- r-minpack.lm +- r-rmarkdown +- r-shiny +update_on: +- regex: flowPloidy_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowPloidy diff --git a/prepare/r-flowplots/PKGBUILD b/prepare/r-flowplots/PKGBUILD new file mode 100644 index 0000000000..a1f00aef8c --- /dev/null +++ b/prepare/r-flowplots/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowPlots +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='flowPlots: analysis plots and data class for gated flow cytometry data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-vcd +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowplots/lilac.py b/prepare/r-flowplots/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowplots/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowplots/lilac.yaml b/prepare/r-flowplots/lilac.yaml new file mode 100644 index 0000000000..bd1670e32b --- /dev/null +++ b/prepare/r-flowplots/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: flowPlots_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowPlots diff --git a/prepare/r-flowsom/PKGBUILD b/prepare/r-flowsom/PKGBUILD new file mode 100644 index 0000000000..556ea7eadf --- /dev/null +++ b/prepare/r-flowsom/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FlowSOM +_pkgver=2.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Using self-organizing maps for visualization and interpretation of cytometry data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-colorramps + r-consensusclusterplus + r-cytoml + r-dplyr + r-flowcore + r-flowworkspace + r-ggforce + r-ggnewscale + r-ggplot2 + r-ggpointdensity + r-ggpubr + r-ggrepel + r-igraph + r-magrittr + r-pheatmap + r-rcolorbrewer + r-rlang + r-rtsne + r-scattermore + r-tidyr + r-xml +) +optdepends=( + r-biocstyle + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowsom/lilac.py b/prepare/r-flowsom/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowsom/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowsom/lilac.yaml b/prepare/r-flowsom/lilac.yaml new file mode 100644 index 0000000000..75b3377ff6 --- /dev/null +++ b/prepare/r-flowsom/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-colorramps +- r-consensusclusterplus +- r-cytoml +- r-dplyr +- r-flowcore +- r-flowworkspace +- r-ggforce +- r-ggnewscale +- r-ggplot2 +- r-ggpointdensity +- r-ggpubr +- r-ggrepel +- r-igraph +- r-magrittr +- r-pheatmap +- r-rcolorbrewer +- r-rlang +- r-rtsne +- r-scattermore +- r-tidyr +- r-xml +update_on: +- regex: FlowSOM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FlowSOM diff --git a/prepare/r-flowsorted.blood.450k/PKGBUILD b/prepare/r-flowsorted.blood.450k/PKGBUILD new file mode 100644 index 0000000000..294b93229b --- /dev/null +++ b/prepare/r-flowsorted.blood.450k/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FlowSorted.Blood.450k +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Illumina HumanMethylation data on sorted blood cell populations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-minfi +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowsorted.blood.450k/lilac.py b/prepare/r-flowsorted.blood.450k/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowsorted.blood.450k/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowsorted.blood.450k/lilac.yaml b/prepare/r-flowsorted.blood.450k/lilac.yaml new file mode 100644 index 0000000000..6ed6ac2ce3 --- /dev/null +++ b/prepare/r-flowsorted.blood.450k/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-minfi +update_on: +- regex: FlowSorted.Blood.450k_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FlowSorted.Blood.450k diff --git a/prepare/r-flowspecs/PKGBUILD b/prepare/r-flowspecs/PKGBUILD new file mode 100644 index 0000000000..75dec89224 --- /dev/null +++ b/prepare/r-flowspecs/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowSpecs +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for processing of high-dimensional cytometry data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-flowcore + r-ggplot2 + r-reshape2 + r-zoo +) +optdepends=( + r-biocstyle + r-depecher + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowspecs/lilac.py b/prepare/r-flowspecs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowspecs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowspecs/lilac.yaml b/prepare/r-flowspecs/lilac.yaml new file mode 100644 index 0000000000..4f647a42d9 --- /dev/null +++ b/prepare/r-flowspecs/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-flowcore +- r-ggplot2 +- r-reshape2 +- r-zoo +update_on: +- regex: flowSpecs_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowSpecs diff --git a/prepare/r-flowstats/PKGBUILD b/prepare/r-flowstats/PKGBUILD new file mode 100644 index 0000000000..b83522a9b3 --- /dev/null +++ b/prepare/r-flowstats/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowStats +_pkgver=4.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical methods for the analysis of flow cytometry data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-fda + r-flowcore + r-flowviz + r-flowworkspace + r-ks + r-ncdfflow + r-rcolorbrewer + r-rrcov +) +optdepends=( + r-ggcyto + r-ggridges + r-graph + r-opencyto + r-rbgl + r-testthat + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowstats/lilac.py b/prepare/r-flowstats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowstats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowstats/lilac.yaml b/prepare/r-flowstats/lilac.yaml new file mode 100644 index 0000000000..5cf993bb96 --- /dev/null +++ b/prepare/r-flowstats/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-fda +- r-flowcore +- r-flowviz +- r-flowworkspace +- r-ks +- r-ncdfflow +- r-rcolorbrewer +- r-rrcov +update_on: +- regex: flowStats_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowStats diff --git a/prepare/r-flowtime/PKGBUILD b/prepare/r-flowtime/PKGBUILD new file mode 100644 index 0000000000..e6b08bb046 --- /dev/null +++ b/prepare/r-flowtime/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowTime +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation and analysis of biological dynamical systems using flow cytometry' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-dplyr + r-flowcore + r-magrittr + r-plyr + r-rlang + r-tibble +) +optdepends=( + r-biocgenerics + r-flowclust + r-flowstats + r-flowviz + r-ggcyto + r-ggplot2 + r-knitr + r-opencyto + r-rmarkdown + r-stats +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowtime/lilac.py b/prepare/r-flowtime/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowtime/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowtime/lilac.yaml b/prepare/r-flowtime/lilac.yaml new file mode 100644 index 0000000000..03d08136cf --- /dev/null +++ b/prepare/r-flowtime/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-flowcore +- r-magrittr +- r-plyr +- r-rlang +- r-tibble +update_on: +- regex: flowTime_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowTime diff --git a/prepare/r-flowtrans/PKGBUILD b/prepare/r-flowtrans/PKGBUILD new file mode 100644 index 0000000000..d427dcf3c8 --- /dev/null +++ b/prepare/r-flowtrans/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowTrans +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Parameter Optimization for Flow Cytometry Data Transformation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-flowclust + r-flowcore + r-flowviz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowtrans/lilac.py b/prepare/r-flowtrans/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowtrans/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowtrans/lilac.yaml b/prepare/r-flowtrans/lilac.yaml new file mode 100644 index 0000000000..382f3a2ab9 --- /dev/null +++ b/prepare/r-flowtrans/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-flowclust +- r-flowcore +- r-flowviz +update_on: +- regex: flowTrans_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowTrans diff --git a/prepare/r-flowutils/PKGBUILD b/prepare/r-flowutils/PKGBUILD new file mode 100644 index 0000000000..6f64a58baf --- /dev/null +++ b/prepare/r-flowutils/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowUtils +_pkgver=1.58.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities for flow cytometry' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-corpcor + r-flowcore + r-graph + r-runit + r-xml +) +optdepends=( + r-gatingmldata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowutils/lilac.py b/prepare/r-flowutils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowutils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowutils/lilac.yaml b/prepare/r-flowutils/lilac.yaml new file mode 100644 index 0000000000..25d1359720 --- /dev/null +++ b/prepare/r-flowutils/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-corpcor +- r-flowcore +- r-graph +- r-runit +- r-xml +update_on: +- regex: flowUtils_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowUtils diff --git a/prepare/r-flowviz/PKGBUILD b/prepare/r-flowviz/PKGBUILD new file mode 100644 index 0000000000..44d2a32432 --- /dev/null +++ b/prepare/r-flowviz/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowViz +_pkgver=1.58.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization for flow cytometry' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-flowcore + r-hexbin + r-idpmisc + r-latticeextra + r-rcolorbrewer +) +optdepends=( + r-colorspace + r-flowstats + r-knitr + r-markdown + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowviz/lilac.py b/prepare/r-flowviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowviz/lilac.yaml b/prepare/r-flowviz/lilac.yaml new file mode 100644 index 0000000000..d02320f24d --- /dev/null +++ b/prepare/r-flowviz/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-flowcore +- r-hexbin +- r-idpmisc +- r-latticeextra +- r-rcolorbrewer +update_on: +- regex: flowViz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowViz diff --git a/prepare/r-flowvs/PKGBUILD b/prepare/r-flowvs/PKGBUILD new file mode 100644 index 0000000000..097e3ed3d9 --- /dev/null +++ b/prepare/r-flowvs/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=flowVS +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Variance stabilization in flow cytometry (and microarrays)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-flowcore + r-flowstats + r-flowviz +) +optdepends=( + r-knitr + r-vsn +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowvs/lilac.py b/prepare/r-flowvs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowvs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowvs/lilac.yaml b/prepare/r-flowvs/lilac.yaml new file mode 100644 index 0000000000..fb7e432e73 --- /dev/null +++ b/prepare/r-flowvs/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-flowcore +- r-flowstats +- r-flowviz +update_on: +- regex: flowVS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowVS diff --git a/prepare/r-flowworkspace/PKGBUILD b/prepare/r-flowworkspace/PKGBUILD new file mode 100644 index 0000000000..ab6e83cd87 --- /dev/null +++ b/prepare/r-flowworkspace/PKGBUILD @@ -0,0 +1,64 @@ +# system requirements: GNU make, C++11 +# Maintainer: Guoyi Zhang + +_pkgname=flowWorkspace +_pkgver=4.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Infrastructure for representing and interacting with gated and ungated cytometry data sets.' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-aws.s3 + r-aws.signature + r-bh + r-biobase + r-biocgenerics + r-cytolib + r-data.table + r-delayedarray + r-digest + r-dplyr + r-flowcore + r-ggplot2 + r-graph + r-latticeextra + r-matrixstats + r-ncdfflow + r-rbgl + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-rgraphviz + r-rhdf5lib + r-rprotobuflib + r-s4vectors + r-scales + r-xml +) +optdepends=( + r-cytoml + r-flowworkspacedata + r-ggcyto + r-knitr + r-opencyto + r-parallel + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-flowworkspace/lilac.py b/prepare/r-flowworkspace/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-flowworkspace/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-flowworkspace/lilac.yaml b/prepare/r-flowworkspace/lilac.yaml new file mode 100644 index 0000000000..26a9e6254f --- /dev/null +++ b/prepare/r-flowworkspace/lilac.yaml @@ -0,0 +1,35 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aws.s3 +- r-aws.signature +- r-bh +- r-biobase +- r-biocgenerics +- r-cytolib +- r-data.table +- r-delayedarray +- r-digest +- r-dplyr +- r-flowcore +- r-ggplot2 +- r-graph +- r-latticeextra +- r-matrixstats +- r-ncdfflow +- r-rbgl +- r-rcpp +- r-rcpparmadillo +- r-rcppparallel +- r-rgraphviz +- r-rhdf5lib +- r-rprotobuflib +- r-s4vectors +- r-scales +- r-xml +update_on: +- regex: flowWorkspace_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/flowWorkspace diff --git a/prepare/r-fmcsr/PKGBUILD b/prepare/r-fmcsr/PKGBUILD new file mode 100644 index 0000000000..828cfe1baf --- /dev/null +++ b/prepare/r-fmcsr/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fmcsR +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mismatch Tolerant Maximum Common Substructure Searching' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-chemminer + r-runit +) +optdepends=( + r-biocstyle + r-knitcitations + r-knitr + r-knitrbootstrap + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fmcsr/lilac.py b/prepare/r-fmcsr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fmcsr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fmcsr/lilac.yaml b/prepare/r-fmcsr/lilac.yaml new file mode 100644 index 0000000000..237546a2f4 --- /dev/null +++ b/prepare/r-fmcsr/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-chemminer +- r-runit +update_on: +- regex: fmcsR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/fmcsR diff --git a/prepare/r-fme/PKGBUILD b/prepare/r-fme/PKGBUILD new file mode 100644 index 0000000000..17d7927bfa --- /dev/null +++ b/prepare/r-fme/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FME +_pkgver=1.3.6.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability and Monte Carlo Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-coda + r-desolve + r-minpack.lm + r-minqa + r-rootsolve +) +optdepends=( + r-diagram +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fme/lilac.py b/prepare/r-fme/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fme/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fme/lilac.yaml b/prepare/r-fme/lilac.yaml new file mode 100644 index 0000000000..00374826b3 --- /dev/null +++ b/prepare/r-fme/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-coda +- r-desolve +- r-minpack.lm +- r-minqa +- r-rootsolve +update_on: +- regex: FME_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=FME diff --git a/prepare/r-fmrs/PKGBUILD b/prepare/r-fmrs/PKGBUILD new file mode 100644 index 0000000000..7ab9e27c26 --- /dev/null +++ b/prepare/r-fmrs/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fmrs +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Variable Selection in Finite Mixture of AFT Regression and FMR' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biocgenerics + r-knitr + r-rmarkdown + r-testthat + r-utils +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fmrs/lilac.py b/prepare/r-fmrs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fmrs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fmrs/lilac.yaml b/prepare/r-fmrs/lilac.yaml new file mode 100644 index 0000000000..3449c8eae9 --- /dev/null +++ b/prepare/r-fmrs/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: fmrs_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/fmrs diff --git a/prepare/r-fmsb/PKGBUILD b/prepare/r-fmsb/PKGBUILD new file mode 100644 index 0000000000..038f45bae6 --- /dev/null +++ b/prepare/r-fmsb/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fmsb +_pkgver=0.7.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for Medical Statistics Book with some Demographic Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-epi + r-vcd +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fmsb/lilac.py b/prepare/r-fmsb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fmsb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fmsb/lilac.yaml b/prepare/r-fmsb/lilac.yaml new file mode 100644 index 0000000000..a112c6e1f1 --- /dev/null +++ b/prepare/r-fmsb/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: fmsb_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fmsb diff --git a/prepare/r-fmstable/PKGBUILD b/prepare/r-fmstable/PKGBUILD new file mode 100644 index 0000000000..55a3ea0dc2 --- /dev/null +++ b/prepare/r-fmstable/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FMStable +_pkgver=0.1-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Finite Moment Stable Distributions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fmstable/lilac.py b/prepare/r-fmstable/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fmstable/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fmstable/lilac.yaml b/prepare/r-fmstable/lilac.yaml new file mode 100644 index 0000000000..24a34da3ad --- /dev/null +++ b/prepare/r-fmstable/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: FMStable_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=FMStable diff --git a/prepare/r-fnn/PKGBUILD b/prepare/r-fnn/PKGBUILD new file mode 100644 index 0000000000..87bd7b45bb --- /dev/null +++ b/prepare/r-fnn/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FNN +_pkgver=1.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast Nearest Neighbor Search Algorithms and Applications' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-chemometrics + r-mvtnorm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fnn/lilac.py b/prepare/r-fnn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fnn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fnn/lilac.yaml b/prepare/r-fnn/lilac.yaml new file mode 100644 index 0000000000..5eda0937c7 --- /dev/null +++ b/prepare/r-fnn/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: FNN_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=FNN diff --git a/prepare/r-fobitools/PKGBUILD b/prepare/r-fobitools/PKGBUILD new file mode 100644 index 0000000000..03e15b3749 --- /dev/null +++ b/prepare/r-fobitools/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fobitools +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools For Manipulating FOBI Ontology' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-clisymbols + r-crayon + r-dplyr + r-fgsea + r-ggplot2 + r-ggraph + r-magrittr + r-ontologyindex + r-purrr + r-recordlinkage + r-stringr + r-textclean + r-tictoc + r-tidygraph + r-tidyr + r-vroom +) +optdepends=( + r-biocstyle + r-covr + r-ggrepel + r-kableextra + r-knitr + r-metabolomicsworkbenchr + r-poma + r-rmarkdown + r-rvest + r-summarizedexperiment + r-testthat + r-tidyverse +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fobitools/lilac.py b/prepare/r-fobitools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fobitools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fobitools/lilac.yaml b/prepare/r-fobitools/lilac.yaml new file mode 100644 index 0000000000..2828af437a --- /dev/null +++ b/prepare/r-fobitools/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clisymbols +- r-crayon +- r-dplyr +- r-fgsea +- r-ggplot2 +- r-ggraph +- r-magrittr +- r-ontologyindex +- r-purrr +- r-recordlinkage +- r-stringr +- r-textclean +- r-tictoc +- r-tidygraph +- r-tidyr +- r-vroom +update_on: +- regex: fobitools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/fobitools diff --git a/prepare/r-foldgo/PKGBUILD b/prepare/r-foldgo/PKGBUILD new file mode 100644 index 0000000000..ea6f7f026a --- /dev/null +++ b/prepare/r-foldgo/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FoldGO +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Package for Fold-specific GO Terms Recognition' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-tidyr + r-topgo +) +optdepends=( + r-devtools + r-kableextra + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-foldgo/lilac.py b/prepare/r-foldgo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-foldgo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-foldgo/lilac.yaml b/prepare/r-foldgo/lilac.yaml new file mode 100644 index 0000000000..6ca9f4c0a9 --- /dev/null +++ b/prepare/r-foldgo/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-tidyr +- r-topgo +update_on: +- regex: FoldGO_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FoldGO diff --git a/prepare/r-fontawesome/PKGBUILD b/prepare/r-fontawesome/PKGBUILD new file mode 100644 index 0000000000..44ffdbb0c2 --- /dev/null +++ b/prepare/r-fontawesome/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fontawesome +_pkgver=0.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Easily Work with 'Font Awesome' Icons" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmltools + r-rlang +) +optdepends=( + r-covr + r-knitr + r-rsvg + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fontawesome/lilac.py b/prepare/r-fontawesome/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fontawesome/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fontawesome/lilac.yaml b/prepare/r-fontawesome/lilac.yaml new file mode 100644 index 0000000000..4a0707ca45 --- /dev/null +++ b/prepare/r-fontawesome/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-rlang +update_on: +- regex: fontawesome_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fontawesome diff --git a/prepare/r-forcats/PKGBUILD b/prepare/r-forcats/PKGBUILD new file mode 100644 index 0000000000..c14dc21b98 --- /dev/null +++ b/prepare/r-forcats/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=forcats +_pkgver=0.5.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Working with Categorical Variables (Factors)' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-ellipsis + r-magrittr + r-rlang + r-tibble +) +optdepends=( + r-covr + r-dplyr + r-ggplot2 + r-knitr + r-readr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-forcats/lilac.py b/prepare/r-forcats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-forcats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-forcats/lilac.yaml b/prepare/r-forcats/lilac.yaml new file mode 100644 index 0000000000..a0bb128603 --- /dev/null +++ b/prepare/r-forcats/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ellipsis +- r-magrittr +- r-rlang +- r-tibble +update_on: +- regex: forcats_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=forcats diff --git a/prepare/r-foreach/PKGBUILD b/prepare/r-foreach/PKGBUILD new file mode 100644 index 0000000000..a1c635a9a0 --- /dev/null +++ b/prepare/r-foreach/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=foreach +_pkgver=1.5.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Provides Foreach Looping Construct' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-iterators +) +optdepends=( + r-domc + r-doparallel + r-knitr + r-randomforest + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-foreach/lilac.py b/prepare/r-foreach/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-foreach/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-foreach/lilac.yaml b/prepare/r-foreach/lilac.yaml new file mode 100644 index 0000000000..54aab585f7 --- /dev/null +++ b/prepare/r-foreach/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-iterators +update_on: +- regex: foreach_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=foreach diff --git a/prepare/r-forecast/PKGBUILD b/prepare/r-forecast/PKGBUILD new file mode 100644 index 0000000000..cea13ce85c --- /dev/null +++ b/prepare/r-forecast/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=forecast +_pkgver=8.16 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Forecasting Functions for Time Series and Linear Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-colorspace + r-fracdiff + r-ggplot2 + r-lmtest + r-magrittr + r-rcpp + r-rcpparmadillo + r-timedate + r-tseries + r-urca + r-zoo +) +optdepends=( + r-forectheta + r-knitr + r-methods + r-rmarkdown + r-rticles + r-seasonal + r-testthat + r-uroot +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-forecast/lilac.py b/prepare/r-forecast/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-forecast/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-forecast/lilac.yaml b/prepare/r-forecast/lilac.yaml new file mode 100644 index 0000000000..2ba2298bf8 --- /dev/null +++ b/prepare/r-forecast/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colorspace +- r-fracdiff +- r-ggplot2 +- r-lmtest +- r-magrittr +- r-rcpp +- r-rcpparmadillo +- r-timedate +- r-tseries +- r-urca +- r-zoo +update_on: +- regex: forecast_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=forecast diff --git a/prepare/r-forestplot/PKGBUILD b/prepare/r-forestplot/PKGBUILD new file mode 100644 index 0000000000..56e2dd68a3 --- /dev/null +++ b/prepare/r-forestplot/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=forestplot +_pkgver=2.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Advanced Forest Plot Using 'grid' Graphics" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-checkmate + r-magrittr +) +optdepends=( + r-abind + r-dplyr + r-knitr + r-rlang + r-rmarkdown + r-rmeta + r-testthat + r-tidyr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-forestplot/lilac.py b/prepare/r-forestplot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-forestplot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-forestplot/lilac.yaml b/prepare/r-forestplot/lilac.yaml new file mode 100644 index 0000000000..c2a5834263 --- /dev/null +++ b/prepare/r-forestplot/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-checkmate +- r-magrittr +update_on: +- regex: forestplot_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=forestplot diff --git a/prepare/r-formattable/PKGBUILD b/prepare/r-formattable/PKGBUILD new file mode 100644 index 0000000000..0f6a761e90 --- /dev/null +++ b/prepare/r-formattable/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=formattable +_pkgver=0.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Create 'Formattable' Data Structures" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmltools + r-htmlwidgets + r-knitr + r-rmarkdown +) +optdepends=( + r-covr + r-dt + r-shiny + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-formattable/lilac.py b/prepare/r-formattable/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-formattable/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-formattable/lilac.yaml b/prepare/r-formattable/lilac.yaml new file mode 100644 index 0000000000..a8f141e81c --- /dev/null +++ b/prepare/r-formattable/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-htmlwidgets +- r-knitr +- r-rmarkdown +update_on: +- regex: formattable_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=formattable diff --git a/prepare/r-formula.tools/PKGBUILD b/prepare/r-formula.tools/PKGBUILD new file mode 100644 index 0000000000..200d8ae87e --- /dev/null +++ b/prepare/r-formula.tools/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=formula.tools +_pkgver=1.7.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Programmatic Utilities for Manipulating Formulas, Expressions, Calls, Assignments and Other R Objects' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-operator.tools +) +optdepends=( + r-magrittr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-formula.tools/lilac.py b/prepare/r-formula.tools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-formula.tools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-formula.tools/lilac.yaml b/prepare/r-formula.tools/lilac.yaml new file mode 100644 index 0000000000..5fbce27291 --- /dev/null +++ b/prepare/r-formula.tools/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-operator.tools +update_on: +- regex: formula.tools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=formula.tools diff --git a/prepare/r-formula/PKGBUILD b/prepare/r-formula/PKGBUILD new file mode 100644 index 0000000000..c894bef813 --- /dev/null +++ b/prepare/r-formula/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Formula +_pkgver=1.2-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Extended Model Formulas' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-formula/lilac.py b/prepare/r-formula/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-formula/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-formula/lilac.yaml b/prepare/r-formula/lilac.yaml new file mode 100644 index 0000000000..20a6600a91 --- /dev/null +++ b/prepare/r-formula/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Formula_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Formula diff --git a/prepare/r-fpc/PKGBUILD b/prepare/r-fpc/PKGBUILD new file mode 100644 index 0000000000..27f15cbadc --- /dev/null +++ b/prepare/r-fpc/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fpc +_pkgver=2.2-9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Flexible Procedures for Clustering' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-diptest + r-flexmix + r-kernlab + r-mclust + r-prabclus + r-robustbase +) +optdepends=( + r-mvtnorm + r-pdfcluster + r-tclust +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fpc/lilac.py b/prepare/r-fpc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fpc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fpc/lilac.yaml b/prepare/r-fpc/lilac.yaml new file mode 100644 index 0000000000..12ffe1019c --- /dev/null +++ b/prepare/r-fpc/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-diptest +- r-flexmix +- r-kernlab +- r-mclust +- r-prabclus +- r-robustbase +update_on: +- regex: fpc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fpc diff --git a/prepare/r-fracdiff/PKGBUILD b/prepare/r-fracdiff/PKGBUILD new file mode 100644 index 0000000000..8d0ffc55f6 --- /dev/null +++ b/prepare/r-fracdiff/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fracdiff +_pkgver=1.5-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-forecast + r-longmemo + r-urca +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fracdiff/lilac.py b/prepare/r-fracdiff/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fracdiff/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fracdiff/lilac.yaml b/prepare/r-fracdiff/lilac.yaml new file mode 100644 index 0000000000..123503f648 --- /dev/null +++ b/prepare/r-fracdiff/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: fracdiff_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fracdiff diff --git a/prepare/r-fraser/PKGBUILD b/prepare/r-fraser/PKGBUILD new file mode 100644 index 0000000000..15ec14b3b3 --- /dev/null +++ b/prepare/r-fraser/PKGBUILD @@ -0,0 +1,74 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FRASER +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Find RAre Splicing Events in RNA-Seq Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-bbmisc + r-biobase + r-biocgenerics + r-biocparallel + r-biomart + r-bsgenome + r-cowplot + r-data.table + r-delayedarray + r-delayedmatrixstats + r-extradistr + r-generics + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggrepel + r-hdf5array + r-iranges + r-matrixstats + r-outrider + r-pcamethods + r-pheatmap + r-plotly + r-prroc + r-r.utils + r-rcolorbrewer + r-rcpp + r-rcpparmadillo + r-rhdf5 + r-rsamtools + r-rsubread + r-s4vectors + r-summarizedexperiment + r-tibble + r-vgam +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-org.hs.eg.db + r-rmarkdown + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fraser/lilac.py b/prepare/r-fraser/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fraser/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fraser/lilac.yaml b/prepare/r-fraser/lilac.yaml new file mode 100644 index 0000000000..e9578298e9 --- /dev/null +++ b/prepare/r-fraser/lilac.yaml @@ -0,0 +1,47 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-bbmisc +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-biomart +- r-bsgenome +- r-cowplot +- r-data.table +- r-delayedarray +- r-delayedmatrixstats +- r-extradistr +- r-generics +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-ggrepel +- r-hdf5array +- r-iranges +- r-matrixstats +- r-outrider +- r-pcamethods +- r-pheatmap +- r-plotly +- r-prroc +- r-r.utils +- r-rcolorbrewer +- r-rcpp +- r-rcpparmadillo +- r-rhdf5 +- r-rsamtools +- r-rsubread +- r-s4vectors +- r-summarizedexperiment +- r-tibble +- r-vgam +update_on: +- regex: FRASER_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FRASER diff --git a/prepare/r-frenchfish/PKGBUILD b/prepare/r-frenchfish/PKGBUILD new file mode 100644 index 0000000000..f46500af2e --- /dev/null +++ b/prepare/r-frenchfish/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=frenchFISH +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-mcmcpack + r-nhpoisson +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-frenchfish/lilac.py b/prepare/r-frenchfish/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-frenchfish/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-frenchfish/lilac.yaml b/prepare/r-frenchfish/lilac.yaml new file mode 100644 index 0000000000..94a795e8ab --- /dev/null +++ b/prepare/r-frenchfish/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mcmcpack +- r-nhpoisson +update_on: +- regex: frenchFISH_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/frenchFISH diff --git a/prepare/r-freqprof/PKGBUILD b/prepare/r-freqprof/PKGBUILD new file mode 100644 index 0000000000..c77a7a09f6 --- /dev/null +++ b/prepare/r-freqprof/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FreqProf +_pkgver=0.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Frequency Profiles Computing and Plotting' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-reshape2 + r-shiny +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-freqprof/lilac.py b/prepare/r-freqprof/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-freqprof/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-freqprof/lilac.yaml b/prepare/r-freqprof/lilac.yaml new file mode 100644 index 0000000000..1b1aecb515 --- /dev/null +++ b/prepare/r-freqprof/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-reshape2 +- r-shiny +update_on: +- regex: FreqProf_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=FreqProf diff --git a/prepare/r-fresh/PKGBUILD b/prepare/r-fresh/PKGBUILD new file mode 100644 index 0000000000..ec62836c64 --- /dev/null +++ b/prepare/r-fresh/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=fresh +_pkgver=0.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Create Custom 'Bootstrap' Themes to Use in 'Shiny'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-htmltools + r-rstudioapi + r-sass + r-shiny +) +optdepends=( + r-bs4dash + r-covr + r-knitr + r-rmarkdown + r-shinydashboard + r-shinywidgets + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fresh/lilac.py b/prepare/r-fresh/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fresh/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fresh/lilac.yaml b/prepare/r-fresh/lilac.yaml new file mode 100644 index 0000000000..083148b3a9 --- /dev/null +++ b/prepare/r-fresh/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-rstudioapi +- r-sass +- r-shiny +update_on: +- regex: fresh_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fresh diff --git a/prepare/r-frgepistasis/PKGBUILD b/prepare/r-frgepistasis/PKGBUILD new file mode 100644 index 0000000000..09766cd321 --- /dev/null +++ b/prepare/r-frgepistasis/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FRGEpistasis +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Epistasis Analysis for Quantitative Traits by Functional Regression Model' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-fda +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-frgepistasis/lilac.py b/prepare/r-frgepistasis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-frgepistasis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-frgepistasis/lilac.yaml b/prepare/r-frgepistasis/lilac.yaml new file mode 100644 index 0000000000..e288fd4700 --- /dev/null +++ b/prepare/r-frgepistasis/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fda +update_on: +- regex: FRGEpistasis_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FRGEpistasis diff --git a/prepare/r-frma/PKGBUILD b/prepare/r-frma/PKGBUILD new file mode 100644 index 0000000000..4d6c52c276 --- /dev/null +++ b/prepare/r-frma/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=frma +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Frozen RMA and Barcode' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-biobase + r-biocgenerics + r-dbi + r-oligo + r-oligoclasses + r-preprocesscore +) +optdepends=( + r-frmaexampledata + r-hgu133afrmavecs +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-frma/lilac.py b/prepare/r-frma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-frma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-frma/lilac.yaml b/prepare/r-frma/lilac.yaml new file mode 100644 index 0000000000..08b7a376e6 --- /dev/null +++ b/prepare/r-frma/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +- r-biocgenerics +- r-dbi +- r-oligo +- r-oligoclasses +- r-preprocesscore +update_on: +- regex: frma_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/frma diff --git a/prepare/r-frmatools/PKGBUILD b/prepare/r-frmatools/PKGBUILD new file mode 100644 index 0000000000..705947c678 --- /dev/null +++ b/prepare/r-frmatools/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=frmaTools +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Frozen RMA Tools' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-biobase + r-dbi + r-preprocesscore +) +optdepends=( + r-affyplm + r-frma + r-frmaexampledata + r-hgu133acdf + r-hgu133afrmavecs + r-hgu133aprobe + r-hgu133atagcdf + r-hgu133atagprobe + r-hgu133plus2cdf + r-hgu133plus2probe + r-oligo + r-pd.huex.1.0.st.v2 + r-pd.hugene.1.0.st.v1 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-frmatools/lilac.py b/prepare/r-frmatools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-frmatools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-frmatools/lilac.yaml b/prepare/r-frmatools/lilac.yaml new file mode 100644 index 0000000000..d2b2d25901 --- /dev/null +++ b/prepare/r-frmatools/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +- r-dbi +- r-preprocesscore +update_on: +- regex: frmaTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/frmaTools diff --git a/prepare/r-fs/PKGBUILD b/prepare/r-fs/PKGBUILD new file mode 100644 index 0000000000..596799f7b3 --- /dev/null +++ b/prepare/r-fs/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=fs +_pkgver=1.5.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Cross-Platform File System Operations Based on 'libuv'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-covr + r-crayon + r-knitr + r-pillar + r-rmarkdown + r-spelling + r-testthat + r-tibble + r-vctrs + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fs/lilac.py b/prepare/r-fs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fs/lilac.yaml b/prepare/r-fs/lilac.yaml new file mode 100644 index 0000000000..32e301366b --- /dev/null +++ b/prepare/r-fs/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: fs_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fs diff --git a/prepare/r-fscanr/PKGBUILD b/prepare/r-fscanr/PKGBUILD new file mode 100644 index 0000000000..ee21e09780 --- /dev/null +++ b/prepare/r-fscanr/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FScanR +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detect Programmed Ribosomal Frameshifting Events from mRNA/cDNA BLASTX Output' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fscanr/lilac.py b/prepare/r-fscanr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fscanr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fscanr/lilac.yaml b/prepare/r-fscanr/lilac.yaml new file mode 100644 index 0000000000..e8978ad929 --- /dev/null +++ b/prepare/r-fscanr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: FScanR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FScanR diff --git a/prepare/r-fselector/PKGBUILD b/prepare/r-fselector/PKGBUILD new file mode 100644 index 0000000000..2c277da1bc --- /dev/null +++ b/prepare/r-fselector/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FSelector +_pkgver=0.33 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Selecting Attributes' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-digest + r-entropy + r-randomforest + r-rweka +) +optdepends=( + r-mlbench + r-rpart +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fselector/lilac.py b/prepare/r-fselector/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fselector/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fselector/lilac.yaml b/prepare/r-fselector/lilac.yaml new file mode 100644 index 0000000000..9903574478 --- /dev/null +++ b/prepare/r-fselector/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-entropy +- r-randomforest +- r-rweka +update_on: +- regex: FSelector_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=FSelector diff --git a/prepare/r-fst/PKGBUILD b/prepare/r-fst/PKGBUILD new file mode 100644 index 0000000000..199d96693e --- /dev/null +++ b/prepare/r-fst/PKGBUILD @@ -0,0 +1,36 @@ +# system requirements: little-endian platform +# Maintainer: Guoyi Zhang + +_pkgname=fst +_pkgver=0.9.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Lightning Fast Serialization of Data Frames' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('AGPL') +depends=( + r + r-rcpp +) +optdepends=( + r-bit64 + r-crayon + r-data.table + r-lintr + r-nanotime + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-fst/lilac.py b/prepare/r-fst/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-fst/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-fst/lilac.yaml b/prepare/r-fst/lilac.yaml new file mode 100644 index 0000000000..af6077818f --- /dev/null +++ b/prepare/r-fst/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: fst_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=fst diff --git a/prepare/r-funchip/PKGBUILD b/prepare/r-funchip/PKGBUILD new file mode 100644 index 0000000000..aebe4a43b7 --- /dev/null +++ b/prepare/r-funchip/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=FunChIP +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clustering and Alignment of ChIP-Seq peaks based on their shapes' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-doparallel + r-fda + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-rcolorbrewer + r-rcpp + r-rsamtools + r-shiny +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-funchip/lilac.py b/prepare/r-funchip/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-funchip/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-funchip/lilac.yaml b/prepare/r-funchip/lilac.yaml new file mode 100644 index 0000000000..6396cd2e72 --- /dev/null +++ b/prepare/r-funchip/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-fda +- r-foreach +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-rcolorbrewer +- r-rcpp +- r-rsamtools +- r-shiny +update_on: +- regex: FunChIP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/FunChIP diff --git a/prepare/r-funtoonorm/PKGBUILD b/prepare/r-funtoonorm/PKGBUILD new file mode 100644 index 0000000000..0005eea5ff --- /dev/null +++ b/prepare/r-funtoonorm/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=funtooNorm +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomeinfodb + r-illuminahumanmethylation450kanno.ilmn12.hg19 + r-illuminahumanmethylation450kmanifest + r-matrixstats + r-minfi + r-pls +) +optdepends=( + r-knitr + r-minfidata + r-prettydoc + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-funtoonorm/lilac.py b/prepare/r-funtoonorm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-funtoonorm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-funtoonorm/lilac.yaml b/prepare/r-funtoonorm/lilac.yaml new file mode 100644 index 0000000000..44bf2e7d02 --- /dev/null +++ b/prepare/r-funtoonorm/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomeinfodb +- r-illuminahumanmethylation450kanno.ilmn12.hg19 +- r-illuminahumanmethylation450kmanifest +- r-matrixstats +- r-minfi +- r-pls +update_on: +- regex: funtooNorm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/funtooNorm diff --git a/prepare/r-furrr/PKGBUILD b/prepare/r-furrr/PKGBUILD new file mode 100644 index 0000000000..2c2c9f861e --- /dev/null +++ b/prepare/r-furrr/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=furrr +_pkgver=0.2.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Apply Mapping Functions in Parallel using Futures' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-ellipsis + r-future + r-globals + r-lifecycle + r-purrr + r-rlang + r-vctrs +) +optdepends=( + r-carrier + r-covr + r-dplyr + r-knitr + r-listenv + r-magrittr + r-rmarkdown + r-testthat + r-tidyselect + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-furrr/lilac.py b/prepare/r-furrr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-furrr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-furrr/lilac.yaml b/prepare/r-furrr/lilac.yaml new file mode 100644 index 0000000000..680947cdaf --- /dev/null +++ b/prepare/r-furrr/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ellipsis +- r-future +- r-globals +- r-lifecycle +- r-purrr +- r-rlang +- r-vctrs +update_on: +- regex: furrr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=furrr diff --git a/prepare/r-future.apply/PKGBUILD b/prepare/r-future.apply/PKGBUILD new file mode 100644 index 0000000000..dac7a911de --- /dev/null +++ b/prepare/r-future.apply/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=future.apply +_pkgver=1.8.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Apply Function to Elements in Parallel using Futures' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-future + r-globals +) +optdepends=( + r-datasets + r-listenv + r-markdown + r-r.rsp + r-stats + r-tools +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-future.apply/lilac.py b/prepare/r-future.apply/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-future.apply/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-future.apply/lilac.yaml b/prepare/r-future.apply/lilac.yaml new file mode 100644 index 0000000000..de22f56dbd --- /dev/null +++ b/prepare/r-future.apply/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-future +- r-globals +update_on: +- regex: future.apply_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=future.apply diff --git a/prepare/r-future/PKGBUILD b/prepare/r-future/PKGBUILD new file mode 100644 index 0000000000..fd04d5388b --- /dev/null +++ b/prepare/r-future/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=future +_pkgver=1.23.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Unified Parallel and Distributed Processing in R for Everyone' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-digest + r-globals + r-listenv + r-parallelly +) +optdepends=( + r-markdown + r-r.rsp + r-rhpcblasctl +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-future/lilac.py b/prepare/r-future/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-future/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-future/lilac.yaml b/prepare/r-future/lilac.yaml new file mode 100644 index 0000000000..847928a08c --- /dev/null +++ b/prepare/r-future/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-globals +- r-listenv +- r-parallelly +update_on: +- regex: future_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=future diff --git a/prepare/r-ga/PKGBUILD b/prepare/r-ga/PKGBUILD new file mode 100644 index 0000000000..0c31662146 --- /dev/null +++ b/prepare/r-ga/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GA +_pkgver=3.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genetic Algorithms' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-cli + r-crayon + r-foreach + r-iterators + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-doparallel + r-dorng + r-knitr + r-parallel + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ga/lilac.py b/prepare/r-ga/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ga/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ga/lilac.yaml b/prepare/r-ga/lilac.yaml new file mode 100644 index 0000000000..168a47f1b2 --- /dev/null +++ b/prepare/r-ga/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cli +- r-crayon +- r-foreach +- r-iterators +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: GA_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=GA diff --git a/prepare/r-ga4ghclient/PKGBUILD b/prepare/r-ga4ghclient/PKGBUILD new file mode 100644 index 0000000000..09d11dcf0b --- /dev/null +++ b/prepare/r-ga4ghclient/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GA4GHclient +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Bioconductor package for accessing GA4GH API data servers' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-dplyr + r-genomeinfodb + r-genomicranges + r-httr + r-iranges + r-jsonlite + r-s4vectors + r-variantannotation +) +optdepends=( + r-annotationdbi + r-biocstyle + r-dt + r-knitr + r-org.hs.eg.db + r-rmarkdown + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ga4ghclient/lilac.py b/prepare/r-ga4ghclient/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ga4ghclient/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ga4ghclient/lilac.yaml b/prepare/r-ga4ghclient/lilac.yaml new file mode 100644 index 0000000000..a044b3ac73 --- /dev/null +++ b/prepare/r-ga4ghclient/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-dplyr +- r-genomeinfodb +- r-genomicranges +- r-httr +- r-iranges +- r-jsonlite +- r-s4vectors +- r-variantannotation +update_on: +- regex: GA4GHclient_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GA4GHclient diff --git a/prepare/r-ga4ghshiny/PKGBUILD b/prepare/r-ga4ghshiny/PKGBUILD new file mode 100644 index 0000000000..edb220f0a7 --- /dev/null +++ b/prepare/r-ga4ghshiny/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GA4GHshiny +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Shiny application for interacting with GA4GH-based data servers' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocgenerics + r-dplyr + r-dt + r-ga4ghclient + r-genomeinfodb + r-genomicfeatures + r-openxlsx + r-purrr + r-s4vectors + r-shiny + r-shinyjs + r-shinythemes + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-org.hs.eg.db + r-rmarkdown + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ga4ghshiny/lilac.py b/prepare/r-ga4ghshiny/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ga4ghshiny/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ga4ghshiny/lilac.yaml b/prepare/r-ga4ghshiny/lilac.yaml new file mode 100644 index 0000000000..623e4ade5c --- /dev/null +++ b/prepare/r-ga4ghshiny/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-dplyr +- r-dt +- r-ga4ghclient +- r-genomeinfodb +- r-genomicfeatures +- r-openxlsx +- r-purrr +- r-s4vectors +- r-shiny +- r-shinyjs +- r-shinythemes +- r-tidyr +update_on: +- regex: GA4GHshiny_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GA4GHshiny diff --git a/prepare/r-gaga/PKGBUILD b/prepare/r-gaga/PKGBUILD new file mode 100644 index 0000000000..b91e805d8b --- /dev/null +++ b/prepare/r-gaga/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gaga +_pkgver=2.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GaGa hierarchical model for high-throughput data analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-coda + r-ebarrays +) +optdepends=( + r-parallel +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gaga/lilac.py b/prepare/r-gaga/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gaga/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gaga/lilac.yaml b/prepare/r-gaga/lilac.yaml new file mode 100644 index 0000000000..5daee779b7 --- /dev/null +++ b/prepare/r-gaga/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-coda +- r-ebarrays +update_on: +- regex: gaga_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gaga diff --git a/prepare/r-gage/PKGBUILD b/prepare/r-gage/PKGBUILD new file mode 100644 index 0000000000..905792e177 --- /dev/null +++ b/prepare/r-gage/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gage +_pkgver=2.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generally Applicable Gene-set Enrichment for Pathway Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-go.db + r-graph + r-keggrest +) +optdepends=( + r-deseq2 + r-edger + r-gagedata + r-genomicalignments + r-gseabase + r-hgu133a.db + r-limma + r-org.hs.eg.db + r-pathview + r-rsamtools + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gage/lilac.py b/prepare/r-gage/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gage/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gage/lilac.yaml b/prepare/r-gage/lilac.yaml new file mode 100644 index 0000000000..2a88e88265 --- /dev/null +++ b/prepare/r-gage/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-go.db +- r-graph +- r-keggrest +update_on: +- regex: gage_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gage diff --git a/prepare/r-gaggle/PKGBUILD b/prepare/r-gaggle/PKGBUILD new file mode 100644 index 0000000000..69a9e421fe --- /dev/null +++ b/prepare/r-gaggle/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gaggle +_pkgver=1.62.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Broadcast data between R and Gaggle' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-graph + r-rjava + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gaggle/lilac.py b/prepare/r-gaggle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gaggle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gaggle/lilac.yaml b/prepare/r-gaggle/lilac.yaml new file mode 100644 index 0000000000..76096c734c --- /dev/null +++ b/prepare/r-gaggle/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +- r-rjava +- r-runit +update_on: +- regex: gaggle_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gaggle diff --git a/prepare/r-gaia/PKGBUILD b/prepare/r-gaia/PKGBUILD new file mode 100644 index 0000000000..b28ff6aea4 --- /dev/null +++ b/prepare/r-gaia/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gaia +_pkgver=2.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GAIA: An R package for genomic analysis of significant chromosomal aberrations.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gaia/lilac.py b/prepare/r-gaia/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gaia/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gaia/lilac.yaml b/prepare/r-gaia/lilac.yaml new file mode 100644 index 0000000000..32c33b2811 --- /dev/null +++ b/prepare/r-gaia/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gaia_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gaia diff --git a/prepare/r-gam/PKGBUILD b/prepare/r-gam/PKGBUILD new file mode 100644 index 0000000000..e181711f43 --- /dev/null +++ b/prepare/r-gam/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gam +_pkgver=1.20 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generalized Additive Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-foreach +) +optdepends=( + r-akima + r-testthat +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gam/lilac.py b/prepare/r-gam/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gam/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gam/lilac.yaml b/prepare/r-gam/lilac.yaml new file mode 100644 index 0000000000..d627cb3bd8 --- /dev/null +++ b/prepare/r-gam/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-foreach +update_on: +- regex: gam_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gam diff --git a/prepare/r-gamlss.data/PKGBUILD b/prepare/r-gamlss.data/PKGBUILD new file mode 100644 index 0000000000..30ca08eeb1 --- /dev/null +++ b/prepare/r-gamlss.data/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gamlss.data +_pkgver=6.0-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data for Generalised Additive Models for Location Scale and Shape' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gamlss.data/lilac.py b/prepare/r-gamlss.data/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gamlss.data/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gamlss.data/lilac.yaml b/prepare/r-gamlss.data/lilac.yaml new file mode 100644 index 0000000000..4ac2dbebcb --- /dev/null +++ b/prepare/r-gamlss.data/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gamlss.data_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gamlss.data diff --git a/prepare/r-gamlss.dist/PKGBUILD b/prepare/r-gamlss.dist/PKGBUILD new file mode 100644 index 0000000000..156ec5b484 --- /dev/null +++ b/prepare/r-gamlss.dist/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gamlss.dist +_pkgver=6.0-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Distributions for Generalized Additive Models for Location Scale and Shape' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gamlss.dist/lilac.py b/prepare/r-gamlss.dist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gamlss.dist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gamlss.dist/lilac.yaml b/prepare/r-gamlss.dist/lilac.yaml new file mode 100644 index 0000000000..f93619fd2e --- /dev/null +++ b/prepare/r-gamlss.dist/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gamlss.dist_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gamlss.dist diff --git a/prepare/r-gamlss/PKGBUILD b/prepare/r-gamlss/PKGBUILD new file mode 100644 index 0000000000..c31d33c5c6 --- /dev/null +++ b/prepare/r-gamlss/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gamlss +_pkgver=5.3-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generalised Additive Models for Location Scale and Shape' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-gamlss.data + r-gamlss.dist +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gamlss/lilac.py b/prepare/r-gamlss/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gamlss/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gamlss/lilac.yaml b/prepare/r-gamlss/lilac.yaml new file mode 100644 index 0000000000..0e0306a11b --- /dev/null +++ b/prepare/r-gamlss/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gamlss.data +- r-gamlss.dist +update_on: +- regex: gamlss_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gamlss diff --git a/prepare/r-gap/PKGBUILD b/prepare/r-gap/PKGBUILD new file mode 100644 index 0000000000..d62958b7cf --- /dev/null +++ b/prepare/r-gap/PKGBUILD @@ -0,0 +1,67 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gap +_pkgver=1.2.3-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genetic Analysis Package' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-bdsmatrix + r-bradleyterry2 + r-calibrate + r-circlize + r-coda + r-cowplot + r-coxme + r-dplyr + r-foreign + r-forestplot + r-gap.datasets + r-genetics + r-ggplot2 + r-grid + r-haplo.stats + r-jsonlite + r-kinship2 + r-lattice + r-magic + r-mass + r-matrix + r-matrixstats + r-mcmcglmm + r-meta + r-metafor + r-mets + r-nlme + r-pedigree + r-pedigreemm + r-plotly + r-plotrix + r-r2jags + r-reshape + r-rmeta + r-rms + r-survival +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gap/lilac.py b/prepare/r-gap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gap/lilac.yaml b/prepare/r-gap/lilac.yaml new file mode 100644 index 0000000000..b4ed47e702 --- /dev/null +++ b/prepare/r-gap/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gap_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gap diff --git a/prepare/r-gapgom/PKGBUILD b/prepare/r-gapgom/PKGBUILD new file mode 100644 index 0000000000..b0df9cd46b --- /dev/null +++ b/prepare/r-gapgom/PKGBUILD @@ -0,0 +1,72 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GAPGOM +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GAPGOM (novel Gene Annotation Prediction and other GO Metrics)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-biobase + r-biocfilecache + r-data.table + r-dplyr + r-fastmatch + r-geoquery + r-go.db + r-gosemsim + r-graph + r-igraph + r-magrittr + r-matrixstats + r-org.hs.eg.db + r-org.mm.eg.db + r-plyr + r-rbgl +) +optdepends=( + r-ggplot2 + r-kableextra + r-knitr + r-org.ag.eg.db + r-org.at.tair.db + r-org.bt.eg.db + r-org.ce.eg.db + r-org.cf.eg.db + r-org.dm.eg.db + r-org.dr.eg.db + r-org.eck12.eg.db + r-org.ecsakai.eg.db + r-org.gg.eg.db + r-org.mmu.eg.db + r-org.pf.plasmo.db + r-org.pt.eg.db + r-org.rn.eg.db + r-org.sc.sgd.db + r-org.ss.eg.db + r-org.xl.eg.db + r-prettydoc + r-profvis + r-pryr + r-reshape2 + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gapgom/lilac.py b/prepare/r-gapgom/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gapgom/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gapgom/lilac.yaml b/prepare/r-gapgom/lilac.yaml new file mode 100644 index 0000000000..d9e8b921f3 --- /dev/null +++ b/prepare/r-gapgom/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocfilecache +- r-data.table +- r-dplyr +- r-fastmatch +- r-geoquery +- r-go.db +- r-gosemsim +- r-graph +- r-igraph +- r-magrittr +- r-matrixstats +- r-org.hs.eg.db +- r-org.mm.eg.db +- r-plyr +- r-rbgl +update_on: +- regex: GAPGOM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GAPGOM diff --git a/prepare/r-gaprediction/PKGBUILD b/prepare/r-gaprediction/PKGBUILD new file mode 100644 index 0000000000..19cc19e45e --- /dev/null +++ b/prepare/r-gaprediction/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GAprediction +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Prediction of gestational age with Illumina HumanMethylation450 data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-glmnet +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gaprediction/lilac.py b/prepare/r-gaprediction/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gaprediction/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gaprediction/lilac.yaml b/prepare/r-gaprediction/lilac.yaml new file mode 100644 index 0000000000..3a3b3ff122 --- /dev/null +++ b/prepare/r-gaprediction/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-glmnet +update_on: +- regex: GAprediction_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GAprediction diff --git a/prepare/r-garfield/PKGBUILD b/prepare/r-garfield/PKGBUILD new file mode 100644 index 0000000000..3cf9b84310 --- /dev/null +++ b/prepare/r-garfield/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=garfield +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-garfield/lilac.py b/prepare/r-garfield/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-garfield/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-garfield/lilac.yaml b/prepare/r-garfield/lilac.yaml new file mode 100644 index 0000000000..6cedce7290 --- /dev/null +++ b/prepare/r-garfield/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: garfield_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/garfield diff --git a/prepare/r-gargle/PKGBUILD b/prepare/r-gargle/PKGBUILD new file mode 100644 index 0000000000..f0af6c57be --- /dev/null +++ b/prepare/r-gargle/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gargle +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities for Working with Google APIs' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-cli + r-fs + r-glue + r-httr + r-jsonlite + r-rappdirs + r-rlang + r-rstudioapi + r-withr +) +optdepends=( + r-aws.ec2metadata + r-aws.signature + r-covr + r-httpuv + r-knitr + r-mockr + r-rmarkdown + r-sodium + r-spelling + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gargle/lilac.py b/prepare/r-gargle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gargle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gargle/lilac.yaml b/prepare/r-gargle/lilac.yaml new file mode 100644 index 0000000000..adaae45d5f --- /dev/null +++ b/prepare/r-gargle/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cli +- r-fs +- r-glue +- r-httr +- r-jsonlite +- r-rappdirs +- r-rlang +- r-rstudioapi +- r-withr +update_on: +- regex: gargle_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gargle diff --git a/prepare/r-gars/PKGBUILD b/prepare/r-gars/PKGBUILD new file mode 100644 index 0000000000..76723c01c1 --- /dev/null +++ b/prepare/r-gars/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GARS +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-damirseq + r-ggplot2 + r-mlseq + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gars/lilac.py b/prepare/r-gars/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gars/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gars/lilac.yaml b/prepare/r-gars/lilac.yaml new file mode 100644 index 0000000000..f59fe65413 --- /dev/null +++ b/prepare/r-gars/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-damirseq +- r-ggplot2 +- r-mlseq +- r-summarizedexperiment +update_on: +- regex: GARS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GARS diff --git a/prepare/r-gatefinder/PKGBUILD b/prepare/r-gatefinder/PKGBUILD new file mode 100644 index 0000000000..e964f97d0a --- /dev/null +++ b/prepare/r-gatefinder/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GateFinder +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Projection-based Gating Strategy Optimization for Flow and Mass Cytometry' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-diptest + r-flowcore + r-flowfp + r-mvoutlier + r-splancs +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gatefinder/lilac.py b/prepare/r-gatefinder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gatefinder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gatefinder/lilac.yaml b/prepare/r-gatefinder/lilac.yaml new file mode 100644 index 0000000000..d24dc5e93d --- /dev/null +++ b/prepare/r-gatefinder/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-diptest +- r-flowcore +- r-flowfp +- r-mvoutlier +- r-splancs +update_on: +- regex: GateFinder_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GateFinder diff --git a/prepare/r-gbm/PKGBUILD b/prepare/r-gbm/PKGBUILD new file mode 100644 index 0000000000..5d72a0ac9b --- /dev/null +++ b/prepare/r-gbm/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gbm +_pkgver=2.1.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generalized Boosted Regression Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-covr + r-gridextra + r-knitr + r-pdp + r-runit + r-splines + r-tinytest + r-vip + r-viridis +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gbm/lilac.py b/prepare/r-gbm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gbm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gbm/lilac.yaml b/prepare/r-gbm/lilac.yaml new file mode 100644 index 0000000000..d1cf974a71 --- /dev/null +++ b/prepare/r-gbm/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gbm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gbm diff --git a/prepare/r-gcapc/PKGBUILD b/prepare/r-gcapc/PKGBUILD new file mode 100644 index 0000000000..85abbb0886 --- /dev/null +++ b/prepare/r-gcapc/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gcapc +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GC Aware Peak Caller' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-matrixstats + r-rsamtools + r-s4vectors +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.mmusculus.ucsc.mm10 + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gcapc/lilac.py b/prepare/r-gcapc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gcapc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gcapc/lilac.yaml b/prepare/r-gcapc/lilac.yaml new file mode 100644 index 0000000000..5944ee738e --- /dev/null +++ b/prepare/r-gcapc/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-matrixstats +- r-rsamtools +- r-s4vectors +update_on: +- regex: gcapc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gcapc diff --git a/prepare/r-gcatest/PKGBUILD b/prepare/r-gcatest/PKGBUILD new file mode 100644 index 0000000000..9be391aa54 --- /dev/null +++ b/prepare/r-gcatest/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gcatest +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genotype Conditional Association TEST' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-lfa +) +optdepends=( + r-ggplot2 + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gcatest/lilac.py b/prepare/r-gcatest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gcatest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gcatest/lilac.yaml b/prepare/r-gcatest/lilac.yaml new file mode 100644 index 0000000000..e9ba92c43e --- /dev/null +++ b/prepare/r-gcatest/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lfa +update_on: +- regex: gcatest_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gcatest diff --git a/prepare/r-gclus/PKGBUILD b/prepare/r-gclus/PKGBUILD new file mode 100644 index 0000000000..699cc665a9 --- /dev/null +++ b/prepare/r-gclus/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gclus +_pkgver=1.3.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clustering Graphics' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gclus/lilac.py b/prepare/r-gclus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gclus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gclus/lilac.yaml b/prepare/r-gclus/lilac.yaml new file mode 100644 index 0000000000..e6a6d370fd --- /dev/null +++ b/prepare/r-gclus/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gclus_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gclus diff --git a/prepare/r-gcrisprtools/PKGBUILD b/prepare/r-gcrisprtools/PKGBUILD new file mode 100644 index 0000000000..09b7ed9d38 --- /dev/null +++ b/prepare/r-gcrisprtools/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gCrisprTools +_pkgver=2.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Suite of Functions for Pooled Crispr Screen QC and Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-complexheatmap + r-ggplot2 + r-limma + r-rmarkdown + r-robustrankaggreg + r-summarizedexperiment +) +optdepends=( + r-annotationdbi + r-biocgenerics + r-edger + r-fgsea + r-knitr + r-markdown + r-msigdbr + r-org.hs.eg.db + r-org.mm.eg.db + r-runit + r-sparrow +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gcrisprtools/lilac.py b/prepare/r-gcrisprtools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gcrisprtools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gcrisprtools/lilac.yaml b/prepare/r-gcrisprtools/lilac.yaml new file mode 100644 index 0000000000..6de47d8fff --- /dev/null +++ b/prepare/r-gcrisprtools/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-complexheatmap +- r-ggplot2 +- r-limma +- r-rmarkdown +- r-robustrankaggreg +- r-summarizedexperiment +update_on: +- regex: gCrisprTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gCrisprTools diff --git a/prepare/r-gcrma/PKGBUILD b/prepare/r-gcrma/PKGBUILD new file mode 100644 index 0000000000..81d4ba899a --- /dev/null +++ b/prepare/r-gcrma/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gcrma +_pkgver=2.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Background Adjustment Using Sequence Information' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-affy + r-affyio + r-biobase + r-biocmanager + r-biostrings + r-xvector +) +optdepends=( + r-affydata + r-hgu95av2cdf + r-hgu95av2probe + r-splines + r-tools +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gcrma/lilac.py b/prepare/r-gcrma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gcrma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gcrma/lilac.yaml b/prepare/r-gcrma/lilac.yaml new file mode 100644 index 0000000000..65995d4598 --- /dev/null +++ b/prepare/r-gcrma/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-affyio +- r-biobase +- r-biocmanager +- r-biostrings +- r-xvector +update_on: +- regex: gcrma_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gcrma diff --git a/prepare/r-gcsconnection/PKGBUILD b/prepare/r-gcsconnection/PKGBUILD new file mode 100644 index 0000000000..524eadfc29 --- /dev/null +++ b/prepare/r-gcsconnection/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GCSConnection +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Creating R Connection with Google Cloud Storage' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-googleauthr + r-googlecloudstorager + r-httr + r-jsonlite + r-rcpp +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gcsconnection/lilac.py b/prepare/r-gcsconnection/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gcsconnection/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gcsconnection/lilac.yaml b/prepare/r-gcsconnection/lilac.yaml new file mode 100644 index 0000000000..1b3acd29be --- /dev/null +++ b/prepare/r-gcsconnection/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-googleauthr +- r-googlecloudstorager +- r-httr +- r-jsonlite +- r-rcpp +update_on: +- regex: GCSConnection_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GCSConnection diff --git a/prepare/r-gcsfilesystem/PKGBUILD b/prepare/r-gcsfilesystem/PKGBUILD new file mode 100644 index 0000000000..5ceef2df9a --- /dev/null +++ b/prepare/r-gcsfilesystem/PKGBUILD @@ -0,0 +1,34 @@ +# system requirements: GCSDokan for Windows, gcsfuse for Linux and macOs +# Maintainer: Guoyi Zhang + +_pkgname=GCSFilesystem +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mounting a Google Cloud bucket to a local directory' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biocstyle + r-gcsconnection + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gcsfilesystem/lilac.py b/prepare/r-gcsfilesystem/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gcsfilesystem/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gcsfilesystem/lilac.yaml b/prepare/r-gcsfilesystem/lilac.yaml new file mode 100644 index 0000000000..d261b9a7e3 --- /dev/null +++ b/prepare/r-gcsfilesystem/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: GCSFilesystem_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GCSFilesystem diff --git a/prepare/r-gcspikelite/PKGBUILD b/prepare/r-gcspikelite/PKGBUILD new file mode 100644 index 0000000000..13fca3eea2 --- /dev/null +++ b/prepare/r-gcspikelite/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gcspikelite +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Spike-in data for GC/MS data and methods within flagme' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gcspikelite/lilac.py b/prepare/r-gcspikelite/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gcspikelite/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gcspikelite/lilac.yaml b/prepare/r-gcspikelite/lilac.yaml new file mode 100644 index 0000000000..f1751b704f --- /dev/null +++ b/prepare/r-gcspikelite/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gcspikelite_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gcspikelite diff --git a/prepare/r-gcsscore/PKGBUILD b/prepare/r-gcsscore/PKGBUILD new file mode 100644 index 0000000000..bde9edf454 --- /dev/null +++ b/prepare/r-gcsscore/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GCSscore +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GCSscore: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affxparser + r-biobase + r-biocmanager + r-data.table + r-devtools + r-dplr + r-rsqlite + r-stringr +) +optdepends=( + r-geoquery + r-r.utils + r-siggenes +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gcsscore/lilac.py b/prepare/r-gcsscore/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gcsscore/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gcsscore/lilac.yaml b/prepare/r-gcsscore/lilac.yaml new file mode 100644 index 0000000000..09cca6f1b7 --- /dev/null +++ b/prepare/r-gcsscore/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affxparser +- r-biobase +- r-biocmanager +- r-data.table +- r-devtools +- r-dplr +- r-rsqlite +- r-stringr +update_on: +- regex: GCSscore_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GCSscore diff --git a/prepare/r-gdata/PKGBUILD b/prepare/r-gdata/PKGBUILD new file mode 100644 index 0000000000..a307da78ff --- /dev/null +++ b/prepare/r-gdata/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: perl (>= 5.10.0) +# Maintainer: Guoyi Zhang + +_pkgname=gdata +_pkgver=2.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Various R Programming Tools for Data Manipulation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-gtools +) +optdepends=( + r-runit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gdata/lilac.py b/prepare/r-gdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gdata/lilac.yaml b/prepare/r-gdata/lilac.yaml new file mode 100644 index 0000000000..a214085bf5 --- /dev/null +++ b/prepare/r-gdata/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gtools +update_on: +- regex: gdata_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gdata diff --git a/prepare/r-gdcrnatools/PKGBUILD b/prepare/r-gdcrnatools/PKGBUILD new file mode 100644 index 0000000000..9628dd1a0a --- /dev/null +++ b/prepare/r-gdcrnatools/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GDCRNATools +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-biomart + r-clusterprofiler + r-deseq2 + r-dose + r-dt + r-edger + r-genomicdatacommons + r-ggplot2 + r-gplots + r-jsonlite + r-limma + r-org.hs.eg.db + r-pathview + r-rjson + r-shiny + r-survminer + r-xml +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gdcrnatools/lilac.py b/prepare/r-gdcrnatools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gdcrnatools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gdcrnatools/lilac.yaml b/prepare/r-gdcrnatools/lilac.yaml new file mode 100644 index 0000000000..c4d982619a --- /dev/null +++ b/prepare/r-gdcrnatools/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-biomart +- r-clusterprofiler +- r-deseq2 +- r-dose +- r-dt +- r-edger +- r-genomicdatacommons +- r-ggplot2 +- r-gplots +- r-jsonlite +- r-limma +- r-org.hs.eg.db +- r-pathview +- r-rjson +- r-shiny +- r-survminer +- r-xml +update_on: +- regex: GDCRNATools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GDCRNATools diff --git a/prepare/r-gdm/PKGBUILD b/prepare/r-gdm/PKGBUILD new file mode 100644 index 0000000000..aa1d476366 --- /dev/null +++ b/prepare/r-gdm/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gdm +_pkgver=1.5.0-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generalized Dissimilarity Modeling' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-doparallel + r-foreach + r-raster + r-rcpp + r-reshape2 + r-vegan +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gdm/lilac.py b/prepare/r-gdm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gdm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gdm/lilac.yaml b/prepare/r-gdm/lilac.yaml new file mode 100644 index 0000000000..775f09f886 --- /dev/null +++ b/prepare/r-gdm/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-foreach +- r-raster +- r-rcpp +- r-reshape2 +- r-vegan +update_on: +- regex: gdm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gdm diff --git a/prepare/r-gdsarray/PKGBUILD b/prepare/r-gdsarray/PKGBUILD new file mode 100644 index 0000000000..40149c582f --- /dev/null +++ b/prepare/r-gdsarray/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GDSArray +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Representing GDS files as array-like objects' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-delayedarray + r-gdsfmt + r-s4vectors + r-seqarray + r-snprelate +) +optdepends=( + r-biocmanager + r-biocstyle + r-knitr + r-markdown + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gdsarray/lilac.py b/prepare/r-gdsarray/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gdsarray/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gdsarray/lilac.yaml b/prepare/r-gdsarray/lilac.yaml new file mode 100644 index 0000000000..aa585e3413 --- /dev/null +++ b/prepare/r-gdsarray/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-delayedarray +- r-gdsfmt +- r-s4vectors +- r-seqarray +- r-snprelate +update_on: +- regex: GDSArray_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GDSArray diff --git a/prepare/r-gdsfmt/PKGBUILD b/prepare/r-gdsfmt/PKGBUILD new file mode 100644 index 0000000000..6bae95ff6e --- /dev/null +++ b/prepare/r-gdsfmt/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gdsfmt +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Interface to CoreArray Genomic Data Structure (GDS) Files' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +optdepends=( + r-biocgenerics + r-crayon + r-digest + r-knitr + r-markdown + r-matrix + r-parallel + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gdsfmt/lilac.py b/prepare/r-gdsfmt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gdsfmt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gdsfmt/lilac.yaml b/prepare/r-gdsfmt/lilac.yaml new file mode 100644 index 0000000000..e8034e4283 --- /dev/null +++ b/prepare/r-gdsfmt/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gdsfmt_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gdsfmt diff --git a/prepare/r-gdtools/PKGBUILD b/prepare/r-gdtools/PKGBUILD new file mode 100644 index 0000000000..f4e04e2e16 --- /dev/null +++ b/prepare/r-gdtools/PKGBUILD @@ -0,0 +1,35 @@ +# system requirements: cairo, freetype2, fontconfig +# Maintainer: Guoyi Zhang + +_pkgname=gdtools +_pkgver=0.2.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities for Graphical Rendering' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-systemfonts +) +optdepends=( + r-curl + r-fontquiver + r-htmltools + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gdtools/lilac.py b/prepare/r-gdtools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gdtools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gdtools/lilac.yaml b/prepare/r-gdtools/lilac.yaml new file mode 100644 index 0000000000..060ef528b6 --- /dev/null +++ b/prepare/r-gdtools/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-systemfonts +update_on: +- regex: gdtools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gdtools diff --git a/prepare/r-geem/PKGBUILD b/prepare/r-geem/PKGBUILD new file mode 100644 index 0000000000..8aba16a166 --- /dev/null +++ b/prepare/r-geem/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=geeM +_pkgver=0.10.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Solve Generalized Estimating Equations' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-geepack + r-mumin + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geem/lilac.py b/prepare/r-geem/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geem/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geem/lilac.yaml b/prepare/r-geem/lilac.yaml new file mode 100644 index 0000000000..36cc2cd9ef --- /dev/null +++ b/prepare/r-geem/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: geeM_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=geeM diff --git a/prepare/r-geepack/PKGBUILD b/prepare/r-geepack/PKGBUILD new file mode 100644 index 0000000000..5220d2d823 --- /dev/null +++ b/prepare/r-geepack/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=geepack +_pkgver=1.3.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generalized Estimating Equation Package' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-broom + r-magrittr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geepack/lilac.py b/prepare/r-geepack/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geepack/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geepack/lilac.yaml b/prepare/r-geepack/lilac.yaml new file mode 100644 index 0000000000..88cfbffbb3 --- /dev/null +++ b/prepare/r-geepack/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-broom +- r-magrittr +update_on: +- regex: geepack_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=geepack diff --git a/prepare/r-geigen/PKGBUILD b/prepare/r-geigen/PKGBUILD new file mode 100644 index 0000000000..b808930f03 --- /dev/null +++ b/prepare/r-geigen/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=geigen +_pkgver=2.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Calculate Generalized Eigenvalues, the Generalized Schur Decomposition and the Generalized Singular Value Decomposition of a Matrix Pair with Lapack' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geigen/lilac.py b/prepare/r-geigen/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geigen/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geigen/lilac.yaml b/prepare/r-geigen/lilac.yaml new file mode 100644 index 0000000000..55a071d864 --- /dev/null +++ b/prepare/r-geigen/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: geigen_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=geigen diff --git a/prepare/r-gem/PKGBUILD b/prepare/r-gem/PKGBUILD new file mode 100644 index 0000000000..7b405a3f56 --- /dev/null +++ b/prepare/r-gem/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GEM +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GEM: fast association study for the interplay of Gene, Environment and Methylation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ggplot2 +) +optdepends=( + r-biocgenerics + r-knitr + r-markdown + r-rmarkdown + r-runit + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gem/lilac.py b/prepare/r-gem/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gem/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gem/lilac.yaml b/prepare/r-gem/lilac.yaml new file mode 100644 index 0000000000..ea9ecbae3a --- /dev/null +++ b/prepare/r-gem/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +update_on: +- regex: GEM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GEM diff --git a/prepare/r-gemini/PKGBUILD b/prepare/r-gemini/PKGBUILD new file mode 100644 index 0000000000..08ded9b26a --- /dev/null +++ b/prepare/r-gemini/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gemini +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-dplyr + r-ggplot2 + r-magrittr + r-mixtools + r-pbmcapply + r-scales +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gemini/lilac.py b/prepare/r-gemini/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gemini/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gemini/lilac.yaml b/prepare/r-gemini/lilac.yaml new file mode 100644 index 0000000000..82ceede42b --- /dev/null +++ b/prepare/r-gemini/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-magrittr +- r-mixtools +- r-pbmcapply +- r-scales +update_on: +- regex: gemini_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gemini diff --git a/prepare/r-genalg/PKGBUILD b/prepare/r-genalg/PKGBUILD new file mode 100644 index 0000000000..195d40bcd4 --- /dev/null +++ b/prepare/r-genalg/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=genalg +_pkgver=0.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Based Genetic Algorithm' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genalg/lilac.py b/prepare/r-genalg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genalg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genalg/lilac.yaml b/prepare/r-genalg/lilac.yaml new file mode 100644 index 0000000000..a43eb5a45b --- /dev/null +++ b/prepare/r-genalg/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: genalg_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=genalg diff --git a/prepare/r-genarise/PKGBUILD b/prepare/r-genarise/PKGBUILD new file mode 100644 index 0000000000..3ce84e4e6e --- /dev/null +++ b/prepare/r-genarise/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=genArise +_pkgver=1.70.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Microarray Analysis tool' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-locfit + r-tkrplot + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genarise/lilac.py b/prepare/r-genarise/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genarise/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genarise/lilac.yaml b/prepare/r-genarise/lilac.yaml new file mode 100644 index 0000000000..c996e5a1b4 --- /dev/null +++ b/prepare/r-genarise/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-locfit +- r-tkrplot +- r-xtable +update_on: +- regex: genArise_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/genArise diff --git a/prepare/r-genbankr/PKGBUILD b/prepare/r-genbankr/PKGBUILD new file mode 100644 index 0000000000..6f227cf10c --- /dev/null +++ b/prepare/r-genbankr/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=genbankr +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Parsing GenBank files into semantically useful objects' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-biostrings + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-rtracklayer + r-s4vectors + r-variantannotation +) +optdepends=( + r-biocstyle + r-knitr + r-rentrez + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genbankr/lilac.py b/prepare/r-genbankr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genbankr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genbankr/lilac.yaml b/prepare/r-genbankr/lilac.yaml new file mode 100644 index 0000000000..e819cd8ec1 --- /dev/null +++ b/prepare/r-genbankr/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biostrings +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-rtracklayer +- r-s4vectors +- r-variantannotation +update_on: +- regex: genbankr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/genbankr diff --git a/prepare/r-geneaccord/PKGBUILD b/prepare/r-geneaccord/PKGBUILD new file mode 100644 index 0000000000..0a9a8ea036 --- /dev/null +++ b/prepare/r-geneaccord/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GeneAccord +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-biomart + r-catools + r-dplyr + r-ggplot2 + r-ggpubr + r-gtools + r-magrittr + r-maxlik + r-rcolorbrewer + r-reshape2 + r-tibble +) +optdepends=( + r-assertthat + r-biocstyle + r-devtools + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geneaccord/lilac.py b/prepare/r-geneaccord/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geneaccord/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geneaccord/lilac.yaml b/prepare/r-geneaccord/lilac.yaml new file mode 100644 index 0000000000..d99505673b --- /dev/null +++ b/prepare/r-geneaccord/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-catools +- r-dplyr +- r-ggplot2 +- r-ggpubr +- r-gtools +- r-magrittr +- r-maxlik +- r-rcolorbrewer +- r-reshape2 +- r-tibble +update_on: +- regex: GeneAccord_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GeneAccord diff --git a/prepare/r-geneanswers/PKGBUILD b/prepare/r-geneanswers/PKGBUILD new file mode 100644 index 0000000000..252ba06def --- /dev/null +++ b/prepare/r-geneanswers/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GeneAnswers +_pkgver=2.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integrated Interpretation of Genes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-annotate + r-biobase + r-downloader + r-heatplus + r-igraph + r-keggrest + r-rbgl + r-rcolorbrewer + r-rcurl + r-rsqlite + r-xml +) +optdepends=( + r-annotationdbi + r-biomart + r-go.db + r-graph + r-org.dm.eg.db + r-org.hs.eg.db + r-org.mm.eg.db + r-org.rn.eg.db + r-reactome.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geneanswers/lilac.py b/prepare/r-geneanswers/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geneanswers/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geneanswers/lilac.yaml b/prepare/r-geneanswers/lilac.yaml new file mode 100644 index 0000000000..95ef6f61f2 --- /dev/null +++ b/prepare/r-geneanswers/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-biobase +- r-downloader +- r-heatplus +- r-igraph +- r-keggrest +- r-rbgl +- r-rcolorbrewer +- r-rcurl +- r-rsqlite +- r-xml +update_on: +- regex: GeneAnswers_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GeneAnswers diff --git a/prepare/r-geneattribution/PKGBUILD b/prepare/r-geneattribution/PKGBUILD new file mode 100644 index 0000000000..ca812b6f1b --- /dev/null +++ b/prepare/r-geneattribution/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=geneAttribution +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identification of candidate genes associated with genetic variation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-org.hs.eg.db + r-rtracklayer +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.hsapiens.ucsc.hg38.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geneattribution/lilac.py b/prepare/r-geneattribution/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geneattribution/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geneattribution/lilac.yaml b/prepare/r-geneattribution/lilac.yaml new file mode 100644 index 0000000000..53691a190a --- /dev/null +++ b/prepare/r-geneattribution/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-org.hs.eg.db +- r-rtracklayer +update_on: +- regex: geneAttribution_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/geneAttribution diff --git a/prepare/r-genebreak/PKGBUILD b/prepare/r-genebreak/PKGBUILD new file mode 100644 index 0000000000..99fea7e1e9 --- /dev/null +++ b/prepare/r-genebreak/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GeneBreak +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Break Detection' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cghbase + r-cghcall + r-genomicranges + r-qdnaseq +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genebreak/lilac.py b/prepare/r-genebreak/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genebreak/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genebreak/lilac.yaml b/prepare/r-genebreak/lilac.yaml new file mode 100644 index 0000000000..1c30805326 --- /dev/null +++ b/prepare/r-genebreak/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cghbase +- r-cghcall +- r-genomicranges +- r-qdnaseq +update_on: +- regex: GeneBreak_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GeneBreak diff --git a/prepare/r-geneclassifiers/PKGBUILD b/prepare/r-geneclassifiers/PKGBUILD new file mode 100644 index 0000000000..e952f81a1c --- /dev/null +++ b/prepare/r-geneclassifiers/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=geneClassifiers +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Application of gene classifiers' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics +) +optdepends=( + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geneclassifiers/lilac.py b/prepare/r-geneclassifiers/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geneclassifiers/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geneclassifiers/lilac.yaml b/prepare/r-geneclassifiers/lilac.yaml new file mode 100644 index 0000000000..a49179eb03 --- /dev/null +++ b/prepare/r-geneclassifiers/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +update_on: +- regex: geneClassifiers_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/geneClassifiers diff --git a/prepare/r-geneexpressionsignature/PKGBUILD b/prepare/r-geneexpressionsignature/PKGBUILD new file mode 100644 index 0000000000..c9084968a9 --- /dev/null +++ b/prepare/r-geneexpressionsignature/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GeneExpressionSignature +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Expression Signature based Similarity Metric' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +optdepends=( + r-apcluster + r-biocstyle + r-geoquery + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geneexpressionsignature/lilac.py b/prepare/r-geneexpressionsignature/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geneexpressionsignature/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geneexpressionsignature/lilac.yaml b/prepare/r-geneexpressionsignature/lilac.yaml new file mode 100644 index 0000000000..7d1102f005 --- /dev/null +++ b/prepare/r-geneexpressionsignature/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: GeneExpressionSignature_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GeneExpressionSignature diff --git a/prepare/r-genefilter/PKGBUILD b/prepare/r-genefilter/PKGBUILD new file mode 100644 index 0000000000..cf0fe1c080 --- /dev/null +++ b/prepare/r-genefilter/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=genefilter +_pkgver=1.76.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='genefilter: methods for filtering genes from high-throughput experiments' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotate + r-annotationdbi + r-biobase + r-biocgenerics +) +optdepends=( + r-all + r-biocstyle + r-class + r-hgu95av2.db + r-knitr + r-rcolorbrewer + r-roc + r-tkwidgets +) +makedepends=( + gcc-fortran +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genefilter/lilac.py b/prepare/r-genefilter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genefilter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genefilter/lilac.yaml b/prepare/r-genefilter/lilac.yaml new file mode 100644 index 0000000000..9bc14c325c --- /dev/null +++ b/prepare/r-genefilter/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-biobase +- r-biocgenerics +update_on: +- regex: genefilter_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/genefilter diff --git a/prepare/r-genefu/PKGBUILD b/prepare/r-genefu/PKGBUILD new file mode 100644 index 0000000000..72ad8f9f31 --- /dev/null +++ b/prepare/r-genefu/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=genefu +_pkgver=2.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Computation of Gene Expression-Based Signatures in Breast Cancer' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-aims + r-amap + r-biomart + r-ic10 + r-impute + r-limma + r-mclust + r-survcomp +) +optdepends=( + r-biobase + r-biocstyle + r-breastcancermainz + r-breastcancernki + r-breastcancertransbig + r-breastcancerunt + r-breastcancerupp + r-breastcancervdx + r-caret + r-genemeta + r-knitr + r-magick + r-rmarkdown + r-rmeta + r-survival + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genefu/lilac.py b/prepare/r-genefu/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genefu/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genefu/lilac.yaml b/prepare/r-genefu/lilac.yaml new file mode 100644 index 0000000000..a66b2280aa --- /dev/null +++ b/prepare/r-genefu/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aims +- r-amap +- r-biomart +- r-ic10 +- r-impute +- r-limma +- r-mclust +- r-survcomp +update_on: +- regex: genefu_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/genefu diff --git a/prepare/r-genega/PKGBUILD b/prepare/r-genega/PKGBUILD new file mode 100644 index 0000000000..83cf05e523 --- /dev/null +++ b/prepare/r-genega/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GeneGA +_pkgver=1.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-hash + r-seqinr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genega/lilac.py b/prepare/r-genega/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genega/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genega/lilac.yaml b/prepare/r-genega/lilac.yaml new file mode 100644 index 0000000000..98f3a14d77 --- /dev/null +++ b/prepare/r-genega/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-hash +- r-seqinr +update_on: +- regex: GeneGA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GeneGA diff --git a/prepare/r-genegeneinter/PKGBUILD b/prepare/r-genegeneinter/PKGBUILD new file mode 100644 index 0000000000..1dbe5a3954 --- /dev/null +++ b/prepare/r-genegeneinter/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GeneGeneInteR +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Testing Gene-Gene Interaction at the Gene Level' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-factominer + r-genomicranges + r-igraph + r-iranges + r-kernlab + r-mvtnorm + r-rsamtools + r-snpstats +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genegeneinter/lilac.py b/prepare/r-genegeneinter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genegeneinter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genegeneinter/lilac.yaml b/prepare/r-genegeneinter/lilac.yaml new file mode 100644 index 0000000000..8c65443250 --- /dev/null +++ b/prepare/r-genegeneinter/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-factominer +- r-genomicranges +- r-igraph +- r-iranges +- r-kernlab +- r-mvtnorm +- r-rsamtools +- r-snpstats +update_on: +- regex: GeneGeneInteR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GeneGeneInteR diff --git a/prepare/r-genelendatabase/PKGBUILD b/prepare/r-genelendatabase/PKGBUILD new file mode 100644 index 0000000000..1cbf29d0ec --- /dev/null +++ b/prepare/r-genelendatabase/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=geneLenDataBase +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Lengths of mRNA transcripts for a number of genomes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-genomicfeatures + r-rtracklayer +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genelendatabase/lilac.py b/prepare/r-genelendatabase/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genelendatabase/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genelendatabase/lilac.yaml b/prepare/r-genelendatabase/lilac.yaml new file mode 100644 index 0000000000..7bbb165d7f --- /dev/null +++ b/prepare/r-genelendatabase/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicfeatures +- r-rtracklayer +update_on: +- regex: geneLenDataBase_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/geneLenDataBase diff --git a/prepare/r-genemeta/PKGBUILD b/prepare/r-genemeta/PKGBUILD new file mode 100644 index 0000000000..8050ab982a --- /dev/null +++ b/prepare/r-genemeta/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GeneMeta +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MetaAnalysis for High Throughput Experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-genefilter +) +optdepends=( + r-rcolorbrewer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genemeta/lilac.py b/prepare/r-genemeta/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genemeta/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genemeta/lilac.yaml b/prepare/r-genemeta/lilac.yaml new file mode 100644 index 0000000000..a5d83cb172 --- /dev/null +++ b/prepare/r-genemeta/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-genefilter +update_on: +- regex: GeneMeta_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GeneMeta diff --git a/prepare/r-genenet/PKGBUILD b/prepare/r-genenet/PKGBUILD new file mode 100644 index 0000000000..48170e84cb --- /dev/null +++ b/prepare/r-genenet/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GeneNet +_pkgver=1.2.16 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Modeling and Inferring Gene Networks' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-corpcor + r-fdrtool + r-longitudinal +) +optdepends=( + r-graph + r-rgraphviz +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genenet/lilac.py b/prepare/r-genenet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genenet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genenet/lilac.yaml b/prepare/r-genenet/lilac.yaml new file mode 100644 index 0000000000..1ae31be011 --- /dev/null +++ b/prepare/r-genenet/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-corpcor +- r-fdrtool +- r-longitudinal +update_on: +- regex: GeneNet_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=GeneNet diff --git a/prepare/r-genenetworkbuilder/PKGBUILD b/prepare/r-genenetworkbuilder/PKGBUILD new file mode 100644 index 0000000000..3f7ef46c3b --- /dev/null +++ b/prepare/r-genenetworkbuilder/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GeneNetworkBuilder +_pkgver=1.36.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-graph + r-htmlwidgets + r-plyr + r-rcpp + r-rgraphviz + r-rjson + r-xml +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-magick + r-rbgl + r-rmarkdown + r-runit + r-shiny + r-simpintlists + r-stringdb +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genenetworkbuilder/lilac.py b/prepare/r-genenetworkbuilder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genenetworkbuilder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genenetworkbuilder/lilac.yaml b/prepare/r-genenetworkbuilder/lilac.yaml new file mode 100644 index 0000000000..b53903edbb --- /dev/null +++ b/prepare/r-genenetworkbuilder/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +- r-htmlwidgets +- r-plyr +- r-rcpp +- r-rgraphviz +- r-rjson +- r-xml +update_on: +- regex: GeneNetworkBuilder_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GeneNetworkBuilder diff --git a/prepare/r-geneoverlap/PKGBUILD b/prepare/r-geneoverlap/PKGBUILD new file mode 100644 index 0000000000..9e8eb33ae3 --- /dev/null +++ b/prepare/r-geneoverlap/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GeneOverlap +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Test and visualize gene overlaps' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-gplots + r-rcolorbrewer +) +optdepends=( + r-biocgenerics + r-biocstyle + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geneoverlap/lilac.py b/prepare/r-geneoverlap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geneoverlap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geneoverlap/lilac.yaml b/prepare/r-geneoverlap/lilac.yaml new file mode 100644 index 0000000000..d58c066029 --- /dev/null +++ b/prepare/r-geneoverlap/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gplots +- r-rcolorbrewer +update_on: +- regex: GeneOverlap_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GeneOverlap diff --git a/prepare/r-geneplast/PKGBUILD b/prepare/r-geneplast/PKGBUILD new file mode 100644 index 0000000000..d3542fdf72 --- /dev/null +++ b/prepare/r-geneplast/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=geneplast +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Evolutionary and plasticity analysis of orthologous groups' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-data.table + r-igraph + r-snow +) +optdepends=( + r-biocgenerics + r-biocstyle + r-fletcher2013b + r-geneplast.data.string.v91 + r-ggplot2 + r-ggpubr + r-knitr + r-plyr + r-rmarkdown + r-rtn + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geneplast/lilac.py b/prepare/r-geneplast/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geneplast/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geneplast/lilac.yaml b/prepare/r-geneplast/lilac.yaml new file mode 100644 index 0000000000..e4bd94cd68 --- /dev/null +++ b/prepare/r-geneplast/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-data.table +- r-igraph +- r-snow +update_on: +- regex: geneplast_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/geneplast diff --git a/prepare/r-geneplotter/PKGBUILD b/prepare/r-geneplotter/PKGBUILD new file mode 100644 index 0000000000..90b9c0f75c --- /dev/null +++ b/prepare/r-geneplotter/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=geneplotter +_pkgver=1.72.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Graphics related functions for Bioconductor' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-rcolorbrewer +) +optdepends=( + r-fibroeset + r-hgu133a.db + r-hgu95av2.db + r-hu6800.db + r-rgraphviz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geneplotter/lilac.py b/prepare/r-geneplotter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geneplotter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geneplotter/lilac.yaml b/prepare/r-geneplotter/lilac.yaml new file mode 100644 index 0000000000..fc3456c750 --- /dev/null +++ b/prepare/r-geneplotter/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-rcolorbrewer +update_on: +- regex: geneplotter_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/geneplotter diff --git a/prepare/r-generecommender/PKGBUILD b/prepare/r-generecommender/PKGBUILD new file mode 100644 index 0000000000..203c6e992f --- /dev/null +++ b/prepare/r-generecommender/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=geneRecommender +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A gene recommender algorithm to identify genes coexpressed with a query set of genes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-generecommender/lilac.py b/prepare/r-generecommender/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-generecommender/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-generecommender/lilac.yaml b/prepare/r-generecommender/lilac.yaml new file mode 100644 index 0000000000..502696b350 --- /dev/null +++ b/prepare/r-generecommender/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: geneRecommender_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/geneRecommender diff --git a/prepare/r-generegionscan/PKGBUILD b/prepare/r-generegionscan/PKGBUILD new file mode 100644 index 0000000000..7a88668c2c --- /dev/null +++ b/prepare/r-generegionscan/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GeneRegionScan +_pkgver=1.50.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GeneRegionScan' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affxparser + r-biobase + r-biostrings + r-rcolorbrewer + r-s4vectors +) +optdepends=( + r-affy + r-annotationdbi + r-bsgenome +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-generegionscan/lilac.py b/prepare/r-generegionscan/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-generegionscan/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-generegionscan/lilac.yaml b/prepare/r-generegionscan/lilac.yaml new file mode 100644 index 0000000000..2a13816af5 --- /dev/null +++ b/prepare/r-generegionscan/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affxparser +- r-biobase +- r-biostrings +- r-rcolorbrewer +- r-s4vectors +update_on: +- regex: GeneRegionScan_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GeneRegionScan diff --git a/prepare/r-generxcluster/PKGBUILD b/prepare/r-generxcluster/PKGBUILD new file mode 100644 index 0000000000..536b8bcfd4 --- /dev/null +++ b/prepare/r-generxcluster/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=geneRxCluster +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='gRx Differential Clustering' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicranges + r-iranges +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-generxcluster/lilac.py b/prepare/r-generxcluster/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-generxcluster/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-generxcluster/lilac.yaml b/prepare/r-generxcluster/lilac.yaml new file mode 100644 index 0000000000..0f0e416c60 --- /dev/null +++ b/prepare/r-generxcluster/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-iranges +update_on: +- regex: geneRxCluster_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/geneRxCluster diff --git a/prepare/r-geneselectmmd/PKGBUILD b/prepare/r-geneselectmmd/PKGBUILD new file mode 100644 index 0000000000..803f3b9c0e --- /dev/null +++ b/prepare/r-geneselectmmd/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GeneSelectMMD +_pkgver=2.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-limma +) +optdepends=( + r-all +) +makedepends=( + gcc-fortran +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geneselectmmd/lilac.py b/prepare/r-geneselectmmd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geneselectmmd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geneselectmmd/lilac.yaml b/prepare/r-geneselectmmd/lilac.yaml new file mode 100644 index 0000000000..0fb41b33cd --- /dev/null +++ b/prepare/r-geneselectmmd/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-limma +update_on: +- regex: GeneSelectMMD_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GeneSelectMMD diff --git a/prepare/r-genesis/PKGBUILD b/prepare/r-genesis/PKGBUILD new file mode 100644 index 0000000000..7507cc17be --- /dev/null +++ b/prepare/r-genesis/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GENESIS +_pkgver=2.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-data.table + r-gdsfmt + r-genomicranges + r-gwastools + r-igraph + r-iranges + r-reshape2 + r-s4vectors + r-seqarray + r-seqvartools + r-snprelate +) +optdepends=( + r-biocstyle + r-compoissonreg + r-compquadform + r-dplyr + r-ggally + r-ggplot2 + r-gwasdata + r-knitr + r-poibin + r-rcolorbrewer + r-rmarkdown + r-spatest + r-survey + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genesis/lilac.py b/prepare/r-genesis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genesis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genesis/lilac.yaml b/prepare/r-genesis/lilac.yaml new file mode 100644 index 0000000000..1d5e57b619 --- /dev/null +++ b/prepare/r-genesis/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-data.table +- r-gdsfmt +- r-genomicranges +- r-gwastools +- r-igraph +- r-iranges +- r-reshape2 +- r-s4vectors +- r-seqarray +- r-seqvartools +- r-snprelate +update_on: +- regex: GENESIS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GENESIS diff --git a/prepare/r-genestructuretools/PKGBUILD b/prepare/r-genestructuretools/PKGBUILD new file mode 100644 index 0000000000..2428158de4 --- /dev/null +++ b/prepare/r-genestructuretools/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GeneStructureTools +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for spliced gene structure manipulation and analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-biostrings + r-bsgenome.mmusculus.ucsc.mm10 + r-data.table + r-genomicranges + r-gviz + r-iranges + r-plyr + r-rtracklayer + r-s4vectors + r-stringdist + r-stringr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genestructuretools/lilac.py b/prepare/r-genestructuretools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genestructuretools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genestructuretools/lilac.yaml b/prepare/r-genestructuretools/lilac.yaml new file mode 100644 index 0000000000..faef5e4294 --- /dev/null +++ b/prepare/r-genestructuretools/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome.mmusculus.ucsc.mm10 +- r-data.table +- r-genomicranges +- r-gviz +- r-iranges +- r-plyr +- r-rtracklayer +- r-s4vectors +- r-stringdist +- r-stringr +update_on: +- regex: GeneStructureTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GeneStructureTools diff --git a/prepare/r-genetclassifier/PKGBUILD b/prepare/r-genetclassifier/PKGBUILD new file mode 100644 index 0000000000..6edb58a4d8 --- /dev/null +++ b/prepare/r-genetclassifier/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=geNetClassifier +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Classify diseases and build associated gene networks using gene expression profiles' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-e1071 + r-ebarrays + r-minet +) +optdepends=( + r-biocgenerics + r-igraph + r-infotheo + r-leukemiaseset + r-rcolorbrewer + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genetclassifier/lilac.py b/prepare/r-genetclassifier/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genetclassifier/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genetclassifier/lilac.yaml b/prepare/r-genetclassifier/lilac.yaml new file mode 100644 index 0000000000..10ee9f59ea --- /dev/null +++ b/prepare/r-genetclassifier/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-e1071 +- r-ebarrays +- r-minet +update_on: +- regex: geNetClassifier_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/geNetClassifier diff --git a/prepare/r-genetics/PKGBUILD b/prepare/r-genetics/PKGBUILD new file mode 100644 index 0000000000..b77a216b2a --- /dev/null +++ b/prepare/r-genetics/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=genetics +_pkgver=1.3.8.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Population Genetics' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-combinat + r-gdata + r-gtools + r-mvtnorm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genetics/lilac.py b/prepare/r-genetics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genetics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genetics/lilac.yaml b/prepare/r-genetics/lilac.yaml new file mode 100644 index 0000000000..98f595de2e --- /dev/null +++ b/prepare/r-genetics/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-combinat +- r-gdata +- r-gtools +- r-mvtnorm +update_on: +- regex: genetics_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=genetics diff --git a/prepare/r-geneticsped/PKGBUILD b/prepare/r-geneticsped/PKGBUILD new file mode 100644 index 0000000000..aae32fdca6 --- /dev/null +++ b/prepare/r-geneticsped/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GeneticsPed +_pkgver=1.56.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pedigree and genetic relationship functions' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-gdata + r-genetics +) +optdepends=( + r-gtools + r-runit +) +makedepends=( + gcc-fortran +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geneticsped/lilac.py b/prepare/r-geneticsped/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geneticsped/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geneticsped/lilac.yaml b/prepare/r-geneticsped/lilac.yaml new file mode 100644 index 0000000000..bf703225b3 --- /dev/null +++ b/prepare/r-geneticsped/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gdata +- r-genetics +update_on: +- regex: GeneticsPed_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GeneticsPed diff --git a/prepare/r-genetonic/PKGBUILD b/prepare/r-genetonic/PKGBUILD new file mode 100644 index 0000000000..49b006cf7c --- /dev/null +++ b/prepare/r-genetonic/PKGBUILD @@ -0,0 +1,72 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GeneTonic +_pkgver=1.6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-backbone + r-bs4dash + r-circlize + r-colorspace + r-colourpicker + r-complexheatmap + r-dendextend + r-deseq2 + r-dplyr + r-dt + r-dynamictreecut + r-expm + r-ggforce + r-ggplot2 + r-ggrepel + r-go.db + r-igraph + r-matrixstats + r-plotly + r-rcolorbrewer + r-rintrojs + r-rlang + r-rmarkdown + r-s4vectors + r-scales + r-shiny + r-shinyace + r-shinycssloaders + r-shinywidgets + r-summarizedexperiment + r-tidyr + r-tippy + r-viridis + r-visnetwork +) +optdepends=( + r-biocstyle + r-clusterprofiler + r-htmltools + r-knitr + r-macrophage + r-magrittr + r-org.hs.eg.db + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genetonic/lilac.py b/prepare/r-genetonic/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genetonic/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genetonic/lilac.yaml b/prepare/r-genetonic/lilac.yaml new file mode 100644 index 0000000000..34a6e7059f --- /dev/null +++ b/prepare/r-genetonic/lilac.yaml @@ -0,0 +1,44 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-backbone +- r-bs4dash +- r-circlize +- r-colorspace +- r-colourpicker +- r-complexheatmap +- r-dendextend +- r-deseq2 +- r-dplyr +- r-dt +- r-dynamictreecut +- r-expm +- r-ggforce +- r-ggplot2 +- r-ggrepel +- r-go.db +- r-igraph +- r-matrixstats +- r-plotly +- r-rcolorbrewer +- r-rintrojs +- r-rlang +- r-rmarkdown +- r-s4vectors +- r-scales +- r-shiny +- r-shinyace +- r-shinycssloaders +- r-shinywidgets +- r-summarizedexperiment +- r-tidyr +- r-tippy +- r-viridis +- r-visnetwork +update_on: +- regex: GeneTonic_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GeneTonic diff --git a/prepare/r-genextender/PKGBUILD b/prepare/r-genextender/PKGBUILD new file mode 100644 index 0000000000..4f9c4108a8 --- /dev/null +++ b/prepare/r-genextender/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=geneXtendeR +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Optimized Functional Annotation Of ChIP-seq Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocstyle + r-data.table + r-dplyr + r-go.db + r-networkd3 + r-org.rn.eg.db + r-rcolorbrewer + r-rtracklayer + r-snowballc + r-tm + r-wordcloud +) +optdepends=( + r-knitr + r-org.ag.eg.db + r-org.bt.eg.db + r-org.ce.eg.db + r-org.cf.eg.db + r-org.dm.eg.db + r-org.dr.eg.db + r-org.gg.eg.db + r-org.hs.eg.db + r-org.mm.eg.db + r-org.pt.eg.db + r-org.sc.sgd.db + r-org.ss.eg.db + r-org.xl.eg.db + r-rmarkdown + r-rtracklayer + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genextender/lilac.py b/prepare/r-genextender/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genextender/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genextender/lilac.yaml b/prepare/r-genextender/lilac.yaml new file mode 100644 index 0000000000..c3aa181701 --- /dev/null +++ b/prepare/r-genextender/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocstyle +- r-data.table +- r-dplyr +- r-go.db +- r-networkd3 +- r-org.rn.eg.db +- r-rcolorbrewer +- r-rtracklayer +- r-snowballc +- r-tm +- r-wordcloud +update_on: +- regex: geneXtendeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/geneXtendeR diff --git a/prepare/r-genie3/PKGBUILD b/prepare/r-genie3/PKGBUILD new file mode 100644 index 0000000000..dc96988d42 --- /dev/null +++ b/prepare/r-genie3/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GENIE3 +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GEne Network Inference with Ensemble of trees' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-reshape2 +) +optdepends=( + r-biobase + r-doparallel + r-dorng + r-foreach + r-knitr + r-methods + r-rmarkdown + r-summarizedexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genie3/lilac.py b/prepare/r-genie3/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genie3/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genie3/lilac.yaml b/prepare/r-genie3/lilac.yaml new file mode 100644 index 0000000000..bc3fb6e36f --- /dev/null +++ b/prepare/r-genie3/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-reshape2 +update_on: +- regex: GENIE3_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GENIE3 diff --git a/prepare/r-genkern/PKGBUILD b/prepare/r-genkern/PKGBUILD new file mode 100644 index 0000000000..148d284382 --- /dev/null +++ b/prepare/r-genkern/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenKern +_pkgver=1.2-60 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for generating and manipulating binned kernel density estimates' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genkern/lilac.py b/prepare/r-genkern/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genkern/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genkern/lilac.yaml b/prepare/r-genkern/lilac.yaml new file mode 100644 index 0000000000..d04a2d533d --- /dev/null +++ b/prepare/r-genkern/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: GenKern_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=GenKern diff --git a/prepare/r-genlasso/PKGBUILD b/prepare/r-genlasso/PKGBUILD new file mode 100644 index 0000000000..35fe885f82 --- /dev/null +++ b/prepare/r-genlasso/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=genlasso +_pkgver=1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Path Algorithm for Generalized Lasso Problems' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-igraph +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genlasso/lilac.py b/prepare/r-genlasso/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genlasso/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genlasso/lilac.yaml b/prepare/r-genlasso/lilac.yaml new file mode 100644 index 0000000000..abe155611f --- /dev/null +++ b/prepare/r-genlasso/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +update_on: +- regex: genlasso_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=genlasso diff --git a/prepare/r-genlib/PKGBUILD b/prepare/r-genlib/PKGBUILD new file mode 100644 index 0000000000..a8ee8145b3 --- /dev/null +++ b/prepare/r-genlib/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GENLIB +_pkgver=1.1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genealogical Data Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bootstrap + r-doparallel + r-foreach + r-kinship2 + r-quadprog + r-rcpp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genlib/lilac.py b/prepare/r-genlib/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genlib/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genlib/lilac.yaml b/prepare/r-genlib/lilac.yaml new file mode 100644 index 0000000000..9915c8d990 --- /dev/null +++ b/prepare/r-genlib/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bootstrap +- r-doparallel +- r-foreach +- r-kinship2 +- r-quadprog +- r-rcpp +update_on: +- regex: GENLIB_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=GENLIB diff --git a/prepare/r-genocn/PKGBUILD b/prepare/r-genocn/PKGBUILD new file mode 100644 index 0000000000..70b412ba1e --- /dev/null +++ b/prepare/r-genocn/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=genoCN +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='genotyping and copy number study tools' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genocn/lilac.py b/prepare/r-genocn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genocn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genocn/lilac.yaml b/prepare/r-genocn/lilac.yaml new file mode 100644 index 0000000000..c59af2fce2 --- /dev/null +++ b/prepare/r-genocn/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: genoCN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/genoCN diff --git a/prepare/r-genogam/PKGBUILD b/prepare/r-genogam/PKGBUILD new file mode 100644 index 0000000000..d75057bd02 --- /dev/null +++ b/prepare/r-genogam/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenoGAM +_pkgver=2.11.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A GAM based framework for analysis of ChIP-Seq data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-biostrings + r-data.table + r-delayedarray + r-deseq2 + r-futile.logger + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-hdf5array + r-iranges + r-rcpp + r-rcpparmadillo + r-rhdf5 + r-rsamtools + r-s4vectors + r-sparseinv + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-chipseq + r-genefilter + r-ggplot2 + r-knitr + r-lsd + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genogam/lilac.py b/prepare/r-genogam/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genogam/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genogam/lilac.yaml b/prepare/r-genogam/lilac.yaml new file mode 100644 index 0000000000..090ab698db --- /dev/null +++ b/prepare/r-genogam/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-biostrings +- r-data.table +- r-delayedarray +- r-deseq2 +- r-futile.logger +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-hdf5array +- r-iranges +- r-rcpp +- r-rcpparmadillo +- r-rhdf5 +- r-rsamtools +- r-s4vectors +- r-sparseinv +- r-summarizedexperiment +update_on: +- regex: GenoGAM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GenoGAM diff --git a/prepare/r-genomation/PKGBUILD b/prepare/r-genomation/PKGBUILD new file mode 100644 index 0000000000..206b834d7e --- /dev/null +++ b/prepare/r-genomation/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=genomation +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Summary, annotation and visualization of genomic data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-bsgenome + r-data.table + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-gridbase + r-impute + r-iranges + r-matrixstats + r-plotrix + r-plyr + r-rcpp + r-readr + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors + r-seqpattern +) +optdepends=( + r-biocgenerics + r-genomationdata + r-knitr + r-rcolorbrewer + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomation/lilac.py b/prepare/r-genomation/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomation/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomation/lilac.yaml b/prepare/r-genomation/lilac.yaml new file mode 100644 index 0000000000..1dc19af93c --- /dev/null +++ b/prepare/r-genomation/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome +- r-data.table +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-gridbase +- r-impute +- r-iranges +- r-matrixstats +- r-plotrix +- r-plyr +- r-rcpp +- r-readr +- r-reshape2 +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-seqpattern +update_on: +- regex: genomation_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/genomation diff --git a/prepare/r-genomeinfodb/PKGBUILD b/prepare/r-genomeinfodb/PKGBUILD new file mode 100644 index 0000000000..932e67f4a2 --- /dev/null +++ b/prepare/r-genomeinfodb/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenomeInfoDb +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities for manipulating chromosome names, including modifying them to follow a particular naming style' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-genomeinfodbdata + r-iranges + r-rcurl + r-s4vectors +) +optdepends=( + r-biocstyle + r-bsgenome + r-bsgenome.celegans.ucsc.ce2 + r-bsgenome.hsapiens.ncbi.grch38 + r-bsgenome.scerevisiae.ucsc.saccer2 + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-knitr + r-rsamtools + r-runit + r-txdb.dmelanogaster.ucsc.dm3.ensgene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomeinfodb/lilac.py b/prepare/r-genomeinfodb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomeinfodb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomeinfodb/lilac.yaml b/prepare/r-genomeinfodb/lilac.yaml new file mode 100644 index 0000000000..65b280b17c --- /dev/null +++ b/prepare/r-genomeinfodb/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomeinfodbdata +- r-iranges +- r-rcurl +- r-s4vectors +update_on: +- regex: GenomeInfoDb_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GenomeInfoDb diff --git a/prepare/r-genomeintervals/PKGBUILD b/prepare/r-genomeintervals/PKGBUILD new file mode 100644 index 0000000000..d62a2d8b4f --- /dev/null +++ b/prepare/r-genomeintervals/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=genomeIntervals +_pkgver=1.50.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Operations on genomic intervals' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-genomeinfodb + r-genomicranges + r-intervals + r-iranges + r-s4vectors +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomeintervals/lilac.py b/prepare/r-genomeintervals/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomeintervals/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomeintervals/lilac.yaml b/prepare/r-genomeintervals/lilac.yaml new file mode 100644 index 0000000000..bce99eafb8 --- /dev/null +++ b/prepare/r-genomeintervals/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomeinfodb +- r-genomicranges +- r-intervals +- r-iranges +- r-s4vectors +update_on: +- regex: genomeIntervals_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/genomeIntervals diff --git a/prepare/r-genomes/PKGBUILD b/prepare/r-genomes/PKGBUILD new file mode 100644 index 0000000000..f26bc9c3fe --- /dev/null +++ b/prepare/r-genomes/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=genomes +_pkgver=3.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genome sequencing project metadata' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-curl + r-readr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomes/lilac.py b/prepare/r-genomes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomes/lilac.yaml b/prepare/r-genomes/lilac.yaml new file mode 100644 index 0000000000..207a1d3e56 --- /dev/null +++ b/prepare/r-genomes/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-readr +update_on: +- regex: genomes_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/genomes diff --git a/prepare/r-genomicalignments/PKGBUILD b/prepare/r-genomicalignments/PKGBUILD new file mode 100644 index 0000000000..3e057979ef --- /dev/null +++ b/prepare/r-genomicalignments/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenomicAlignments +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Representation and manipulation of short genomic alignments' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-genomeinfodb + r-genomicranges + r-iranges + r-rsamtools + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-bsgenome + r-bsgenome.dmelanogaster.ucsc.dm3 + r-bsgenome.hsapiens.ucsc.hg19 + r-deseq2 + r-edger + r-genomicfeatures + r-pasillabamsubset + r-rnaseqdata.hnrnpc.bam.chr14 + r-rtracklayer + r-runit + r-shortread + r-txdb.dmelanogaster.ucsc.dm3.ensgene + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomicalignments/lilac.py b/prepare/r-genomicalignments/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomicalignments/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomicalignments/lilac.yaml b/prepare/r-genomicalignments/lilac.yaml new file mode 100644 index 0000000000..eab3594a96 --- /dev/null +++ b/prepare/r-genomicalignments/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rsamtools +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: GenomicAlignments_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GenomicAlignments diff --git a/prepare/r-genomicdatacommons/PKGBUILD b/prepare/r-genomicdatacommons/PKGBUILD new file mode 100644 index 0000000000..fdea7ecac2 --- /dev/null +++ b/prepare/r-genomicdatacommons/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenomicDataCommons +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='NIH / NCI Genomic Data Commons Access' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-dplyr + r-genomicranges + r-httr + r-iranges + r-jsonlite + r-magrittr + r-rappdirs + r-readr + r-rlang + r-s4vectors + r-summarizedexperiment + r-tibble + r-xml2 +) +optdepends=( + r-biocparallel + r-biocstyle + r-dt + r-genomicalignments + r-ggplot2 + r-knitr + r-listviewer + r-rmarkdown + r-rsamtools + r-testthat + r-txdb.hsapiens.ucsc.hg38.knowngene + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomicdatacommons/lilac.py b/prepare/r-genomicdatacommons/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomicdatacommons/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomicdatacommons/lilac.yaml b/prepare/r-genomicdatacommons/lilac.yaml new file mode 100644 index 0000000000..64b59c02dc --- /dev/null +++ b/prepare/r-genomicdatacommons/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-genomicranges +- r-httr +- r-iranges +- r-jsonlite +- r-magrittr +- r-rappdirs +- r-readr +- r-rlang +- r-s4vectors +- r-summarizedexperiment +- r-tibble +- r-xml2 +update_on: +- regex: GenomicDataCommons_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GenomicDataCommons diff --git a/prepare/r-genomicdistributions/PKGBUILD b/prepare/r-genomicdistributions/PKGBUILD new file mode 100644 index 0000000000..a242f76b1a --- /dev/null +++ b/prepare/r-genomicdistributions/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenomicDistributions +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GenomicDistributions: fast analysis of genomic intervals with Bioconductor' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-biostrings + r-data.table + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-plyr + r-reshape2 +) +optdepends=( + r-annotationfilter + r-biocstyle + r-bsgenome + r-ensembldb + r-extrafont + r-genomicfeatures + r-knitr + r-rmarkdown + r-rtracklayer + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomicdistributions/lilac.py b/prepare/r-genomicdistributions/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomicdistributions/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomicdistributions/lilac.yaml b/prepare/r-genomicdistributions/lilac.yaml new file mode 100644 index 0000000000..0f7a42700f --- /dev/null +++ b/prepare/r-genomicdistributions/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-data.table +- r-dplyr +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-plyr +- r-reshape2 +update_on: +- regex: GenomicDistributions_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GenomicDistributions diff --git a/prepare/r-genomicfeatures/PKGBUILD b/prepare/r-genomicfeatures/PKGBUILD new file mode 100644 index 0000000000..1dbae7db39 --- /dev/null +++ b/prepare/r-genomicfeatures/PKGBUILD @@ -0,0 +1,66 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenomicFeatures +_pkgver=1.46.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Conveniently import and query gene models' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biobase + r-biocgenerics + r-biocio + r-biomart + r-biostrings + r-dbi + r-genomeinfodb + r-genomicranges + r-iranges + r-rcurl + r-rsqlite + r-rtracklayer + r-s4vectors + r-xvector +) +optdepends=( + r-biocstyle + r-bsgenome + r-bsgenome.celegans.ucsc.ce11 + r-bsgenome.dmelanogaster.ucsc.dm3 + r-bsgenome.hsapiens.ucsc.hg19 + r-ensembldb + r-fdb.ucsc.trnas + r-genomicalignments + r-knitr + r-mirbase.db + r-org.hs.eg.db + r-org.mm.eg.db + r-pasillabamsubset + r-rmariadb + r-rsamtools + r-runit + r-snplocs.hsapiens.dbsnp144.grch38 + r-txdb.celegans.ucsc.ce11.ensgene + r-txdb.dmelanogaster.ucsc.dm3.ensgene + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.hsapiens.ucsc.hg19.lincrnastranscripts + r-txdb.hsapiens.ucsc.hg38.knowngene + r-txdb.mmusculus.ucsc.mm10.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomicfeatures/lilac.py b/prepare/r-genomicfeatures/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomicfeatures/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomicfeatures/lilac.yaml b/prepare/r-genomicfeatures/lilac.yaml new file mode 100644 index 0000000000..1beba8cee4 --- /dev/null +++ b/prepare/r-genomicfeatures/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-biocio +- r-biomart +- r-biostrings +- r-dbi +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rcurl +- r-rsqlite +- r-rtracklayer +- r-s4vectors +- r-xvector +update_on: +- regex: GenomicFeatures_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GenomicFeatures diff --git a/prepare/r-genomicfiles/PKGBUILD b/prepare/r-genomicfiles/PKGBUILD new file mode 100644 index 0000000000..3113c9d664 --- /dev/null +++ b/prepare/r-genomicfiles/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenomicFiles +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Distributed computing by file or by range' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-matrixgenerics + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-biocstyle + r-biostrings + r-deepsnv + r-genefilter + r-homo.sapiens + r-rnaseqdata.hnrnpc.bam.chr14 + r-runit + r-snpstats +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomicfiles/lilac.py b/prepare/r-genomicfiles/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomicfiles/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomicfiles/lilac.yaml b/prepare/r-genomicfiles/lilac.yaml new file mode 100644 index 0000000000..6105035801 --- /dev/null +++ b/prepare/r-genomicfiles/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-matrixgenerics +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: GenomicFiles_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GenomicFiles diff --git a/prepare/r-genomicinstability/PKGBUILD b/prepare/r-genomicinstability/PKGBUILD new file mode 100644 index 0000000000..7f84b99dc9 --- /dev/null +++ b/prepare/r-genomicinstability/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=genomicInstability +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genomic Instability estimation for scRNA-Seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-checkmate + r-mixtools + r-summarizedexperiment +) +optdepends=( + r-experimenthub + r-proc + r-singlecellexperiment +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomicinstability/lilac.py b/prepare/r-genomicinstability/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomicinstability/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomicinstability/lilac.yaml b/prepare/r-genomicinstability/lilac.yaml new file mode 100644 index 0000000000..9bcf54df60 --- /dev/null +++ b/prepare/r-genomicinstability/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-checkmate +- r-mixtools +- r-summarizedexperiment +update_on: +- regex: genomicInstability_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/genomicInstability diff --git a/prepare/r-genomicinteractions/PKGBUILD b/prepare/r-genomicinteractions/PKGBUILD new file mode 100644 index 0000000000..faf2ed65c8 --- /dev/null +++ b/prepare/r-genomicinteractions/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenomicInteractions +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities for handling genomic interaction data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-data.table + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gridextra + r-gviz + r-igraph + r-interactionset + r-iranges + r-rsamtools + r-rtracklayer + r-s4vectors + r-stringr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomicinteractions/lilac.py b/prepare/r-genomicinteractions/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomicinteractions/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomicinteractions/lilac.yaml b/prepare/r-genomicinteractions/lilac.yaml new file mode 100644 index 0000000000..006b09d6c8 --- /dev/null +++ b/prepare/r-genomicinteractions/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-data.table +- r-dplyr +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-gridextra +- r-gviz +- r-igraph +- r-interactionset +- r-iranges +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-stringr +update_on: +- regex: GenomicInteractions_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GenomicInteractions diff --git a/prepare/r-genomicozone/PKGBUILD b/prepare/r-genomicozone/PKGBUILD new file mode 100644 index 0000000000..00b28d7f6c --- /dev/null +++ b/prepare/r-genomicozone/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenomicOZone +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Delineate outstanding genomic zones of differential gene activity' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biomart + r-ckmeans.1d.dp + r-genomeinfodb + r-genomicranges + r-ggbio + r-ggplot2 + r-gridextra + r-iranges + r-lsr + r-plyr + r-rdpack + r-s4vectors +) +optdepends=( + r-geoquery + r-knitr + r-readxl + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomicozone/lilac.py b/prepare/r-genomicozone/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomicozone/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomicozone/lilac.yaml b/prepare/r-genomicozone/lilac.yaml new file mode 100644 index 0000000000..500c24debc --- /dev/null +++ b/prepare/r-genomicozone/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-ckmeans.1d.dp +- r-genomeinfodb +- r-genomicranges +- r-ggbio +- r-ggplot2 +- r-gridextra +- r-iranges +- r-lsr +- r-plyr +- r-rdpack +- r-s4vectors +update_on: +- regex: GenomicOZone_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GenomicOZone diff --git a/prepare/r-genomicranges/PKGBUILD b/prepare/r-genomicranges/PKGBUILD new file mode 100644 index 0000000000..646908e7a2 --- /dev/null +++ b/prepare/r-genomicranges/PKGBUILD @@ -0,0 +1,68 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenomicRanges +_pkgver=1.46.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Representation and manipulation of genomic intervals' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-genomeinfodb + r-iranges + r-s4vectors + r-xvector +) +optdepends=( + r-annotate + r-annotationdbi + r-annotationhub + r-biobase + r-biocstyle + r-biostrings + r-bsgenome + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.mmusculus.ucsc.mm10 + r-bsgenome.scerevisiae.ucsc.saccer2 + r-deseq2 + r-dexseq + r-digest + r-edger + r-genomicalignments + r-genomicfeatures + r-gviz + r-hgu95av2.db + r-hgu95av2probe + r-kegggraph + r-keggrest + r-knitr + r-matrix + r-pasillabamsubset + r-rmarkdown + r-rnaseqdata.hnrnpc.bam.chr14 + r-rsamtools + r-rtracklayer + r-runit + r-summarizedexperiment + r-txdb.athaliana.biomart.plantsmart22 + r-txdb.dmelanogaster.ucsc.dm3.ensgene + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.mmusculus.ucsc.mm10.knowngene + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomicranges/lilac.py b/prepare/r-genomicranges/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomicranges/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomicranges/lilac.yaml b/prepare/r-genomicranges/lilac.yaml new file mode 100644 index 0000000000..a0e1f0933e --- /dev/null +++ b/prepare/r-genomicranges/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomeinfodb +- r-iranges +- r-s4vectors +- r-xvector +update_on: +- regex: GenomicRanges_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GenomicRanges diff --git a/prepare/r-genomicscores/PKGBUILD b/prepare/r-genomicscores/PKGBUILD new file mode 100644 index 0000000000..223d7c531c --- /dev/null +++ b/prepare/r-genomicscores/PKGBUILD @@ -0,0 +1,61 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenomicScores +_pkgver=2.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Infrastructure to work with genomewide position-specific scores' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationhub + r-biobase + r-biocfilecache + r-biocgenerics + r-biocmanager + r-biostrings + r-delayedarray + r-genomeinfodb + r-genomicranges + r-hdf5array + r-iranges + r-rhdf5 + r-s4vectors + r-xml +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-data.table + r-dt + r-gwascat + r-knitr + r-mafdb.1kgenomes.phase1.hs37d5 + r-magrittr + r-phastcons100way.ucsc.hg19 + r-rcolorbrewer + r-rmarkdown + r-runit + r-shiny + r-shinycustomloader + r-shinydashboard + r-shinyjs + r-snplocs.hsapiens.dbsnp144.grch37 + r-txdb.hsapiens.ucsc.hg19.knowngene + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomicscores/lilac.py b/prepare/r-genomicscores/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomicscores/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomicscores/lilac.yaml b/prepare/r-genomicscores/lilac.yaml new file mode 100644 index 0000000000..bdd4088303 --- /dev/null +++ b/prepare/r-genomicscores/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-biobase +- r-biocfilecache +- r-biocgenerics +- r-biocmanager +- r-biostrings +- r-delayedarray +- r-genomeinfodb +- r-genomicranges +- r-hdf5array +- r-iranges +- r-rhdf5 +- r-s4vectors +- r-xml +update_on: +- regex: GenomicScores_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GenomicScores diff --git a/prepare/r-genomicstate/PKGBUILD b/prepare/r-genomicstate/PKGBUILD new file mode 100644 index 0000000000..f2a4e4191d --- /dev/null +++ b/prepare/r-genomicstate/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenomicState +_pkgver=0.99.15 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Build and access GenomicState objects for use with derfinder tools from sources like Gencode' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-annotationhub + r-bumphunter + r-derfinder + r-genomeinfodb + r-genomicfeatures + r-iranges + r-org.hs.eg.db + r-rtracklayer +) +optdepends=( + r-annotationhubdata + r-biocstyle + r-covr + r-derfinderplot + r-genomicranges + r-glue + r-knitr + r-refmanager + r-rmarkdown + r-sessioninfo + r-testthat +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomicstate/lilac.py b/prepare/r-genomicstate/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomicstate/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomicstate/lilac.yaml b/prepare/r-genomicstate/lilac.yaml new file mode 100644 index 0000000000..295d6fc7bc --- /dev/null +++ b/prepare/r-genomicstate/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-bumphunter +- r-derfinder +- r-genomeinfodb +- r-genomicfeatures +- r-iranges +- r-org.hs.eg.db +- r-rtracklayer +update_on: +- regex: GenomicState_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GenomicState diff --git a/prepare/r-genomicsupersignature/PKGBUILD b/prepare/r-genomicsupersignature/PKGBUILD new file mode 100644 index 0000000000..c25441bc77 --- /dev/null +++ b/prepare/r-genomicsupersignature/PKGBUILD @@ -0,0 +1,61 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenomicSuperSignature +_pkgver=1.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interpretation of RNA-seq experiments through robust, efficient comparison to public databases' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocfilecache + r-complexheatmap + r-dplyr + r-flextable + r-ggplot2 + r-ggpubr + r-plotly + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-bcellviper + r-biocmanager + r-biocstyle + r-circlize + r-cluster + r-clusterprofiler + r-devtools + r-enrichmentbrowser + r-forcats + r-knitr + r-msigdbr + r-pkgdown + r-rcolorbrewer + r-readr + r-reshape2 + r-rmarkdown + r-roxygen2 + r-stats + r-testthat + r-tibble + r-usethis + r-utils + r-wordcloud +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomicsupersignature/lilac.py b/prepare/r-genomicsupersignature/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomicsupersignature/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomicsupersignature/lilac.yaml b/prepare/r-genomicsupersignature/lilac.yaml new file mode 100644 index 0000000000..b3ea459336 --- /dev/null +++ b/prepare/r-genomicsupersignature/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocfilecache +- r-complexheatmap +- r-dplyr +- r-flextable +- r-ggplot2 +- r-ggpubr +- r-plotly +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: GenomicSuperSignature_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GenomicSuperSignature diff --git a/prepare/r-genomictools.filehandler/PKGBUILD b/prepare/r-genomictools.filehandler/PKGBUILD new file mode 100644 index 0000000000..6fe9f45f95 --- /dev/null +++ b/prepare/r-genomictools.filehandler/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenomicTools.fileHandler +_pkgver=0.1.5.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='File Handlers for Genomic Data Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-snpstats +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomictools.filehandler/lilac.py b/prepare/r-genomictools.filehandler/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomictools.filehandler/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomictools.filehandler/lilac.yaml b/prepare/r-genomictools.filehandler/lilac.yaml new file mode 100644 index 0000000000..47fcd9a7a8 --- /dev/null +++ b/prepare/r-genomictools.filehandler/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-snpstats +update_on: +- regex: GenomicTools.fileHandler_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=GenomicTools.fileHandler diff --git a/prepare/r-genomictools/PKGBUILD b/prepare/r-genomictools/PKGBUILD new file mode 100644 index 0000000000..de3d2a1b8f --- /dev/null +++ b/prepare/r-genomictools/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenomicTools +_pkgver=0.2.9.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Collection of Tools for Genomic Data Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-circlize + r-data.table + r-genomictools.filehandler + r-gmwt + r-rcpp + r-rcpparmadillo + r-snpstats + r-stringr +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomictools/lilac.py b/prepare/r-genomictools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomictools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomictools/lilac.yaml b/prepare/r-genomictools/lilac.yaml new file mode 100644 index 0000000000..84f550a454 --- /dev/null +++ b/prepare/r-genomictools/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circlize +- r-data.table +- r-genomictools.filehandler +- r-gmwt +- r-rcpp +- r-rcpparmadillo +- r-snpstats +- r-stringr +update_on: +- regex: GenomicTools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=GenomicTools diff --git a/prepare/r-genomictuples/PKGBUILD b/prepare/r-genomictuples/PKGBUILD new file mode 100644 index 0000000000..5e403cba8b --- /dev/null +++ b/prepare/r-genomictuples/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenomicTuples +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Representation and Manipulation of Genomic Tuples' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-data.table + r-genomeinfodb + r-genomicranges + r-iranges + r-rcpp + r-s4vectors +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genomictuples/lilac.py b/prepare/r-genomictuples/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genomictuples/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genomictuples/lilac.yaml b/prepare/r-genomictuples/lilac.yaml new file mode 100644 index 0000000000..8475deec27 --- /dev/null +++ b/prepare/r-genomictuples/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-data.table +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rcpp +- r-s4vectors +update_on: +- regex: GenomicTuples_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GenomicTuples diff --git a/prepare/r-genotypeeval/PKGBUILD b/prepare/r-genotypeeval/PKGBUILD new file mode 100644 index 0000000000..be303e9e8f --- /dev/null +++ b/prepare/r-genotypeeval/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=genotypeeval +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='QA/QC of a gVCF or VCF file' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-rtracklayer + r-variantannotation +) +optdepends=( + r-rmarkdown + r-snplocs.hsapiens.dbsnp141.grch38 + r-testthat + r-txdb.hsapiens.ucsc.hg38.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genotypeeval/lilac.py b/prepare/r-genotypeeval/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genotypeeval/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genotypeeval/lilac.yaml b/prepare/r-genotypeeval/lilac.yaml new file mode 100644 index 0000000000..bb9b659c8c --- /dev/null +++ b/prepare/r-genotypeeval/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-rtracklayer +- r-variantannotation +update_on: +- regex: genotypeeval_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/genotypeeval diff --git a/prepare/r-genphen/PKGBUILD b/prepare/r-genphen/PKGBUILD new file mode 100644 index 0000000000..a94d285758 --- /dev/null +++ b/prepare/r-genphen/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=genphen +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='genphen: tool for quantification of genotype-phenotype associations in genome wide association studies (GWAS)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-doparallel + r-e1071 + r-foreach + r-ranger + r-rcpp + r-rpref + r-rstan +) +optdepends=( + r-ape + r-ggplot2 + r-ggrepel + r-gridextra + r-knitr + r-reshape + r-testthat + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genphen/lilac.py b/prepare/r-genphen/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genphen/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genphen/lilac.yaml b/prepare/r-genphen/lilac.yaml new file mode 100644 index 0000000000..d107a220d0 --- /dev/null +++ b/prepare/r-genphen/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-doparallel +- r-e1071 +- r-foreach +- r-ranger +- r-rcpp +- r-rpref +- r-rstan +update_on: +- regex: genphen_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/genphen diff --git a/prepare/r-gensa/PKGBUILD b/prepare/r-gensa/PKGBUILD new file mode 100644 index 0000000000..0d764145ac --- /dev/null +++ b/prepare/r-gensa/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenSA +_pkgver=1.1.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generalized Simulated Annealing' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gensa/lilac.py b/prepare/r-gensa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gensa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gensa/lilac.yaml b/prepare/r-gensa/lilac.yaml new file mode 100644 index 0000000000..bc7d866d47 --- /dev/null +++ b/prepare/r-gensa/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: GenSA_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=GenSA diff --git a/prepare/r-genvisr/PKGBUILD b/prepare/r-genvisr/PKGBUILD new file mode 100644 index 0000000000..d134a62bde --- /dev/null +++ b/prepare/r-genvisr/PKGBUILD @@ -0,0 +1,62 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GenVisR +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genomic Visualizations in R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocgenerics + r-biomart + r-biostrings + r-bsgenome + r-data.table + r-dbi + r-ffield + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-gridextra + r-gtable + r-gtools + r-iranges + r-plyr + r-reshape2 + r-rsamtools + r-scales + r-variantannotation + r-viridis +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.hsapiens.ucsc.hg38 + r-formatr + r-knitr + r-rmarkdown + r-rmysql + r-roxygen2 + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.hsapiens.ucsc.hg38.knowngene + r-vdiffr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-genvisr/lilac.py b/prepare/r-genvisr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-genvisr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-genvisr/lilac.yaml b/prepare/r-genvisr/lilac.yaml new file mode 100644 index 0000000000..87ef6ee84d --- /dev/null +++ b/prepare/r-genvisr/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-biomart +- r-biostrings +- r-bsgenome +- r-data.table +- r-dbi +- r-ffield +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-gridextra +- r-gtable +- r-gtools +- r-iranges +- r-plyr +- r-reshape2 +- r-rsamtools +- r-scales +- r-variantannotation +- r-viridis +update_on: +- regex: GenVisR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GenVisR diff --git a/prepare/r-geodiff/PKGBUILD b/prepare/r-geodiff/PKGBUILD new file mode 100644 index 0000000000..5b594e2aca --- /dev/null +++ b/prepare/r-geodiff/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GeoDiff +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Count model based differential expression and normalization on GeoMx RNA data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-geomxtools + r-lme4 + r-nanostringnctools + r-plyr + r-rcpp + r-rcpparmadillo + r-robust + r-roptim + r-testthat + r-withr +) +optdepends=( + r-dplyr + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geodiff/lilac.py b/prepare/r-geodiff/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geodiff/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geodiff/lilac.yaml b/prepare/r-geodiff/lilac.yaml new file mode 100644 index 0000000000..de2bd6f526 --- /dev/null +++ b/prepare/r-geodiff/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-geomxtools +- r-lme4 +- r-nanostringnctools +- r-plyr +- r-rcpp +- r-rcpparmadillo +- r-robust +- r-roptim +- r-testthat +- r-withr +update_on: +- regex: GeoDiff_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GeoDiff diff --git a/prepare/r-geoexplorer/PKGBUILD b/prepare/r-geoexplorer/PKGBUILD new file mode 100644 index 0000000000..73368080ac --- /dev/null +++ b/prepare/r-geoexplorer/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GEOexplorer +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GEOexplorer: an R/Bioconductor package for gene expression analysis and visualisation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-dt + r-factoextra + r-geoquery + r-ggplot2 + r-heatmaply + r-htmltools + r-impute + r-limma + r-maptools + r-pheatmap + r-plotly + r-scales + r-shiny + r-shinybs + r-shinybusy + r-shinyheatmaply + r-stringr + r-umap +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat + r-usethis +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geoexplorer/lilac.py b/prepare/r-geoexplorer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geoexplorer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geoexplorer/lilac.yaml b/prepare/r-geoexplorer/lilac.yaml new file mode 100644 index 0000000000..6bb6787a49 --- /dev/null +++ b/prepare/r-geoexplorer/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-dt +- r-factoextra +- r-geoquery +- r-ggplot2 +- r-heatmaply +- r-htmltools +- r-impute +- r-limma +- r-maptools +- r-pheatmap +- r-plotly +- r-scales +- r-shiny +- r-shinybs +- r-shinybusy +- r-shinyheatmaply +- r-stringr +- r-umap +update_on: +- regex: GEOexplorer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GEOexplorer diff --git a/prepare/r-geofastq/PKGBUILD b/prepare/r-geofastq/PKGBUILD new file mode 100644 index 0000000000..82cfa0b4b1 --- /dev/null +++ b/prepare/r-geofastq/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GEOfastq +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Downloads ENA Fastqs With GEO Accessions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-doparallel + r-foreach + r-plyr + r-rcurl + r-rvest + r-stringr + r-xml2 +) +optdepends=( + r-bioccheck + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geofastq/lilac.py b/prepare/r-geofastq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geofastq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geofastq/lilac.yaml b/prepare/r-geofastq/lilac.yaml new file mode 100644 index 0000000000..9cfa9937e6 --- /dev/null +++ b/prepare/r-geofastq/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-foreach +- r-plyr +- r-rcurl +- r-rvest +- r-stringr +- r-xml2 +update_on: +- regex: GEOfastq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GEOfastq diff --git a/prepare/r-geomap/PKGBUILD b/prepare/r-geomap/PKGBUILD new file mode 100644 index 0000000000..bb3d93df2b --- /dev/null +++ b/prepare/r-geomap/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GEOmap +_pkgver=2.4-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Topographic and Geologic Mapping' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-fields + r-mba + r-rpmg + r-splancs +) +optdepends=( + r-geomapdata + r-maps + r-rfoc +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geomap/lilac.py b/prepare/r-geomap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geomap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geomap/lilac.yaml b/prepare/r-geomap/lilac.yaml new file mode 100644 index 0000000000..ad7732ec18 --- /dev/null +++ b/prepare/r-geomap/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fields +- r-mba +- r-rpmg +- r-splancs +update_on: +- regex: GEOmap_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=GEOmap diff --git a/prepare/r-geometadb/PKGBUILD b/prepare/r-geometadb/PKGBUILD new file mode 100644 index 0000000000..6c7fd00a40 --- /dev/null +++ b/prepare/r-geometadb/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GEOmetadb +_pkgver=1.56.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A compilation of metadata from NCBI GEO' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-geoquery + r-rsqlite +) +optdepends=( + r-dplyr + r-knitr + r-rmarkdown + r-tm + r-wordcloud +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geometadb/lilac.py b/prepare/r-geometadb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geometadb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geometadb/lilac.yaml b/prepare/r-geometadb/lilac.yaml new file mode 100644 index 0000000000..4b9e77fa2f --- /dev/null +++ b/prepare/r-geometadb/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-geoquery +- r-rsqlite +update_on: +- regex: GEOmetadb_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GEOmetadb diff --git a/prepare/r-geometry/PKGBUILD b/prepare/r-geometry/PKGBUILD new file mode 100644 index 0000000000..d132a8172a --- /dev/null +++ b/prepare/r-geometry/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=geometry +_pkgver=0.4.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mesh Generation and Surface Tessellation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-linprog + r-lpsolve + r-magic + r-rcpp + r-rcppprogress +) +optdepends=( + r-r.matlab + r-rgl + r-spelling + r-testthat + r-tripack +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geometry/lilac.py b/prepare/r-geometry/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geometry/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geometry/lilac.yaml b/prepare/r-geometry/lilac.yaml new file mode 100644 index 0000000000..0f81ebef72 --- /dev/null +++ b/prepare/r-geometry/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-linprog +- r-lpsolve +- r-magic +- r-rcpp +- r-rcppprogress +update_on: +- regex: geometry_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=geometry diff --git a/prepare/r-geomxtools/PKGBUILD b/prepare/r-geomxtools/PKGBUILD new file mode 100644 index 0000000000..431960a400 --- /dev/null +++ b/prepare/r-geomxtools/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GeomxTools +_pkgver=2.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='NanoString GeoMx Tools' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-biocgenerics + r-data.table + r-dplyr + r-envstats + r-lmertest + r-nanostringnctools + r-outliers + r-readxl + r-reshape2 + r-rjson + r-s4vectors +) +optdepends=( + r-ggiraph + r-knitr + r-parallel + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geomxtools/lilac.py b/prepare/r-geomxtools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geomxtools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geomxtools/lilac.yaml b/prepare/r-geomxtools/lilac.yaml new file mode 100644 index 0000000000..88d74e20bd --- /dev/null +++ b/prepare/r-geomxtools/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-data.table +- r-dplyr +- r-envstats +- r-lmertest +- r-nanostringnctools +- r-outliers +- r-readxl +- r-reshape2 +- r-rjson +- r-s4vectors +update_on: +- regex: GeomxTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GeomxTools diff --git a/prepare/r-geoquery/PKGBUILD b/prepare/r-geoquery/PKGBUILD new file mode 100644 index 0000000000..fc4935cc06 --- /dev/null +++ b/prepare/r-geoquery/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GEOquery +_pkgver=2.62.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Get data from NCBI Gene Expression Omnibus (GEO)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-data.table + r-dplyr + r-httr + r-limma + r-magrittr + r-r.utils + r-readr + r-tidyr + r-xml2 +) +optdepends=( + r-biocgenerics + r-covr + r-knitr + r-markdown + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geoquery/lilac.py b/prepare/r-geoquery/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geoquery/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geoquery/lilac.yaml b/prepare/r-geoquery/lilac.yaml new file mode 100644 index 0000000000..ef690b88f9 --- /dev/null +++ b/prepare/r-geoquery/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-data.table +- r-dplyr +- r-httr +- r-limma +- r-magrittr +- r-r.utils +- r-readr +- r-tidyr +- r-xml2 +update_on: +- regex: GEOquery_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GEOquery diff --git a/prepare/r-geosubmission/PKGBUILD b/prepare/r-geosubmission/PKGBUILD new file mode 100644 index 0000000000..f0561d8983 --- /dev/null +++ b/prepare/r-geosubmission/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GEOsubmission +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Prepares microarray data for submission to GEO' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geosubmission/lilac.py b/prepare/r-geosubmission/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geosubmission/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geosubmission/lilac.yaml b/prepare/r-geosubmission/lilac.yaml new file mode 100644 index 0000000000..0b19351607 --- /dev/null +++ b/prepare/r-geosubmission/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +update_on: +- regex: GEOsubmission_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GEOsubmission diff --git a/prepare/r-gep2pep/PKGBUILD b/prepare/r-gep2pep/PKGBUILD new file mode 100644 index 0000000000..96ce952160 --- /dev/null +++ b/prepare/r-gep2pep/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gep2pep +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Creation and Analysis of Pathway Expression Profiles (PEPs)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-digest + r-foreach + r-gseabase + r-iterators + r-repo + r-rhdf5 + r-xml +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat + r-writexls +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gep2pep/lilac.py b/prepare/r-gep2pep/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gep2pep/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gep2pep/lilac.yaml b/prepare/r-gep2pep/lilac.yaml new file mode 100644 index 0000000000..b51f43204c --- /dev/null +++ b/prepare/r-gep2pep/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-digest +- r-foreach +- r-gseabase +- r-iterators +- r-repo +- r-rhdf5 +- r-xml +update_on: +- regex: gep2pep_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gep2pep diff --git a/prepare/r-gert/PKGBUILD b/prepare/r-gert/PKGBUILD new file mode 100644 index 0000000000..cf33e37f65 --- /dev/null +++ b/prepare/r-gert/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: libgit2 (>= 0.26): libgit2-devel (rpm) orlibgit2-dev (deb) +# Maintainer: Guoyi Zhang + +_pkgname=gert +_pkgver=1.5.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Simple Git Client for R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-askpass + r-credentials + r-openssl + r-rstudioapi + r-sys + r-zip +) +optdepends=( + r-knitr + r-rmarkdown + r-spelling + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gert/lilac.py b/prepare/r-gert/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gert/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gert/lilac.yaml b/prepare/r-gert/lilac.yaml new file mode 100644 index 0000000000..4cf4a2e484 --- /dev/null +++ b/prepare/r-gert/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-askpass +- r-credentials +- r-openssl +- r-rstudioapi +- r-sys +- r-zip +update_on: +- regex: gert_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gert diff --git a/prepare/r-gesper/PKGBUILD b/prepare/r-gesper/PKGBUILD new file mode 100644 index 0000000000..4c8fef1842 --- /dev/null +++ b/prepare/r-gesper/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gespeR +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene-Specific Phenotype EstimatoR' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biomart + r-cellhts2 + r-doparallel + r-dplyr + r-foreach + r-ggplot2 + r-glmnet + r-reshape2 +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gesper/lilac.py b/prepare/r-gesper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gesper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gesper/lilac.yaml b/prepare/r-gesper/lilac.yaml new file mode 100644 index 0000000000..387031a3c8 --- /dev/null +++ b/prepare/r-gesper/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biomart +- r-cellhts2 +- r-doparallel +- r-dplyr +- r-foreach +- r-ggplot2 +- r-glmnet +- r-reshape2 +update_on: +- regex: gespeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gespeR diff --git a/prepare/r-getdee2/PKGBUILD b/prepare/r-getdee2/PKGBUILD new file mode 100644 index 0000000000..748f624611 --- /dev/null +++ b/prepare/r-getdee2/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=getDEE2 +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Programmatic access to the DEE2 RNA expression dataset' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-htm2txt + r-summarizedexperiment +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-getdee2/lilac.py b/prepare/r-getdee2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-getdee2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-getdee2/lilac.yaml b/prepare/r-getdee2/lilac.yaml new file mode 100644 index 0000000000..c919d3e39b --- /dev/null +++ b/prepare/r-getdee2/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htm2txt +- r-summarizedexperiment +update_on: +- regex: getDEE2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/getDEE2 diff --git a/prepare/r-getopt/PKGBUILD b/prepare/r-getopt/PKGBUILD new file mode 100644 index 0000000000..95f9b03a96 --- /dev/null +++ b/prepare/r-getopt/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=getopt +_pkgver=1.20.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="C-Like 'getopt' Behavior" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-getopt/lilac.py b/prepare/r-getopt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-getopt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-getopt/lilac.yaml b/prepare/r-getopt/lilac.yaml new file mode 100644 index 0000000000..0a0d08c7c3 --- /dev/null +++ b/prepare/r-getopt/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: getopt_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=getopt diff --git a/prepare/r-getoptlong/PKGBUILD b/prepare/r-getoptlong/PKGBUILD new file mode 100644 index 0000000000..bbf4b56654 --- /dev/null +++ b/prepare/r-getoptlong/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: Perl, Getopt::Long +# Maintainer: Guoyi Zhang + +_pkgname=GetoptLong +_pkgver=1.0.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Parsing Command-Line Arguments and Simple Variable Interpolation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-crayon + r-globaloptions + r-rjson +) +optdepends=( + r-knitr + r-markdown + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-getoptlong/lilac.py b/prepare/r-getoptlong/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-getoptlong/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-getoptlong/lilac.yaml b/prepare/r-getoptlong/lilac.yaml new file mode 100644 index 0000000000..b1b289c502 --- /dev/null +++ b/prepare/r-getoptlong/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-crayon +- r-globaloptions +- r-rjson +update_on: +- regex: GetoptLong_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=GetoptLong diff --git a/prepare/r-getpass/PKGBUILD b/prepare/r-getpass/PKGBUILD new file mode 100644 index 0000000000..8d2f14d2b3 --- /dev/null +++ b/prepare/r-getpass/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=getPass +_pkgver=0.2-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Masked User Input' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-rstudioapi +) +optdepends=( + r-argon2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-getpass/lilac.py b/prepare/r-getpass/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-getpass/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-getpass/lilac.yaml b/prepare/r-getpass/lilac.yaml new file mode 100644 index 0000000000..08857eb14a --- /dev/null +++ b/prepare/r-getpass/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rstudioapi +update_on: +- regex: getPass_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=getPass diff --git a/prepare/r-geva/PKGBUILD b/prepare/r-geva/PKGBUILD new file mode 100644 index 0000000000..53d5fb355e --- /dev/null +++ b/prepare/r-geva/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=geva +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Expression Variation Analysis (GEVA)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-dbscan + r-fastcluster + r-matrixstats +) +optdepends=( + r-devtools + r-knitr + r-limma + r-rmarkdown + r-roxygen2 + r-testthat + r-topgo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-geva/lilac.py b/prepare/r-geva/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-geva/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-geva/lilac.yaml b/prepare/r-geva/lilac.yaml new file mode 100644 index 0000000000..0b0dc84e8e --- /dev/null +++ b/prepare/r-geva/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dbscan +- r-fastcluster +- r-matrixstats +update_on: +- regex: geva_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/geva diff --git a/prepare/r-gewist/PKGBUILD b/prepare/r-gewist/PKGBUILD new file mode 100644 index 0000000000..8d8f89a719 --- /dev/null +++ b/prepare/r-gewist/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GEWIST +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Environment Wide Interaction Search Threshold' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-car +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gewist/lilac.py b/prepare/r-gewist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gewist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gewist/lilac.yaml b/prepare/r-gewist/lilac.yaml new file mode 100644 index 0000000000..45c8ae9f65 --- /dev/null +++ b/prepare/r-gewist/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-car +update_on: +- regex: GEWIST_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GEWIST diff --git a/prepare/r-ggalluvial/PKGBUILD b/prepare/r-ggalluvial/PKGBUILD new file mode 100644 index 0000000000..d469449071 --- /dev/null +++ b/prepare/r-ggalluvial/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggalluvial +_pkgver=0.12.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Alluvial Plots in 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-ggplot2 + r-lazyeval + r-rlang + r-tidyr + r-tidyselect +) +optdepends=( + r-alluvial + r-babynames + r-ggfittext + r-ggrepel + r-grid + r-htmltools + r-knitr + r-rmarkdown + r-sessioninfo + r-shiny + r-sp + r-testthat + r-vdiffr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggalluvial/lilac.py b/prepare/r-ggalluvial/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggalluvial/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggalluvial/lilac.yaml b/prepare/r-ggalluvial/lilac.yaml new file mode 100644 index 0000000000..8fad0e5b61 --- /dev/null +++ b/prepare/r-ggalluvial/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-lazyeval +- r-rlang +- r-tidyr +- r-tidyselect +update_on: +- regex: ggalluvial_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggalluvial diff --git a/prepare/r-ggally/PKGBUILD b/prepare/r-ggally/PKGBUILD new file mode 100644 index 0000000000..a23e5c0c71 --- /dev/null +++ b/prepare/r-ggally/PKGBUILD @@ -0,0 +1,64 @@ +# system requirements: openssl +# Maintainer: Guoyi Zhang + +_pkgname=GGally +_pkgver=2.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Extension to 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-forcats + r-ggplot2 + r-gtable + r-lifecycle + r-plyr + r-progress + r-rcolorbrewer + r-reshape + r-rlang + r-scales + r-tidyr +) +optdepends=( + r-broom + r-broom.helpers + r-chemometrics + r-crosstalk + r-emmeans + r-geosphere + r-ggforce + r-hmisc + r-igraph + r-intergraph + r-knitr + r-labelled + r-mapproj + r-maps + r-network + r-nnet + r-rmarkdown + r-roxygen2 + r-scagnostics + r-sna + r-spelling + r-survival + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggally/lilac.py b/prepare/r-ggally/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggally/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggally/lilac.yaml b/prepare/r-ggally/lilac.yaml new file mode 100644 index 0000000000..f0ebf9c8ec --- /dev/null +++ b/prepare/r-ggally/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-forcats +- r-ggplot2 +- r-gtable +- r-lifecycle +- r-plyr +- r-progress +- r-rcolorbrewer +- r-reshape +- r-rlang +- r-scales +- r-tidyr +update_on: +- regex: GGally_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=GGally diff --git a/prepare/r-ggalt/PKGBUILD b/prepare/r-ggalt/PKGBUILD new file mode 100644 index 0000000000..59f77ed1f4 --- /dev/null +++ b/prepare/r-ggalt/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggalt +_pkgver=0.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Extra Coordinate Systems, 'Geoms', Statistical Transformations, Scales and Fonts for 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('AGPL') +depends=( + r + r-ash + r-dplyr + r-extrafont + r-ggplot2 + r-gtable + r-maps + r-plotly + r-proj4 + r-rcolorbrewer + r-scales + r-tibble +) +optdepends=( + r-ggthemes + r-gridextra + r-knitr + r-reshape2 + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggalt/lilac.py b/prepare/r-ggalt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggalt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggalt/lilac.yaml b/prepare/r-ggalt/lilac.yaml new file mode 100644 index 0000000000..54bf8465c2 --- /dev/null +++ b/prepare/r-ggalt/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ash +- r-dplyr +- r-extrafont +- r-ggplot2 +- r-gtable +- r-maps +- r-plotly +- r-proj4 +- r-rcolorbrewer +- r-scales +- r-tibble +update_on: +- regex: ggalt_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggalt diff --git a/prepare/r-gganimate/PKGBUILD b/prepare/r-gganimate/PKGBUILD new file mode 100644 index 0000000000..43437c364a --- /dev/null +++ b/prepare/r-gganimate/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gganimate +_pkgver=1.0.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Grammar of Animated Graphics' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-ggplot2 + r-glue + r-plyr + r-progress + r-rlang + r-scales + r-stringi + r-tweenr +) +optdepends=( + r-av + r-base64enc + r-covr + r-gifski + r-htmltools + r-knitr + r-magick + r-ragg + r-rmarkdown + r-svglite + r-testthat + r-transformr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gganimate/lilac.py b/prepare/r-gganimate/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gganimate/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gganimate/lilac.yaml b/prepare/r-gganimate/lilac.yaml new file mode 100644 index 0000000000..435c1f3edb --- /dev/null +++ b/prepare/r-gganimate/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-glue +- r-plyr +- r-progress +- r-rlang +- r-scales +- r-stringi +- r-tweenr +update_on: +- regex: gganimate_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gganimate diff --git a/prepare/r-ggbeeswarm/PKGBUILD b/prepare/r-ggbeeswarm/PKGBUILD new file mode 100644 index 0000000000..2aece114bb --- /dev/null +++ b/prepare/r-ggbeeswarm/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggbeeswarm +_pkgver=0.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Categorical Scatter (Violin Point) Plots' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-beeswarm + r-ggplot2 + r-vipor +) +optdepends=( + r-gridextra +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggbeeswarm/lilac.py b/prepare/r-ggbeeswarm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggbeeswarm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggbeeswarm/lilac.yaml b/prepare/r-ggbeeswarm/lilac.yaml new file mode 100644 index 0000000000..c57a3bddf5 --- /dev/null +++ b/prepare/r-ggbeeswarm/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beeswarm +- r-ggplot2 +- r-vipor +update_on: +- regex: ggbeeswarm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggbeeswarm diff --git a/prepare/r-ggbio/PKGBUILD b/prepare/r-ggbio/PKGBUILD new file mode 100644 index 0000000000..dc7750d0f6 --- /dev/null +++ b/prepare/r-ggbio/PKGBUILD @@ -0,0 +1,65 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggbio +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization tools for genomic data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-annotationfilter + r-biobase + r-biocgenerics + r-biostrings + r-biovizbase + r-bsgenome + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggally + r-ggplot2 + r-gridextra + r-gtable + r-hmisc + r-iranges + r-organismdbi + r-reshape2 + r-rlang + r-rsamtools + r-rtracklayer + r-s4vectors + r-scales + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-ensdb.hsapiens.v75 + r-homo.sapiens + r-knitr + r-testthat + r-tinytex + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.mmusculus.ucsc.mm9.knowngene + r-vsn +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggbio/lilac.py b/prepare/r-ggbio/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggbio/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggbio/lilac.yaml b/prepare/r-ggbio/lilac.yaml new file mode 100644 index 0000000000..4495c5ead1 --- /dev/null +++ b/prepare/r-ggbio/lilac.yaml @@ -0,0 +1,36 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationfilter +- r-biobase +- r-biocgenerics +- r-biostrings +- r-biovizbase +- r-bsgenome +- r-ensembldb +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggally +- r-ggplot2 +- r-gridextra +- r-gtable +- r-hmisc +- r-iranges +- r-organismdbi +- r-reshape2 +- r-rlang +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-scales +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: ggbio_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ggbio diff --git a/prepare/r-ggcorrplot/PKGBUILD b/prepare/r-ggcorrplot/PKGBUILD new file mode 100644 index 0000000000..96bc059800 --- /dev/null +++ b/prepare/r-ggcorrplot/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggcorrplot +_pkgver=0.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Visualization of a Correlation Matrix using 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-reshape2 +) +optdepends=( + r-knitr + r-spelling +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggcorrplot/lilac.py b/prepare/r-ggcorrplot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggcorrplot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggcorrplot/lilac.yaml b/prepare/r-ggcorrplot/lilac.yaml new file mode 100644 index 0000000000..39b713cd76 --- /dev/null +++ b/prepare/r-ggcorrplot/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-reshape2 +update_on: +- regex: ggcorrplot_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggcorrplot diff --git a/prepare/r-ggcyto/PKGBUILD b/prepare/r-ggcyto/PKGBUILD new file mode 100644 index 0000000000..1b2ea824d5 --- /dev/null +++ b/prepare/r-ggcyto/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggcyto +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualize Cytometry data with ggplot' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-data.table + r-flowcore + r-flowworkspace + r-ggplot2 + r-gridextra + r-hexbin + r-ncdfflow + r-plyr + r-rcolorbrewer + r-rlang + r-scales +) +optdepends=( + r-flowstats + r-flowviz + r-flowworkspacedata + r-ggridges + r-knitr + r-opencyto + r-rmarkdown + r-testthat + r-vdiffr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggcyto/lilac.py b/prepare/r-ggcyto/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggcyto/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggcyto/lilac.yaml b/prepare/r-ggcyto/lilac.yaml new file mode 100644 index 0000000000..ea4d5fa561 --- /dev/null +++ b/prepare/r-ggcyto/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-flowcore +- r-flowworkspace +- r-ggplot2 +- r-gridextra +- r-hexbin +- r-ncdfflow +- r-plyr +- r-rcolorbrewer +- r-rlang +- r-scales +update_on: +- regex: ggcyto_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ggcyto diff --git a/prepare/r-ggdendro/PKGBUILD b/prepare/r-ggdendro/PKGBUILD new file mode 100644 index 0000000000..a77dd04318 --- /dev/null +++ b/prepare/r-ggdendro/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggdendro +_pkgver=0.1.22 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Create Dendrograms and Tree Diagrams Using 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 +) +optdepends=( + r-cluster + r-knitr + r-rmarkdown + r-rpart + r-scales + r-spelling + r-testthat + r-tree +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggdendro/lilac.py b/prepare/r-ggdendro/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggdendro/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggdendro/lilac.yaml b/prepare/r-ggdendro/lilac.yaml new file mode 100644 index 0000000000..a9bebb3bd1 --- /dev/null +++ b/prepare/r-ggdendro/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +update_on: +- regex: ggdendro_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggdendro diff --git a/prepare/r-ggdist/PKGBUILD b/prepare/r-ggdist/PKGBUILD new file mode 100644 index 0000000000..45c2574e47 --- /dev/null +++ b/prepare/r-ggdist/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggdist +_pkgver=3.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualizations of Distributions and Uncertainty' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-distributional + r-dplyr + r-ggplot2 + r-hdinterval + r-rlang + r-scales + r-tibble + r-tidyselect + r-vctrs + r-withr +) +optdepends=( + r-beeswarm + r-broom + r-covr + r-cowplot + r-fda + r-forcats + r-gdtools + r-knitr + r-modelr + r-pkgdown + r-png + r-posterior + r-purrr + r-rmarkdown + r-svglite + r-testthat + r-tidyr + r-vdiffr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggdist/lilac.py b/prepare/r-ggdist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggdist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggdist/lilac.yaml b/prepare/r-ggdist/lilac.yaml new file mode 100644 index 0000000000..b67210a8ae --- /dev/null +++ b/prepare/r-ggdist/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-distributional +- r-dplyr +- r-ggplot2 +- r-hdinterval +- r-rlang +- r-scales +- r-tibble +- r-tidyselect +- r-vctrs +- r-withr +update_on: +- regex: ggdist_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggdist diff --git a/prepare/r-ggextra/PKGBUILD b/prepare/r-ggextra/PKGBUILD new file mode 100644 index 0000000000..92e6ae6783 --- /dev/null +++ b/prepare/r-ggextra/PKGBUILD @@ -0,0 +1,47 @@ +# system requirements: pandoc with https support +# Maintainer: Guoyi Zhang + +_pkgname=ggExtra +_pkgver=0.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Add Marginal Histograms to 'ggplot2', and More 'ggplot2' Enhancements" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-colourpicker + r-ggplot2 + r-gtable + r-miniui + r-r6 + r-scales + r-shiny + r-shinyjs +) +optdepends=( + r-devtools + r-fontquiver + r-knitr + r-rmarkdown + r-rstudioapi + r-svglite + r-testthat + r-vdiffr + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggextra/lilac.py b/prepare/r-ggextra/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggextra/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggextra/lilac.yaml b/prepare/r-ggextra/lilac.yaml new file mode 100644 index 0000000000..75b7cef8c6 --- /dev/null +++ b/prepare/r-ggextra/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colourpicker +- r-ggplot2 +- r-gtable +- r-miniui +- r-r6 +- r-scales +- r-shiny +- r-shinyjs +update_on: +- regex: ggExtra_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggExtra diff --git a/prepare/r-ggfittext/PKGBUILD b/prepare/r-ggfittext/PKGBUILD new file mode 100644 index 0000000000..89c1b05073 --- /dev/null +++ b/prepare/r-ggfittext/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggfittext +_pkgver=0.9.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Fit Text Inside a Box in 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-shades + r-stringi +) +optdepends=( + r-knitr + r-rmarkdown + r-spelling + r-testthat + r-vdiffr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggfittext/lilac.py b/prepare/r-ggfittext/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggfittext/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggfittext/lilac.yaml b/prepare/r-ggfittext/lilac.yaml new file mode 100644 index 0000000000..7920fd41df --- /dev/null +++ b/prepare/r-ggfittext/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-shades +- r-stringi +update_on: +- regex: ggfittext_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggfittext diff --git a/prepare/r-ggforce/PKGBUILD b/prepare/r-ggforce/PKGBUILD new file mode 100644 index 0000000000..b660be1241 --- /dev/null +++ b/prepare/r-ggforce/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggforce +_pkgver=0.3.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Accelerating 'ggplot2'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-ggplot2 + r-gtable + r-polyclip + r-rcpp + r-rcppeigen + r-rlang + r-scales + r-tidyselect + r-tweenr + r-withr +) +optdepends=( + r-concaveman + r-covr + r-deldir + r-reshape2 + r-sessioninfo + r-units +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggforce/lilac.py b/prepare/r-ggforce/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggforce/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggforce/lilac.yaml b/prepare/r-ggforce/lilac.yaml new file mode 100644 index 0000000000..3a4bbda4be --- /dev/null +++ b/prepare/r-ggforce/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gtable +- r-polyclip +- r-rcpp +- r-rcppeigen +- r-rlang +- r-scales +- r-tidyselect +- r-tweenr +- r-withr +update_on: +- regex: ggforce_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggforce diff --git a/prepare/r-ggformula/PKGBUILD b/prepare/r-ggformula/PKGBUILD new file mode 100644 index 0000000000..232b1c17aa --- /dev/null +++ b/prepare/r-ggformula/PKGBUILD @@ -0,0 +1,61 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggformula +_pkgver=0.10.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Formula Interface to the Grammar of Graphics' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-ggforce + r-ggplot2 + r-ggridges + r-ggstance + r-labelled + r-magrittr + r-mosaiccore + r-rlang + r-scales + r-stringr + r-tibble +) +optdepends=( + r-broom + r-covr + r-dplyr + r-ggplot2movies + r-ggthemes + r-knitr + r-lattice + r-lubridate + r-maps + r-maptools + r-mosaic + r-mosaicdata + r-palmerpenguins + r-purrr + r-rgeos + r-rmarkdown + r-sf + r-survival + r-testthat + r-tidyr + r-vdiffr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggformula/lilac.py b/prepare/r-ggformula/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggformula/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggformula/lilac.yaml b/prepare/r-ggformula/lilac.yaml new file mode 100644 index 0000000000..5c6863ed22 --- /dev/null +++ b/prepare/r-ggformula/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggforce +- r-ggplot2 +- r-ggridges +- r-ggstance +- r-labelled +- r-magrittr +- r-mosaiccore +- r-rlang +- r-scales +- r-stringr +- r-tibble +update_on: +- regex: ggformula_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggformula diff --git a/prepare/r-ggfortify/PKGBUILD b/prepare/r-ggfortify/PKGBUILD new file mode 100644 index 0000000000..e17a6d2af7 --- /dev/null +++ b/prepare/r-ggfortify/PKGBUILD @@ -0,0 +1,66 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggfortify +_pkgver=0.4.14 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data Visualization Tools for Statistical Analysis Results' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-ggplot2 + r-gridextra + r-scales + r-stringr + r-tibble + r-tidyr +) +optdepends=( + r-changepoint + r-cluster + r-dlm + r-fgarch + r-forecast + r-ggrepel + r-glmnet + r-grdevices + r-kfas + r-knitr + r-lfda + r-lintr + r-mapdata + r-markdown + r-mass + r-mswm + r-nlme + r-raster + r-rocr + r-sp + r-stats + r-strucchange + r-survival + r-testthat + r-timeseries + r-tseries + r-utils + r-vars + r-xts + r-zoo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggfortify/lilac.py b/prepare/r-ggfortify/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggfortify/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggfortify/lilac.yaml b/prepare/r-ggfortify/lilac.yaml new file mode 100644 index 0000000000..9da944f5b5 --- /dev/null +++ b/prepare/r-ggfortify/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-gridextra +- r-scales +- r-stringr +- r-tibble +- r-tidyr +update_on: +- regex: ggfortify_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggfortify diff --git a/prepare/r-ggfun/PKGBUILD b/prepare/r-ggfun/PKGBUILD new file mode 100644 index 0000000000..9c8f6c7d44 --- /dev/null +++ b/prepare/r-ggfun/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggfun +_pkgver=0.0.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Miscellaneous Functions for 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ggplot2 + r-rlang +) +optdepends=( + r-ggplotify + r-knitr + r-prettydoc + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggfun/lilac.py b/prepare/r-ggfun/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggfun/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggfun/lilac.yaml b/prepare/r-ggfun/lilac.yaml new file mode 100644 index 0000000000..9aac31048f --- /dev/null +++ b/prepare/r-ggfun/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-rlang +update_on: +- regex: ggfun_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggfun diff --git a/prepare/r-gghalves/PKGBUILD b/prepare/r-gghalves/PKGBUILD new file mode 100644 index 0000000000..bfb658151d --- /dev/null +++ b/prepare/r-gghalves/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gghalves +_pkgver=0.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Compose Half-Half Plots Using Your Favourite Geoms' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-ggplot2 + r-gtable +) +optdepends=( + r-dplyr + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gghalves/lilac.py b/prepare/r-gghalves/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gghalves/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gghalves/lilac.yaml b/prepare/r-gghalves/lilac.yaml new file mode 100644 index 0000000000..441e95c913 --- /dev/null +++ b/prepare/r-gghalves/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gtable +update_on: +- regex: gghalves_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gghalves diff --git a/prepare/r-gghighlight/PKGBUILD b/prepare/r-gghighlight/PKGBUILD new file mode 100644 index 0000000000..c634ca8fb8 --- /dev/null +++ b/prepare/r-gghighlight/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gghighlight +_pkgver=0.3.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Highlight Lines and Points in 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-ggplot2 + r-ggrepel + r-lifecycle + r-purrr + r-rlang + r-tibble +) +optdepends=( + r-knitr + r-rmarkdown + r-sf + r-testthat + r-vdiffr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gghighlight/lilac.py b/prepare/r-gghighlight/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gghighlight/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gghighlight/lilac.yaml b/prepare/r-gghighlight/lilac.yaml new file mode 100644 index 0000000000..2e12b8b6fd --- /dev/null +++ b/prepare/r-gghighlight/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-ggrepel +- r-lifecycle +- r-purrr +- r-rlang +- r-tibble +update_on: +- regex: gghighlight_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gghighlight diff --git a/prepare/r-ggiraph/PKGBUILD b/prepare/r-ggiraph/PKGBUILD new file mode 100644 index 0000000000..f4ef70bdd4 --- /dev/null +++ b/prepare/r-ggiraph/PKGBUILD @@ -0,0 +1,48 @@ +# system requirements: C++11, libpng +# Maintainer: Guoyi Zhang + +_pkgname=ggiraph +_pkgver=0.8.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Make 'ggplot2' Graphics Interactive" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-htmltools + r-htmlwidgets + r-purrr + r-rcpp + r-rlang + r-systemfonts + r-uuid +) +optdepends=( + r-dplyr + r-ggrepel + r-hexbin + r-knitr + r-maps + r-quantreg + r-rmarkdown + r-sf + r-shiny + r-tinytest + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggiraph/lilac.py b/prepare/r-ggiraph/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggiraph/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggiraph/lilac.yaml b/prepare/r-ggiraph/lilac.yaml new file mode 100644 index 0000000000..f5c2d5f82d --- /dev/null +++ b/prepare/r-ggiraph/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-htmltools +- r-htmlwidgets +- r-purrr +- r-rcpp +- r-rlang +- r-systemfonts +- r-uuid +update_on: +- regex: ggiraph_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggiraph diff --git a/prepare/r-ggm/PKGBUILD b/prepare/r-ggm/PKGBUILD new file mode 100644 index 0000000000..e358f9fab9 --- /dev/null +++ b/prepare/r-ggm/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggm +_pkgver=2.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Graphical Markov Models with Mixed Graphs' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-graph + r-igraph +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggm/lilac.py b/prepare/r-ggm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggm/lilac.yaml b/prepare/r-ggm/lilac.yaml new file mode 100644 index 0000000000..15651e8e07 --- /dev/null +++ b/prepare/r-ggm/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +- r-igraph +update_on: +- regex: ggm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggm diff --git a/prepare/r-ggmcmc/PKGBUILD b/prepare/r-ggmcmc/PKGBUILD new file mode 100644 index 0000000000..5a9cd18af2 --- /dev/null +++ b/prepare/r-ggmcmc/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggmcmc +_pkgver=1.5.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Analyzing MCMC Simulations from Bayesian Inference' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-ggally + r-ggplot2 + r-tidyr +) +optdepends=( + r-cairo + r-coda + r-extrafont + r-ggthemes + r-gridextra + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggmcmc/lilac.py b/prepare/r-ggmcmc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggmcmc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggmcmc/lilac.yaml b/prepare/r-ggmcmc/lilac.yaml new file mode 100644 index 0000000000..4d1188249e --- /dev/null +++ b/prepare/r-ggmcmc/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggally +- r-ggplot2 +- r-tidyr +update_on: +- regex: ggmcmc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggmcmc diff --git a/prepare/r-ggmsa/PKGBUILD b/prepare/r-ggmsa/PKGBUILD new file mode 100644 index 0000000000..e0e2b222d4 --- /dev/null +++ b/prepare/r-ggmsa/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggmsa +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Plot Multiple Sequence Alignment using 'ggplot2'" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-aplot + r-biostrings + r-dplyr + r-ggalt + r-ggforce + r-ggplot2 + r-magrittr + r-r4rna + r-rcolorbrewer + r-seqmagick + r-tidyr +) +optdepends=( + r-ape + r-biocstyle + r-cowplot + r-gggenes + r-ggnewscale + r-ggtree + r-ggtreeextra + r-kableextra + r-knitr + r-phangorn + r-readxl + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggmsa/lilac.py b/prepare/r-ggmsa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggmsa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggmsa/lilac.yaml b/prepare/r-ggmsa/lilac.yaml new file mode 100644 index 0000000000..c9d60e0672 --- /dev/null +++ b/prepare/r-ggmsa/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aplot +- r-biostrings +- r-dplyr +- r-ggalt +- r-ggforce +- r-ggplot2 +- r-magrittr +- r-r4rna +- r-rcolorbrewer +- r-seqmagick +- r-tidyr +update_on: +- regex: ggmsa_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ggmsa diff --git a/prepare/r-ggnetwork/PKGBUILD b/prepare/r-ggnetwork/PKGBUILD new file mode 100644 index 0000000000..08a3986653 --- /dev/null +++ b/prepare/r-ggnetwork/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggnetwork +_pkgver=0.5.10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Geometries to Plot Networks with 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-ggrepel + r-igraph + r-network + r-sna +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggnetwork/lilac.py b/prepare/r-ggnetwork/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggnetwork/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggnetwork/lilac.yaml b/prepare/r-ggnetwork/lilac.yaml new file mode 100644 index 0000000000..9d747526ec --- /dev/null +++ b/prepare/r-ggnetwork/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-ggrepel +- r-igraph +- r-network +- r-sna +update_on: +- regex: ggnetwork_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggnetwork diff --git a/prepare/r-ggnewscale/PKGBUILD b/prepare/r-ggnewscale/PKGBUILD new file mode 100644 index 0000000000..0d6da5e451 --- /dev/null +++ b/prepare/r-ggnewscale/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggnewscale +_pkgver=0.4.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Multiple Fill and Colour Scales in 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 +) +optdepends=( + r-covr + r-testthat + r-vdiffr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggnewscale/lilac.py b/prepare/r-ggnewscale/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggnewscale/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggnewscale/lilac.yaml b/prepare/r-ggnewscale/lilac.yaml new file mode 100644 index 0000000000..c39d7ad68a --- /dev/null +++ b/prepare/r-ggnewscale/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +update_on: +- regex: ggnewscale_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggnewscale diff --git a/prepare/r-ggpa/PKGBUILD b/prepare/r-ggpa/PKGBUILD new file mode 100644 index 0000000000..60d6be4a7d --- /dev/null +++ b/prepare/r-ggpa/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=GGPA +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggally + r-matrixstats + r-network + r-rcpp + r-rcpparmadillo + r-scales + r-sna +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggpa/lilac.py b/prepare/r-ggpa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggpa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggpa/lilac.yaml b/prepare/r-ggpa/lilac.yaml new file mode 100644 index 0000000000..179c867c7d --- /dev/null +++ b/prepare/r-ggpa/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggally +- r-matrixstats +- r-network +- r-rcpp +- r-rcpparmadillo +- r-scales +- r-sna +update_on: +- regex: GGPA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GGPA diff --git a/prepare/r-ggplot.multistats/PKGBUILD b/prepare/r-ggplot.multistats/PKGBUILD new file mode 100644 index 0000000000..f06ec075d5 --- /dev/null +++ b/prepare/r-ggplot.multistats/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggplot.multistats +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multiple Summary Statistics for Binned Stats/Geometries' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-hexbin + r-rlang + r-scales +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggplot.multistats/lilac.py b/prepare/r-ggplot.multistats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggplot.multistats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggplot.multistats/lilac.yaml b/prepare/r-ggplot.multistats/lilac.yaml new file mode 100644 index 0000000000..32869cab3f --- /dev/null +++ b/prepare/r-ggplot.multistats/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-hexbin +- r-rlang +- r-scales +update_on: +- regex: ggplot.multistats_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggplot.multistats diff --git a/prepare/r-ggplot2/PKGBUILD b/prepare/r-ggplot2/PKGBUILD new file mode 100644 index 0000000000..d547152015 --- /dev/null +++ b/prepare/r-ggplot2/PKGBUILD @@ -0,0 +1,64 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggplot2 +_pkgver=3.3.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Create Elegant Data Visualisations Using the Grammar of Graphics' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-digest + r-glue + r-gtable + r-isoband + r-rlang + r-scales + r-tibble + r-withr +) +optdepends=( + r-covr + r-dplyr + r-ggplot2movies + r-hexbin + r-hmisc + r-interp + r-knitr + r-lattice + r-mapproj + r-maps + r-maptools + r-multcomp + r-munsell + r-nlme + r-profvis + r-quantreg + r-ragg + r-rcolorbrewer + r-rgeos + r-rmarkdown + r-rpart + r-sf + r-sp + r-svglite + r-testthat + r-vdiffr + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggplot2/lilac.py b/prepare/r-ggplot2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggplot2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggplot2/lilac.yaml b/prepare/r-ggplot2/lilac.yaml new file mode 100644 index 0000000000..90a2d40c95 --- /dev/null +++ b/prepare/r-ggplot2/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-glue +- r-gtable +- r-isoband +- r-rlang +- r-scales +- r-tibble +- r-withr +update_on: +- regex: ggplot2_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggplot2 diff --git a/prepare/r-ggplotify/PKGBUILD b/prepare/r-ggplotify/PKGBUILD new file mode 100644 index 0000000000..ba55b718fc --- /dev/null +++ b/prepare/r-ggplotify/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggplotify +_pkgver=0.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Convert Plot to 'grob' or 'ggplot' Object" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ggplot2 + r-gridgraphics + r-yulab.utils +) +optdepends=( + r-aplot + r-colorspace + r-cowplot + r-ggimage + r-knitr + r-lattice + r-prettydoc + r-rmarkdown + r-utils + r-vcd +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggplotify/lilac.py b/prepare/r-ggplotify/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggplotify/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggplotify/lilac.yaml b/prepare/r-ggplotify/lilac.yaml new file mode 100644 index 0000000000..c7d5372821 --- /dev/null +++ b/prepare/r-ggplotify/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gridgraphics +- r-yulab.utils +update_on: +- regex: ggplotify_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggplotify diff --git a/prepare/r-ggpmisc/PKGBUILD b/prepare/r-ggpmisc/PKGBUILD new file mode 100644 index 0000000000..93dba8a0a9 --- /dev/null +++ b/prepare/r-ggpmisc/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggpmisc +_pkgver=0.4.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Miscellaneous Extensions to 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-generics + r-ggplot2 + r-ggpp + r-lmodel2 + r-lubridate + r-plyr + r-polynom + r-quantreg + r-rlang + r-scales + r-splus2r + r-tibble +) +optdepends=( + r-broom + r-broom.mixed + r-gginnards + r-ggrepel + r-knitr + r-nlme + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggpmisc/lilac.py b/prepare/r-ggpmisc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggpmisc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggpmisc/lilac.yaml b/prepare/r-ggpmisc/lilac.yaml new file mode 100644 index 0000000000..68d7ef3ca4 --- /dev/null +++ b/prepare/r-ggpmisc/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-generics +- r-ggplot2 +- r-ggpp +- r-lmodel2 +- r-lubridate +- r-plyr +- r-polynom +- r-quantreg +- r-rlang +- r-scales +- r-splus2r +- r-tibble +update_on: +- regex: ggpmisc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggpmisc diff --git a/prepare/r-ggpointdensity/PKGBUILD b/prepare/r-ggpointdensity/PKGBUILD new file mode 100644 index 0000000000..4b81d3eb9c --- /dev/null +++ b/prepare/r-ggpointdensity/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggpointdensity +_pkgver=0.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Cross Between a 2D Density Plot and a Scatter Plot' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 +) +optdepends=( + r-dplyr + r-viridis +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggpointdensity/lilac.py b/prepare/r-ggpointdensity/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggpointdensity/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggpointdensity/lilac.yaml b/prepare/r-ggpointdensity/lilac.yaml new file mode 100644 index 0000000000..9c22e56ee2 --- /dev/null +++ b/prepare/r-ggpointdensity/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +update_on: +- regex: ggpointdensity_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggpointdensity diff --git a/prepare/r-ggpp/PKGBUILD b/prepare/r-ggpp/PKGBUILD new file mode 100644 index 0000000000..93de40535d --- /dev/null +++ b/prepare/r-ggpp/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggpp +_pkgver=0.4.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Grammar Extensions to 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-ggplot2 + r-glue + r-gridextra + r-lubridate + r-magrittr + r-polynom + r-rlang + r-scales + r-stringr + r-tibble + r-xts + r-zoo +) +optdepends=( + r-gginnards + r-ggrepel + r-knitr + r-magick + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggpp/lilac.py b/prepare/r-ggpp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggpp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggpp/lilac.yaml b/prepare/r-ggpp/lilac.yaml new file mode 100644 index 0000000000..1dfab0fb8c --- /dev/null +++ b/prepare/r-ggpp/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-glue +- r-gridextra +- r-lubridate +- r-magrittr +- r-polynom +- r-rlang +- r-scales +- r-stringr +- r-tibble +- r-xts +- r-zoo +update_on: +- regex: ggpp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggpp diff --git a/prepare/r-ggprism/PKGBUILD b/prepare/r-ggprism/PKGBUILD new file mode 100644 index 0000000000..d5933d54f6 --- /dev/null +++ b/prepare/r-ggprism/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggprism +_pkgver=1.0.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="A 'ggplot2' Extension Inspired by 'GraphPad Prism'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-digest + r-ggplot2 + r-glue + r-gtable + r-rlang + r-scales + r-tibble +) +optdepends=( + r-covr + r-dplyr + r-ggbeeswarm + r-ggnewscale + r-knitr + r-magrittr + r-patchwork + r-rmarkdown + r-rstatix + r-tidyr + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggprism/lilac.py b/prepare/r-ggprism/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggprism/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggprism/lilac.yaml b/prepare/r-ggprism/lilac.yaml new file mode 100644 index 0000000000..aeef4d0ae9 --- /dev/null +++ b/prepare/r-ggprism/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-ggplot2 +- r-glue +- r-gtable +- r-rlang +- r-scales +- r-tibble +update_on: +- regex: ggprism_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggprism diff --git a/prepare/r-ggpubr/PKGBUILD b/prepare/r-ggpubr/PKGBUILD new file mode 100644 index 0000000000..acf390c812 --- /dev/null +++ b/prepare/r-ggpubr/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggpubr +_pkgver=0.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'ggplot2' Based Publication Ready Plots" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-cowplot + r-dplyr + r-ggplot2 + r-ggrepel + r-ggsci + r-ggsignif + r-glue + r-gridextra + r-magrittr + r-polynom + r-purrr + r-rlang + r-rstatix + r-scales + r-tibble + r-tidyr +) +optdepends=( + r-grdevices + r-gtable + r-knitr + r-rcolorbrewer +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggpubr/lilac.py b/prepare/r-ggpubr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggpubr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggpubr/lilac.yaml b/prepare/r-ggpubr/lilac.yaml new file mode 100644 index 0000000000..b694f394ad --- /dev/null +++ b/prepare/r-ggpubr/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cowplot +- r-dplyr +- r-ggplot2 +- r-ggrepel +- r-ggsci +- r-ggsignif +- r-glue +- r-gridextra +- r-magrittr +- r-polynom +- r-purrr +- r-rlang +- r-rstatix +- r-scales +- r-tibble +- r-tidyr +update_on: +- regex: ggpubr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggpubr diff --git a/prepare/r-ggraph/PKGBUILD b/prepare/r-ggraph/PKGBUILD new file mode 100644 index 0000000000..e14b62cece --- /dev/null +++ b/prepare/r-ggraph/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggraph +_pkgver=2.0.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Implementation of Grammar of Graphics for Graphs and Networks' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-digest + r-dplyr + r-ggforce + r-ggplot2 + r-ggrepel + r-graphlayouts + r-gtable + r-igraph + r-rcpp + r-rlang + r-scales + r-tidygraph + r-viridis + r-withr +) +optdepends=( + r-covr + r-deldir + r-gganimate + r-knitr + r-network + r-purrr + r-rmarkdown + r-seriation + r-tibble +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggraph/lilac.py b/prepare/r-ggraph/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggraph/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggraph/lilac.yaml b/prepare/r-ggraph/lilac.yaml new file mode 100644 index 0000000000..2df54fffca --- /dev/null +++ b/prepare/r-ggraph/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-dplyr +- r-ggforce +- r-ggplot2 +- r-ggrepel +- r-graphlayouts +- r-gtable +- r-igraph +- r-rcpp +- r-rlang +- r-scales +- r-tidygraph +- r-viridis +- r-withr +update_on: +- regex: ggraph_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggraph diff --git a/prepare/r-ggrastr/PKGBUILD b/prepare/r-ggrastr/PKGBUILD new file mode 100644 index 0000000000..e283c445a5 --- /dev/null +++ b/prepare/r-ggrastr/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggrastr +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Rasterize Layers for 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-cairo + r-ggbeeswarm + r-ggplot2 + r-png + r-ragg +) +optdepends=( + r-knitr + r-maps + r-rmarkdown + r-sf +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggrastr/lilac.py b/prepare/r-ggrastr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggrastr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggrastr/lilac.yaml b/prepare/r-ggrastr/lilac.yaml new file mode 100644 index 0000000000..df11568fc7 --- /dev/null +++ b/prepare/r-ggrastr/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cairo +- r-ggbeeswarm +- r-ggplot2 +- r-png +- r-ragg +update_on: +- regex: ggrastr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggrastr diff --git a/prepare/r-ggrepel/PKGBUILD b/prepare/r-ggrepel/PKGBUILD new file mode 100644 index 0000000000..0223c0698b --- /dev/null +++ b/prepare/r-ggrepel/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggrepel +_pkgver=0.9.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Automatically Position Non-Overlapping Text Labels with 'ggplot2'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-rcpp + r-rlang + r-scales +) +optdepends=( + r-devtools + r-dplyr + r-ggbeeswarm + r-gridextra + r-knitr + r-magrittr + r-prettydoc + r-readr + r-rmarkdown + r-stringr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggrepel/lilac.py b/prepare/r-ggrepel/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggrepel/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggrepel/lilac.yaml b/prepare/r-ggrepel/lilac.yaml new file mode 100644 index 0000000000..4bcbbbc7fd --- /dev/null +++ b/prepare/r-ggrepel/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-rcpp +- r-rlang +- r-scales +update_on: +- regex: ggrepel_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggrepel diff --git a/prepare/r-ggridges/PKGBUILD b/prepare/r-ggridges/PKGBUILD new file mode 100644 index 0000000000..da3c06a53f --- /dev/null +++ b/prepare/r-ggridges/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggridges +_pkgver=0.5.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Ridgeline Plots in 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-plyr + r-scales + r-withr +) +optdepends=( + r-covr + r-dplyr + r-forcats + r-ggplot2movies + r-knitr + r-patchwork + r-rmarkdown + r-testthat + r-vdiffr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggridges/lilac.py b/prepare/r-ggridges/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggridges/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggridges/lilac.yaml b/prepare/r-ggridges/lilac.yaml new file mode 100644 index 0000000000..18f4267362 --- /dev/null +++ b/prepare/r-ggridges/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-plyr +- r-scales +- r-withr +update_on: +- regex: ggridges_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggridges diff --git a/prepare/r-ggsci/PKGBUILD b/prepare/r-ggsci/PKGBUILD new file mode 100644 index 0000000000..86f5a18aec --- /dev/null +++ b/prepare/r-ggsci/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggsci +_pkgver=2.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-scales +) +optdepends=( + r-gridextra + r-knitr + r-reshape2 + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggsci/lilac.py b/prepare/r-ggsci/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggsci/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggsci/lilac.yaml b/prepare/r-ggsci/lilac.yaml new file mode 100644 index 0000000000..6add0b541e --- /dev/null +++ b/prepare/r-ggsci/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-scales +update_on: +- regex: ggsci_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggsci diff --git a/prepare/r-ggseqlogo/PKGBUILD b/prepare/r-ggseqlogo/PKGBUILD new file mode 100644 index 0000000000..7f8fad59ca --- /dev/null +++ b/prepare/r-ggseqlogo/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggseqlogo +_pkgver=0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="A 'ggplot2' Extension for Drawing Publication-Ready Sequence Logos" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-ggplot2 +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggseqlogo/lilac.py b/prepare/r-ggseqlogo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggseqlogo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggseqlogo/lilac.yaml b/prepare/r-ggseqlogo/lilac.yaml new file mode 100644 index 0000000000..8d19fe5ee5 --- /dev/null +++ b/prepare/r-ggseqlogo/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +update_on: +- regex: ggseqlogo_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggseqlogo diff --git a/prepare/r-ggside/PKGBUILD b/prepare/r-ggside/PKGBUILD new file mode 100644 index 0000000000..0cb3a4a5d6 --- /dev/null +++ b/prepare/r-ggside/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggside +_pkgver=0.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Side Grammar Graphics' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-ggplot2 + r-glue + r-gtable + r-rlang + r-scales +) +optdepends=( + r-dplyr + r-ggdendro + r-knitr + r-rmarkdown + r-testthat + r-tidyr + r-vdiffr + r-viridis +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggside/lilac.py b/prepare/r-ggside/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggside/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggside/lilac.yaml b/prepare/r-ggside/lilac.yaml new file mode 100644 index 0000000000..6c7c10e560 --- /dev/null +++ b/prepare/r-ggside/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-glue +- r-gtable +- r-rlang +- r-scales +update_on: +- regex: ggside_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggside diff --git a/prepare/r-ggsignif/PKGBUILD b/prepare/r-ggsignif/PKGBUILD new file mode 100644 index 0000000000..21cd66d67c --- /dev/null +++ b/prepare/r-ggsignif/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggsignif +_pkgver=0.6.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Significance Brackets for 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 +) +optdepends=( + r-knitr + r-rmarkdown + r-spelling + r-testthat + r-vdiffr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggsignif/lilac.py b/prepare/r-ggsignif/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggsignif/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggsignif/lilac.yaml b/prepare/r-ggsignif/lilac.yaml new file mode 100644 index 0000000000..7f3174f003 --- /dev/null +++ b/prepare/r-ggsignif/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +update_on: +- regex: ggsignif_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggsignif diff --git a/prepare/r-ggspavis/PKGBUILD b/prepare/r-ggspavis/PKGBUILD new file mode 100644 index 0000000000..0d373c63fe --- /dev/null +++ b/prepare/r-ggspavis/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggspavis +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization functions for spatially resolved transcriptomics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-ggplot2 + r-ggside + r-singlecellexperiment + r-spatialexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-bumpymatrix + r-knitr + r-rmarkdown + r-scater + r-scran + r-stexampledata + r-testthat + r-uwot +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggspavis/lilac.py b/prepare/r-ggspavis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggspavis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggspavis/lilac.yaml b/prepare/r-ggspavis/lilac.yaml new file mode 100644 index 0000000000..11f9ddcdcf --- /dev/null +++ b/prepare/r-ggspavis/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-ggside +- r-singlecellexperiment +- r-spatialexperiment +- r-summarizedexperiment +update_on: +- regex: ggspavis_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ggspavis diff --git a/prepare/r-ggstance/PKGBUILD b/prepare/r-ggstance/PKGBUILD new file mode 100644 index 0000000000..20bd33a5d3 --- /dev/null +++ b/prepare/r-ggstance/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggstance +_pkgver=0.3.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Horizontal 'ggplot2' Components" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-plyr + r-rlang + r-withr +) +optdepends=( + r-covr + r-hmisc + r-testthat + r-vdiffr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggstance/lilac.py b/prepare/r-ggstance/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggstance/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggstance/lilac.yaml b/prepare/r-ggstance/lilac.yaml new file mode 100644 index 0000000000..62157b2f98 --- /dev/null +++ b/prepare/r-ggstance/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-plyr +- r-rlang +- r-withr +update_on: +- regex: ggstance_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggstance diff --git a/prepare/r-ggstar/PKGBUILD b/prepare/r-ggstar/PKGBUILD new file mode 100644 index 0000000000..21afb1cc61 --- /dev/null +++ b/prepare/r-ggstar/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggstar +_pkgver=1.0.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Multiple Geometric Shape Point Layer for 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ggplot2 + r-gridextra + r-scales +) +optdepends=( + r-knitr + r-markdown + r-prettydoc + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggstar/lilac.py b/prepare/r-ggstar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggstar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggstar/lilac.yaml b/prepare/r-ggstar/lilac.yaml new file mode 100644 index 0000000000..852b4377a1 --- /dev/null +++ b/prepare/r-ggstar/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gridextra +- r-scales +update_on: +- regex: ggstar_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggstar diff --git a/prepare/r-ggtext/PKGBUILD b/prepare/r-ggtext/PKGBUILD new file mode 100644 index 0000000000..e7813f744a --- /dev/null +++ b/prepare/r-ggtext/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggtext +_pkgver=0.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Improved Text Rendering Support for 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-gridtext + r-rlang + r-scales +) +optdepends=( + r-cowplot + r-dplyr + r-glue + r-knitr + r-rmarkdown + r-testthat + r-vdiffr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggtext/lilac.py b/prepare/r-ggtext/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggtext/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggtext/lilac.yaml b/prepare/r-ggtext/lilac.yaml new file mode 100644 index 0000000000..ec2614b71b --- /dev/null +++ b/prepare/r-ggtext/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gridtext +- r-rlang +- r-scales +update_on: +- regex: ggtext_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggtext diff --git a/prepare/r-ggthemes/PKGBUILD b/prepare/r-ggthemes/PKGBUILD new file mode 100644 index 0000000000..01e5b3a77f --- /dev/null +++ b/prepare/r-ggthemes/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggthemes +_pkgver=4.2.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Extra Themes, Scales and Geoms for 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-purrr + r-scales + r-stringr + r-tibble +) +optdepends=( + r-covr + r-dplyr + r-extrafont + r-glue + r-knitr + r-lattice + r-lintr + r-mapproj + r-maps + r-pander + r-rlang + r-rmarkdown + r-spelling + r-testthat + r-tidyr + r-vdiffr + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggthemes/lilac.py b/prepare/r-ggthemes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggthemes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggthemes/lilac.yaml b/prepare/r-ggthemes/lilac.yaml new file mode 100644 index 0000000000..d6ef87aadc --- /dev/null +++ b/prepare/r-ggthemes/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-purrr +- r-scales +- r-stringr +- r-tibble +update_on: +- regex: ggthemes_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggthemes diff --git a/prepare/r-ggtree/PKGBUILD b/prepare/r-ggtree/PKGBUILD new file mode 100644 index 0000000000..9aa10b4344 --- /dev/null +++ b/prepare/r-ggtree/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggtree +_pkgver=3.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='an R package for visualization of tree and annotation data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ape + r-aplot + r-dplyr + r-ggfun + r-ggplot2 + r-magrittr + r-purrr + r-rlang + r-scales + r-tidyr + r-tidytree + r-treeio + r-yulab.utils +) +optdepends=( + r-emojifont + r-ggimage + r-ggplotify + r-grdevices + r-knitr + r-prettydoc + r-rmarkdown + r-stats + r-testthat + r-tibble +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggtree/lilac.py b/prepare/r-ggtree/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggtree/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggtree/lilac.yaml b/prepare/r-ggtree/lilac.yaml new file mode 100644 index 0000000000..293638b276 --- /dev/null +++ b/prepare/r-ggtree/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-aplot +- r-dplyr +- r-ggfun +- r-ggplot2 +- r-magrittr +- r-purrr +- r-rlang +- r-scales +- r-tidyr +- r-tidytree +- r-treeio +- r-yulab.utils +update_on: +- regex: ggtree_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ggtree diff --git a/prepare/r-ggtreeextra/PKGBUILD b/prepare/r-ggtreeextra/PKGBUILD new file mode 100644 index 0000000000..c647b3a7ee --- /dev/null +++ b/prepare/r-ggtreeextra/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggtreeExtra +_pkgver=1.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggnewscale + r-ggplot2 + r-ggtree + r-rlang +) +optdepends=( + r-ggstar + r-knitr + r-markdown + r-patchwork + r-prettydoc + r-rmarkdown + r-testthat + r-treeio +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggtreeextra/lilac.py b/prepare/r-ggtreeextra/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggtreeextra/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggtreeextra/lilac.yaml b/prepare/r-ggtreeextra/lilac.yaml new file mode 100644 index 0000000000..b5e1324621 --- /dev/null +++ b/prepare/r-ggtreeextra/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggnewscale +- r-ggplot2 +- r-ggtree +- r-rlang +update_on: +- regex: ggtreeExtra_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ggtreeExtra diff --git a/prepare/r-ggvis/PKGBUILD b/prepare/r-ggvis/PKGBUILD new file mode 100644 index 0000000000..09dd389be2 --- /dev/null +++ b/prepare/r-ggvis/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggvis +_pkgver=0.4.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive Grammar of Graphics' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-dplyr + r-htmltools + r-jsonlite + r-magrittr + r-rlang + r-shiny +) +optdepends=( + r-knitr + r-lubridate + r-mass + r-mgcv + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggvis/lilac.py b/prepare/r-ggvis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggvis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggvis/lilac.yaml b/prepare/r-ggvis/lilac.yaml new file mode 100644 index 0000000000..810633a649 --- /dev/null +++ b/prepare/r-ggvis/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-dplyr +- r-htmltools +- r-jsonlite +- r-magrittr +- r-rlang +- r-shiny +update_on: +- regex: ggvis_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggvis diff --git a/prepare/r-ggwordcloud/PKGBUILD b/prepare/r-ggwordcloud/PKGBUILD new file mode 100644 index 0000000000..cdba3bae63 --- /dev/null +++ b/prepare/r-ggwordcloud/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ggwordcloud +_pkgver=0.5.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="A Word Cloud Geom for 'ggplot2'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-colorspace + r-ggplot2 + r-png + r-rcpp + r-scales +) +optdepends=( + r-covr + r-dplyr + r-ggrepel + r-knitr + r-rmarkdown + r-testthat + r-tidyr + r-wordcloud + r-wordcloud2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ggwordcloud/lilac.py b/prepare/r-ggwordcloud/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ggwordcloud/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ggwordcloud/lilac.yaml b/prepare/r-ggwordcloud/lilac.yaml new file mode 100644 index 0000000000..2fc74c6d87 --- /dev/null +++ b/prepare/r-ggwordcloud/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colorspace +- r-ggplot2 +- r-png +- r-rcpp +- r-scales +update_on: +- regex: ggwordcloud_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ggwordcloud diff --git a/prepare/r-gh/PKGBUILD b/prepare/r-gh/PKGBUILD new file mode 100644 index 0000000000..4604577001 --- /dev/null +++ b/prepare/r-gh/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gh +_pkgver=1.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'GitHub' 'API'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-cli + r-gitcreds + r-httr + r-ini + r-jsonlite +) +optdepends=( + r-covr + r-knitr + r-mockery + r-rmarkdown + r-rprojroot + r-spelling + r-testthat + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gh/lilac.py b/prepare/r-gh/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gh/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gh/lilac.yaml b/prepare/r-gh/lilac.yaml new file mode 100644 index 0000000000..88743dc69d --- /dev/null +++ b/prepare/r-gh/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cli +- r-gitcreds +- r-httr +- r-ini +- r-jsonlite +update_on: +- regex: gh_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gh diff --git a/prepare/r-gigsea/PKGBUILD b/prepare/r-gigsea/PKGBUILD new file mode 100644 index 0000000000..4be8f0d133 --- /dev/null +++ b/prepare/r-gigsea/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GIGSEA +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genotype Imputed Gene Set Enrichment Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-locfdr +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gigsea/lilac.py b/prepare/r-gigsea/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gigsea/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gigsea/lilac.yaml b/prepare/r-gigsea/lilac.yaml new file mode 100644 index 0000000000..4d4b629c5c --- /dev/null +++ b/prepare/r-gigsea/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-locfdr +update_on: +- regex: GIGSEA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GIGSEA diff --git a/prepare/r-girafe/PKGBUILD b/prepare/r-girafe/PKGBUILD new file mode 100644 index 0000000000..ef5c50a18d --- /dev/null +++ b/prepare/r-girafe/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=girafe +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genome Intervals and Read Alignments for Functional Exploration' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-biostrings + r-genomeintervals + r-intervals + r-iranges + r-rsamtools + r-s4vectors + r-shortread +) +optdepends=( + r-genomeintervals + r-mass + r-org.mm.eg.db + r-rcolorbrewer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-girafe/lilac.py b/prepare/r-girafe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-girafe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-girafe/lilac.yaml b/prepare/r-girafe/lilac.yaml new file mode 100644 index 0000000000..a16529ac18 --- /dev/null +++ b/prepare/r-girafe/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biostrings +- r-genomeintervals +- r-intervals +- r-iranges +- r-rsamtools +- r-s4vectors +- r-shortread +update_on: +- regex: girafe_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/girafe diff --git a/prepare/r-gispa/PKGBUILD b/prepare/r-gispa/PKGBUILD new file mode 100644 index 0000000000..ef439b726e --- /dev/null +++ b/prepare/r-gispa/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GISPA +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GISPA: Method for Gene Integrated Set Profile Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-changepoint + r-data.table + r-genefilter + r-gseabase + r-hh + r-latticeextra + r-plyr + r-scatterplot3d +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gispa/lilac.py b/prepare/r-gispa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gispa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gispa/lilac.yaml b/prepare/r-gispa/lilac.yaml new file mode 100644 index 0000000000..ad0ec9bd31 --- /dev/null +++ b/prepare/r-gispa/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-changepoint +- r-data.table +- r-genefilter +- r-gseabase +- r-hh +- r-latticeextra +- r-plyr +- r-scatterplot3d +update_on: +- regex: GISPA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GISPA diff --git a/prepare/r-gistr/PKGBUILD b/prepare/r-gistr/PKGBUILD new file mode 100644 index 0000000000..f7f97f2c1e --- /dev/null +++ b/prepare/r-gistr/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gistr +_pkgver=0.9.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Work with 'GitHub' 'Gists'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-assertthat + r-crul + r-dplyr + r-httr + r-jsonlite + r-knitr + r-magrittr + r-rmarkdown +) +optdepends=( + r-git2r + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gistr/lilac.py b/prepare/r-gistr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gistr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gistr/lilac.yaml b/prepare/r-gistr/lilac.yaml new file mode 100644 index 0000000000..593ffbb67e --- /dev/null +++ b/prepare/r-gistr/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-crul +- r-dplyr +- r-httr +- r-jsonlite +- r-knitr +- r-magrittr +- r-rmarkdown +update_on: +- regex: gistr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gistr diff --git a/prepare/r-git2r/PKGBUILD b/prepare/r-git2r/PKGBUILD new file mode 100644 index 0000000000..7f31a0b155 --- /dev/null +++ b/prepare/r-git2r/PKGBUILD @@ -0,0 +1,30 @@ +# system requirements: By default, git2r uses a system installation of thelibgit2 headers and library. However, if a system installationis not available, builds and uses a bundled version of thelibgit2 source. zlib headers and library. OpenSSL headers andlibrary (non-macOS). LibSSH2 (optional on non-Windows) toenable the SSH transport. +# Maintainer: Guoyi Zhang + +_pkgname=git2r +_pkgver=0.29.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Provides Access to Git Repositories' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-getpass +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-git2r/lilac.py b/prepare/r-git2r/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-git2r/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-git2r/lilac.yaml b/prepare/r-git2r/lilac.yaml new file mode 100644 index 0000000000..5089784efc --- /dev/null +++ b/prepare/r-git2r/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: git2r_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=git2r diff --git a/prepare/r-gitcreds/PKGBUILD b/prepare/r-gitcreds/PKGBUILD new file mode 100644 index 0000000000..3bb56ab96b --- /dev/null +++ b/prepare/r-gitcreds/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: git +# Maintainer: Guoyi Zhang + +_pkgname=gitcreds +_pkgver=0.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Query 'git' Credentials from 'R'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-codetools + r-knitr + r-mockery + r-oskeyring + r-rmarkdown + r-testthat + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gitcreds/lilac.py b/prepare/r-gitcreds/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gitcreds/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gitcreds/lilac.yaml b/prepare/r-gitcreds/lilac.yaml new file mode 100644 index 0000000000..43b33caeaa --- /dev/null +++ b/prepare/r-gitcreds/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gitcreds_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gitcreds diff --git a/prepare/r-glad/PKGBUILD b/prepare/r-glad/PKGBUILD new file mode 100644 index 0000000000..02b8bced24 --- /dev/null +++ b/prepare/r-glad/PKGBUILD @@ -0,0 +1,28 @@ +# system requirements: gsl. Note: users should have GSL installed. Windowsusers: 'consult the README file available in the inst directoryof the source distribution for necessary configurationinstructions'. +# Maintainer: Guoyi Zhang + +_pkgname=GLAD +_pkgver=2.58.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gain and Loss Analysis of DNA' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-aws +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-glad/lilac.py b/prepare/r-glad/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-glad/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-glad/lilac.yaml b/prepare/r-glad/lilac.yaml new file mode 100644 index 0000000000..51f6d7cae0 --- /dev/null +++ b/prepare/r-glad/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aws +update_on: +- regex: GLAD_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GLAD diff --git a/prepare/r-gladiatox/PKGBUILD b/prepare/r-gladiatox/PKGBUILD new file mode 100644 index 0000000000..5a2e1a5675 --- /dev/null +++ b/prepare/r-gladiatox/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GladiaTOX +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Package for Processing High Content Screening data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-brew + r-data.table + r-dbi + r-ggplot2 + r-ggrepel + r-numderiv + r-rcolorbrewer + r-rcurl + r-rjsonio + r-rmysql + r-rsqlite + r-stringr + r-tidyr + r-xml + r-xtable +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gladiatox/lilac.py b/prepare/r-gladiatox/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gladiatox/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gladiatox/lilac.yaml b/prepare/r-gladiatox/lilac.yaml new file mode 100644 index 0000000000..3cad636948 --- /dev/null +++ b/prepare/r-gladiatox/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-brew +- r-data.table +- r-dbi +- r-ggplot2 +- r-ggrepel +- r-numderiv +- r-rcolorbrewer +- r-rcurl +- r-rjsonio +- r-rmysql +- r-rsqlite +- r-stringr +- r-tidyr +- r-xml +- r-xtable +update_on: +- regex: GladiaTOX_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GladiaTOX diff --git a/prepare/r-glasso/PKGBUILD b/prepare/r-glasso/PKGBUILD new file mode 100644 index 0000000000..4a6bb39542 --- /dev/null +++ b/prepare/r-glasso/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=glasso +_pkgver=1.11 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Graphical Lasso: Estimation of Gaussian Graphical Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-glasso/lilac.py b/prepare/r-glasso/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-glasso/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-glasso/lilac.yaml b/prepare/r-glasso/lilac.yaml new file mode 100644 index 0000000000..1b6e60ed63 --- /dev/null +++ b/prepare/r-glasso/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: glasso_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=glasso diff --git a/prepare/r-gld/PKGBUILD b/prepare/r-gld/PKGBUILD new file mode 100644 index 0000000000..d661eed1f3 --- /dev/null +++ b/prepare/r-gld/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gld +_pkgver=2.6.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimation and Use of the Generalised (Tukey) Lambda Distribution' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-e1071 + r-lmom +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gld/lilac.py b/prepare/r-gld/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gld/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gld/lilac.yaml b/prepare/r-gld/lilac.yaml new file mode 100644 index 0000000000..ec75c9551a --- /dev/null +++ b/prepare/r-gld/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-e1071 +- r-lmom +update_on: +- regex: gld_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gld diff --git a/prepare/r-glimma/PKGBUILD b/prepare/r-glimma/PKGBUILD new file mode 100644 index 0000000000..6b9169ff4b --- /dev/null +++ b/prepare/r-glimma/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Glimma +_pkgver=2.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive HTML graphics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-deseq2 + r-edger + r-htmlwidgets + r-jsonlite + r-limma + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-annotationhub + r-biocstyle + r-genomicranges + r-iranges + r-knitr + r-pryr + r-rmarkdown + r-scater + r-scran + r-scrnaseq + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-glimma/lilac.py b/prepare/r-glimma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-glimma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-glimma/lilac.yaml b/prepare/r-glimma/lilac.yaml new file mode 100644 index 0000000000..8f9ba38858 --- /dev/null +++ b/prepare/r-glimma/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-deseq2 +- r-edger +- r-htmlwidgets +- r-jsonlite +- r-limma +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: Glimma_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Glimma diff --git a/prepare/r-glm2/PKGBUILD b/prepare/r-glm2/PKGBUILD new file mode 100644 index 0000000000..38a36b03de --- /dev/null +++ b/prepare/r-glm2/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=glm2 +_pkgver=1.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fitting Generalized Linear Models' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-glm2/lilac.py b/prepare/r-glm2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-glm2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-glm2/lilac.yaml b/prepare/r-glm2/lilac.yaml new file mode 100644 index 0000000000..67c30171e6 --- /dev/null +++ b/prepare/r-glm2/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: glm2_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=glm2 diff --git a/prepare/r-glmgampoi/PKGBUILD b/prepare/r-glmgampoi/PKGBUILD new file mode 100644 index 0000000000..2cd9e4a331 --- /dev/null +++ b/prepare/r-glmgampoi/PKGBUILD @@ -0,0 +1,55 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=glmGamPoi +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fit a Gamma-Poisson Generalized Linear Model' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-beachmat + r-biocgenerics + r-delayedarray + r-delayedmatrixstats + r-hdf5array + r-matrixstats + r-rcpp + r-rcpparmadillo + r-summarizedexperiment +) +optdepends=( + r-beachmat + r-bench + r-biocparallel + r-biocstyle + r-deseq2 + r-edger + r-ggplot2 + r-knitr + r-limma + r-mass + r-muscdata + r-rmarkdown + r-scran + r-statmod + r-tenxpbmcdata + r-testthat + r-zoo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-glmgampoi/lilac.py b/prepare/r-glmgampoi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-glmgampoi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-glmgampoi/lilac.yaml b/prepare/r-glmgampoi/lilac.yaml new file mode 100644 index 0000000000..1e8357eb46 --- /dev/null +++ b/prepare/r-glmgampoi/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beachmat +- r-biocgenerics +- r-delayedarray +- r-delayedmatrixstats +- r-hdf5array +- r-matrixstats +- r-rcpp +- r-rcpparmadillo +- r-summarizedexperiment +update_on: +- regex: glmGamPoi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/glmGamPoi diff --git a/prepare/r-glmmtmb/PKGBUILD b/prepare/r-glmmtmb/PKGBUILD new file mode 100644 index 0000000000..265840fc78 --- /dev/null +++ b/prepare/r-glmmtmb/PKGBUILD @@ -0,0 +1,61 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=glmmTMB +_pkgver=1.1.2.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generalized Linear Mixed Models using Template Model Builder' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('AGPL') +depends=( + r + r-lme4 + r-numderiv + r-rcppeigen + r-tmb +) +optdepends=( + r-bbmle + r-boot + r-broom + r-broom.mixed + r-car + r-coda + r-dharma + r-dotwhisker + r-effects + r-emmeans + r-estimability + r-ggplot2 + r-huxtable + r-knitr + r-lattice + r-mass + r-mlmrev + r-multcomp + r-mumin + r-mvabund + r-plyr + r-png + r-pscl + r-reshape2 + r-rmarkdown + r-testthat + r-texreg + r-xtable +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-glmmtmb/lilac.py b/prepare/r-glmmtmb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-glmmtmb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-glmmtmb/lilac.yaml b/prepare/r-glmmtmb/lilac.yaml new file mode 100644 index 0000000000..46b810745b --- /dev/null +++ b/prepare/r-glmmtmb/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lme4 +- r-numderiv +- r-rcppeigen +- r-tmb +update_on: +- regex: glmmTMB_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=glmmTMB diff --git a/prepare/r-glmnet/PKGBUILD b/prepare/r-glmnet/PKGBUILD new file mode 100644 index 0000000000..7f5db2f45b --- /dev/null +++ b/prepare/r-glmnet/PKGBUILD @@ -0,0 +1,41 @@ +# system requirements: C++14 +# Maintainer: Guoyi Zhang + +_pkgname=glmnet +_pkgver=4.1-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Lasso and Elastic-Net Regularized Generalized Linear Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-foreach + r-rcpp + r-rcppeigen + r-shape +) +optdepends=( + r-knitr + r-lars + r-rmarkdown + r-testthat + r-xfun +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-glmnet/lilac.py b/prepare/r-glmnet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-glmnet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-glmnet/lilac.yaml b/prepare/r-glmnet/lilac.yaml new file mode 100644 index 0000000000..598dc9498e --- /dev/null +++ b/prepare/r-glmnet/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-foreach +- r-rcpp +- r-rcppeigen +- r-shape +update_on: +- regex: glmnet_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=glmnet diff --git a/prepare/r-glmpca/PKGBUILD b/prepare/r-glmpca/PKGBUILD new file mode 100644 index 0000000000..60e42c1588 --- /dev/null +++ b/prepare/r-glmpca/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=glmpca +_pkgver=0.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dimension Reduction of Non-Normally Distributed Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +optdepends=( + r-covr + r-ggplot2 + r-knitr + r-logisticpca + r-markdown + r-matrix + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-glmpca/lilac.py b/prepare/r-glmpca/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-glmpca/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-glmpca/lilac.yaml b/prepare/r-glmpca/lilac.yaml new file mode 100644 index 0000000000..dba3264327 --- /dev/null +++ b/prepare/r-glmpca/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: glmpca_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=glmpca diff --git a/prepare/r-glmsparsenet/PKGBUILD b/prepare/r-glmsparsenet/PKGBUILD new file mode 100644 index 0000000000..bf8f2bd28a --- /dev/null +++ b/prepare/r-glmsparsenet/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=glmSparseNet +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Network Centrality Metrics for Elastic-Net Regularized Models' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-dplyr + r-forcats + r-futile.logger + r-ggplot2 + r-glmnet + r-glue + r-httr + r-loose.rock + r-multiassayexperiment + r-readr + r-reshape2 + r-sparsebn + r-sparsebnutils + r-stringr + r-summarizedexperiment + r-survminer +) +optdepends=( + r-biocstyle + r-curatedtcgadata + r-knitr + r-proc + r-rmarkdown + r-survcomp + r-survival + r-tcgautils + r-testthat + r-venndiagram +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-glmsparsenet/lilac.py b/prepare/r-glmsparsenet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-glmsparsenet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-glmsparsenet/lilac.yaml b/prepare/r-glmsparsenet/lilac.yaml new file mode 100644 index 0000000000..01dc04d87f --- /dev/null +++ b/prepare/r-glmsparsenet/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-dplyr +- r-forcats +- r-futile.logger +- r-ggplot2 +- r-glmnet +- r-glue +- r-httr +- r-loose.rock +- r-multiassayexperiment +- r-readr +- r-reshape2 +- r-sparsebn +- r-sparsebnutils +- r-stringr +- r-summarizedexperiment +- r-survminer +update_on: +- regex: glmSparseNet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/glmSparseNet diff --git a/prepare/r-globalancova/PKGBUILD b/prepare/r-globalancova/PKGBUILD new file mode 100644 index 0000000000..dd69faddab --- /dev/null +++ b/prepare/r-globalancova/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GlobalAncova +_pkgver=4.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Global test for groups of variables via model comparisons' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotate + r-annotationdbi + r-biobase + r-corpcor + r-dendextend + r-globaltest + r-gseabase + r-vgam +) +optdepends=( + r-go.db + r-golubesets + r-hu6800.db + r-rgraphviz + r-vsn +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-globalancova/lilac.py b/prepare/r-globalancova/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-globalancova/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-globalancova/lilac.yaml b/prepare/r-globalancova/lilac.yaml new file mode 100644 index 0000000000..36355aee68 --- /dev/null +++ b/prepare/r-globalancova/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-biobase +- r-corpcor +- r-dendextend +- r-globaltest +- r-gseabase +- r-vgam +update_on: +- regex: GlobalAncova_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GlobalAncova diff --git a/prepare/r-globaloptions/PKGBUILD b/prepare/r-globaloptions/PKGBUILD new file mode 100644 index 0000000000..ddb1453ab5 --- /dev/null +++ b/prepare/r-globaloptions/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GlobalOptions +_pkgver=0.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generate Functions to Get or Set Global Options' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-getoptlong + r-knitr + r-markdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-globaloptions/lilac.py b/prepare/r-globaloptions/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-globaloptions/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-globaloptions/lilac.yaml b/prepare/r-globaloptions/lilac.yaml new file mode 100644 index 0000000000..c861c57be9 --- /dev/null +++ b/prepare/r-globaloptions/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: GlobalOptions_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=GlobalOptions diff --git a/prepare/r-globals/PKGBUILD b/prepare/r-globals/PKGBUILD new file mode 100644 index 0000000000..36581d40d9 --- /dev/null +++ b/prepare/r-globals/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=globals +_pkgver=0.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identify Global Objects in R Expressions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-globals/lilac.py b/prepare/r-globals/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-globals/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-globals/lilac.yaml b/prepare/r-globals/lilac.yaml new file mode 100644 index 0000000000..62e295063b --- /dev/null +++ b/prepare/r-globals/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: globals_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=globals diff --git a/prepare/r-globalseq/PKGBUILD b/prepare/r-globalseq/PKGBUILD new file mode 100644 index 0000000000..302a2d8375 --- /dev/null +++ b/prepare/r-globalseq/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=globalSeq +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Global Test for Counts' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-s4vectors + r-summarizedexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-globalseq/lilac.py b/prepare/r-globalseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-globalseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-globalseq/lilac.yaml b/prepare/r-globalseq/lilac.yaml new file mode 100644 index 0000000000..660a18bbd8 --- /dev/null +++ b/prepare/r-globalseq/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: globalSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/globalSeq diff --git a/prepare/r-globaltest/PKGBUILD b/prepare/r-globaltest/PKGBUILD new file mode 100644 index 0000000000..0eef2bcdef --- /dev/null +++ b/prepare/r-globaltest/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=globaltest +_pkgver=5.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotate + r-annotationdbi + r-biobase +) +optdepends=( + r-boot + r-go.db + r-golubesets + r-gseabase + r-gss + r-hu6800.db + r-keggrest + r-lungexpression + r-mass + r-mstate + r-org.hs.eg.db + r-penalized + r-rgraphviz + r-rpart + r-vsn +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-globaltest/lilac.py b/prepare/r-globaltest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-globaltest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-globaltest/lilac.yaml b/prepare/r-globaltest/lilac.yaml new file mode 100644 index 0000000000..e5efee6ba9 --- /dev/null +++ b/prepare/r-globaltest/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-biobase +update_on: +- regex: globaltest_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/globaltest diff --git a/prepare/r-gmapr/PKGBUILD b/prepare/r-gmapr/PKGBUILD new file mode 100644 index 0000000000..f26d87cf05 --- /dev/null +++ b/prepare/r-gmapr/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gmapR +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R interface to the GMAP/GSNAP/GSTRUCT suite' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-rsamtools + r-rtracklayer + r-s4vectors + r-variantannotation +) +optdepends=( + r-bsgenome.dmelanogaster.ucsc.dm3 + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.scerevisiae.ucsc.saccer3 + r-lungcancerlines + r-org.hs.eg.db + r-runit + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gmapr/lilac.py b/prepare/r-gmapr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gmapr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gmapr/lilac.yaml b/prepare/r-gmapr/lilac.yaml new file mode 100644 index 0000000000..675ba85c16 --- /dev/null +++ b/prepare/r-gmapr/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-variantannotation +update_on: +- regex: gmapR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gmapR diff --git a/prepare/r-gmicr/PKGBUILD b/prepare/r-gmicr/PKGBUILD new file mode 100644 index 0000000000..913258971a --- /dev/null +++ b/prepare/r-gmicr/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GmicR +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-ape + r-bnlearn + r-category + r-data.table + r-doparallel + r-dt + r-foreach + r-gostats + r-grain + r-grbase + r-gseabase + r-org.hs.eg.db + r-org.mm.eg.db + r-reshape2 + r-shiny + r-wgcna +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gmicr/lilac.py b/prepare/r-gmicr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gmicr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gmicr/lilac.yaml b/prepare/r-gmicr/lilac.yaml new file mode 100644 index 0000000000..41ba86e153 --- /dev/null +++ b/prepare/r-gmicr/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-ape +- r-bnlearn +- r-category +- r-data.table +- r-doparallel +- r-dt +- r-foreach +- r-gostats +- r-grain +- r-grbase +- r-gseabase +- r-org.hs.eg.db +- r-org.mm.eg.db +- r-reshape2 +- r-shiny +- r-wgcna +update_on: +- regex: GmicR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GmicR diff --git a/prepare/r-gmm/PKGBUILD b/prepare/r-gmm/PKGBUILD new file mode 100644 index 0000000000..42a4f9a889 --- /dev/null +++ b/prepare/r-gmm/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gmm +_pkgver=1.6-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generalized Method of Moments and Generalized Empirical Likelihood' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-sandwich +) +optdepends=( + r-car + r-knitr + r-mass + r-mvtnorm + r-stabledist + r-timedate + r-timeseries +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gmm/lilac.py b/prepare/r-gmm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gmm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gmm/lilac.yaml b/prepare/r-gmm/lilac.yaml new file mode 100644 index 0000000000..fce6532773 --- /dev/null +++ b/prepare/r-gmm/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-sandwich +update_on: +- regex: gmm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gmm diff --git a/prepare/r-gmodels/PKGBUILD b/prepare/r-gmodels/PKGBUILD new file mode 100644 index 0000000000..310fbfd00f --- /dev/null +++ b/prepare/r-gmodels/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gmodels +_pkgver=2.18.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Various R Programming Tools for Model Fitting' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-gdata +) +optdepends=( + r-gplots + r-gtools + r-lme4 + r-matrix + r-nlme +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gmodels/lilac.py b/prepare/r-gmodels/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gmodels/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gmodels/lilac.yaml b/prepare/r-gmodels/lilac.yaml new file mode 100644 index 0000000000..b750587979 --- /dev/null +++ b/prepare/r-gmodels/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gdata +update_on: +- regex: gmodels_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gmodels diff --git a/prepare/r-gmoviz/PKGBUILD b/prepare/r-gmoviz/PKGBUILD new file mode 100644 index 0000000000..107b703c9a --- /dev/null +++ b/prepare/r-gmoviz/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gmoviz +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Seamless visualization of complex genomic variations in GMOs and edited cell lines' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-circlize + r-colorspace + r-complexheatmap + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-gridbase + r-iranges + r-pracma + r-rsamtools + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocmanager + r-biocstyle + r-knitr + r-pasillabamsubset + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gmoviz/lilac.py b/prepare/r-gmoviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gmoviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gmoviz/lilac.yaml b/prepare/r-gmoviz/lilac.yaml new file mode 100644 index 0000000000..4751769eeb --- /dev/null +++ b/prepare/r-gmoviz/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-circlize +- r-colorspace +- r-complexheatmap +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-gridbase +- r-iranges +- r-pracma +- r-rsamtools +- r-rtracklayer +- r-s4vectors +update_on: +- regex: gmoviz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gmoviz diff --git a/prepare/r-gmp/PKGBUILD b/prepare/r-gmp/PKGBUILD new file mode 100644 index 0000000000..be76d6af0c --- /dev/null +++ b/prepare/r-gmp/PKGBUILD @@ -0,0 +1,32 @@ +# system requirements: gmp (>= 4.2.3) +# Maintainer: Guoyi Zhang + +_pkgname=gmp +_pkgver=0.6-2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multiple Precision Arithmetic' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-mass + r-rmpfr + r-round +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gmp/lilac.py b/prepare/r-gmp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gmp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gmp/lilac.yaml b/prepare/r-gmp/lilac.yaml new file mode 100644 index 0000000000..8089198a23 --- /dev/null +++ b/prepare/r-gmp/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gmp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gmp diff --git a/prepare/r-gmrp/PKGBUILD b/prepare/r-gmrp/PKGBUILD new file mode 100644 index 0000000000..76ec12e929 --- /dev/null +++ b/prepare/r-gmrp/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GMRP +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GWAS-based Mendelian Randomization and Path Analyses' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-diagram + r-genomicranges + r-plotrix +) +optdepends=( + r-biocgenerics + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gmrp/lilac.py b/prepare/r-gmrp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gmrp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gmrp/lilac.yaml b/prepare/r-gmrp/lilac.yaml new file mode 100644 index 0000000000..9ae347db8e --- /dev/null +++ b/prepare/r-gmrp/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-diagram +- r-genomicranges +- r-plotrix +update_on: +- regex: GMRP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GMRP diff --git a/prepare/r-gmwt/PKGBUILD b/prepare/r-gmwt/PKGBUILD new file mode 100644 index 0000000000..a0294d0489 --- /dev/null +++ b/prepare/r-gmwt/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gMWT +_pkgver=1.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generalized Mann-Whitney Type Tests' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-clinfun + r-rcpp + r-rcpparmadillo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gmwt/lilac.py b/prepare/r-gmwt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gmwt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gmwt/lilac.yaml b/prepare/r-gmwt/lilac.yaml new file mode 100644 index 0000000000..17a3a2b92e --- /dev/null +++ b/prepare/r-gmwt/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clinfun +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: gMWT_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gMWT diff --git a/prepare/r-gnet2/PKGBUILD b/prepare/r-gnet2/PKGBUILD new file mode 100644 index 0000000000..04d8464daf --- /dev/null +++ b/prepare/r-gnet2/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GNET2 +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Constructing gene regulatory networks from expression data through functional module inference' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Apache') +depends=( + r + r-diagrammer + r-dplyr + r-ggplot2 + r-igraph + r-matrixstats + r-rcpp + r-reshape2 + r-summarizedexperiment + r-xgboost +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gnet2/lilac.py b/prepare/r-gnet2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gnet2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gnet2/lilac.yaml b/prepare/r-gnet2/lilac.yaml new file mode 100644 index 0000000000..d04eabcb72 --- /dev/null +++ b/prepare/r-gnet2/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-diagrammer +- r-dplyr +- r-ggplot2 +- r-igraph +- r-matrixstats +- r-rcpp +- r-reshape2 +- r-summarizedexperiment +- r-xgboost +update_on: +- regex: GNET2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GNET2 diff --git a/prepare/r-gnm/PKGBUILD b/prepare/r-gnm/PKGBUILD new file mode 100644 index 0000000000..cd3f1b992e --- /dev/null +++ b/prepare/r-gnm/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gnm +_pkgver=1.1-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generalized Nonlinear Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-qvcalc + r-relimp +) +optdepends=( + r-testthat + r-vcdextra +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gnm/lilac.py b/prepare/r-gnm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gnm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gnm/lilac.yaml b/prepare/r-gnm/lilac.yaml new file mode 100644 index 0000000000..a4c7f8c9fa --- /dev/null +++ b/prepare/r-gnm/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-qvcalc +- r-relimp +update_on: +- regex: gnm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gnm diff --git a/prepare/r-go.db/PKGBUILD b/prepare/r-go.db/PKGBUILD new file mode 100644 index 0000000000..466c5ee2c0 --- /dev/null +++ b/prepare/r-go.db/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GO.db +_pkgver=3.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A set of annotation maps describing the entire Gene Ontology' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi +) +optdepends=( + r-dbi +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-go.db/lilac.py b/prepare/r-go.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-go.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-go.db/lilac.yaml b/prepare/r-go.db/lilac.yaml new file mode 100644 index 0000000000..9aecd7218e --- /dev/null +++ b/prepare/r-go.db/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +update_on: +- regex: GO.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GO.db diff --git a/prepare/r-goexpress/PKGBUILD b/prepare/r-goexpress/PKGBUILD new file mode 100644 index 0000000000..80f692e752 --- /dev/null +++ b/prepare/r-goexpress/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GOexpress +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualise microarray and RNAseq data using gene ontology annotations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biomart + r-ggplot2 + r-gplots + r-randomforest + r-rcolorbrewer + r-rcurl + r-stringr +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-goexpress/lilac.py b/prepare/r-goexpress/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-goexpress/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-goexpress/lilac.yaml b/prepare/r-goexpress/lilac.yaml new file mode 100644 index 0000000000..aea4b3b218 --- /dev/null +++ b/prepare/r-goexpress/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biomart +- r-ggplot2 +- r-gplots +- r-randomforest +- r-rcolorbrewer +- r-rcurl +- r-stringr +update_on: +- regex: GOexpress_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GOexpress diff --git a/prepare/r-gofkernel/PKGBUILD b/prepare/r-gofkernel/PKGBUILD new file mode 100644 index 0000000000..cf2053ce4e --- /dev/null +++ b/prepare/r-gofkernel/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GoFKernel +_pkgver=2.1-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Testing Goodness-of-Fit with the Kernel Density Estimator' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gofkernel/lilac.py b/prepare/r-gofkernel/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gofkernel/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gofkernel/lilac.yaml b/prepare/r-gofkernel/lilac.yaml new file mode 100644 index 0000000000..cb277a4fbc --- /dev/null +++ b/prepare/r-gofkernel/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: GoFKernel_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=GoFKernel diff --git a/prepare/r-goftest/PKGBUILD b/prepare/r-goftest/PKGBUILD new file mode 100644 index 0000000000..f0f7c818b4 --- /dev/null +++ b/prepare/r-goftest/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=goftest +_pkgver=1.2-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Classical Goodness-of-Fit Tests for Univariate Distributions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-goftest/lilac.py b/prepare/r-goftest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-goftest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-goftest/lilac.yaml b/prepare/r-goftest/lilac.yaml new file mode 100644 index 0000000000..685058eae3 --- /dev/null +++ b/prepare/r-goftest/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: goftest_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=goftest diff --git a/prepare/r-gofuncr/PKGBUILD b/prepare/r-gofuncr/PKGBUILD new file mode 100644 index 0000000000..e743d7cf1b --- /dev/null +++ b/prepare/r-gofuncr/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GOfuncR +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene ontology enrichment using FUNC' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-genomicranges + r-gtools + r-iranges + r-mapplots + r-rcpp + r-vioplot +) +optdepends=( + r-biocstyle + r-homo.sapiens + r-knitr + r-markdown + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gofuncr/lilac.py b/prepare/r-gofuncr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gofuncr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gofuncr/lilac.yaml b/prepare/r-gofuncr/lilac.yaml new file mode 100644 index 0000000000..cd96af8c35 --- /dev/null +++ b/prepare/r-gofuncr/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-genomicranges +- r-gtools +- r-iranges +- r-mapplots +- r-rcpp +- r-vioplot +update_on: +- regex: GOfuncR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GOfuncR diff --git a/prepare/r-golem/PKGBUILD b/prepare/r-golem/PKGBUILD new file mode 100644 index 0000000000..d53207ee4b --- /dev/null +++ b/prepare/r-golem/PKGBUILD @@ -0,0 +1,63 @@ +# Maintainer: Guoyi Zhang + +_pkgname=golem +_pkgver=0.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Framework for Robust Shiny Applications' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-attempt + r-cli + r-config + r-crayon + r-desc + r-dockerfiler + r-fs + r-here + r-htmltools + r-jsonlite + r-pkgload + r-remotes + r-rlang + r-roxygen2 + r-rstudioapi + r-shiny + r-testthat + r-usethis + r-yaml +) +optdepends=( + r-covr + r-devtools + r-glue + r-knitr + r-pkgbuild + r-pkgdown + r-processx + r-purrr + r-rcmdcheck + r-rmarkdown + r-rsconnect + r-spelling + r-stringr + r-tools + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-golem/lilac.py b/prepare/r-golem/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-golem/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-golem/lilac.yaml b/prepare/r-golem/lilac.yaml new file mode 100644 index 0000000000..b48e003033 --- /dev/null +++ b/prepare/r-golem/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-attempt +- r-cli +- r-config +- r-crayon +- r-desc +- r-dockerfiler +- r-fs +- r-here +- r-htmltools +- r-jsonlite +- r-pkgload +- r-remotes +- r-rlang +- r-roxygen2 +- r-rstudioapi +- r-shiny +- r-testthat +- r-usethis +- r-yaml +update_on: +- regex: golem_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=golem diff --git a/prepare/r-googleauthr/PKGBUILD b/prepare/r-googleauthr/PKGBUILD new file mode 100644 index 0000000000..fc564b0f69 --- /dev/null +++ b/prepare/r-googleauthr/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=googleAuthR +_pkgver=1.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Authenticate and Create Google APIs' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-assertthat + r-cli + r-digest + r-gargle + r-httr + r-jsonlite + r-memoise + r-rlang +) +optdepends=( + r-bigqueryr + r-covr + r-devtools + r-formatr + r-googleanalyticsr + r-knitr + r-miniui + r-rmarkdown + r-roxygen2 + r-rstudioapi + r-shiny + r-testthat + r-usethis +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-googleauthr/lilac.py b/prepare/r-googleauthr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-googleauthr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-googleauthr/lilac.yaml b/prepare/r-googleauthr/lilac.yaml new file mode 100644 index 0000000000..7650d0d424 --- /dev/null +++ b/prepare/r-googleauthr/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-cli +- r-digest +- r-gargle +- r-httr +- r-jsonlite +- r-memoise +- r-rlang +update_on: +- regex: googleAuthR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=googleAuthR diff --git a/prepare/r-googlecloudstorager/PKGBUILD b/prepare/r-googlecloudstorager/PKGBUILD new file mode 100644 index 0000000000..611f03501b --- /dev/null +++ b/prepare/r-googlecloudstorager/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=googleCloudStorageR +_pkgver=0.7.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interface with Google Cloud Storage API' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-assertthat + r-cli + r-curl + r-googleauthr + r-httr + r-jsonlite + r-openssl + r-yaml + r-zip +) +optdepends=( + r-fs + r-googlecomputeenginer + r-knitr + r-readr + r-rmarkdown + r-sodium + r-testthat + r-usethis +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-googlecloudstorager/lilac.py b/prepare/r-googlecloudstorager/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-googlecloudstorager/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-googlecloudstorager/lilac.yaml b/prepare/r-googlecloudstorager/lilac.yaml new file mode 100644 index 0000000000..c12abe7d5b --- /dev/null +++ b/prepare/r-googlecloudstorager/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-cli +- r-curl +- r-googleauthr +- r-httr +- r-jsonlite +- r-openssl +- r-yaml +- r-zip +update_on: +- regex: googleCloudStorageR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=googleCloudStorageR diff --git a/prepare/r-googledrive/PKGBUILD b/prepare/r-googledrive/PKGBUILD new file mode 100644 index 0000000000..44a6f42d9b --- /dev/null +++ b/prepare/r-googledrive/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=googledrive +_pkgver=2.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Interface to Google Drive' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-cli + r-gargle + r-glue + r-httr + r-jsonlite + r-lifecycle + r-magrittr + r-pillar + r-purrr + r-rlang + r-tibble + r-uuid + r-vctrs + r-withr +) +optdepends=( + r-covr + r-curl + r-downlit + r-dplyr + r-knitr + r-mockr + r-rmarkdown + r-roxygen2 + r-sodium + r-spelling + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-googledrive/lilac.py b/prepare/r-googledrive/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-googledrive/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-googledrive/lilac.yaml b/prepare/r-googledrive/lilac.yaml new file mode 100644 index 0000000000..1616e22a51 --- /dev/null +++ b/prepare/r-googledrive/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cli +- r-gargle +- r-glue +- r-httr +- r-jsonlite +- r-lifecycle +- r-magrittr +- r-pillar +- r-purrr +- r-rlang +- r-tibble +- r-uuid +- r-vctrs +- r-withr +update_on: +- regex: googledrive_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=googledrive diff --git a/prepare/r-googlesheets4/PKGBUILD b/prepare/r-googlesheets4/PKGBUILD new file mode 100644 index 0000000000..3f5bd91c3f --- /dev/null +++ b/prepare/r-googlesheets4/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=googlesheets4 +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Access Google Sheets using the Sheets API V4' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-cellranger + r-cli + r-curl + r-gargle + r-glue + r-googledrive + r-httr + r-ids + r-magrittr + r-purrr + r-rematch2 + r-rlang + r-tibble + r-vctrs +) +optdepends=( + r-covr + r-readr + r-rmarkdown + r-sodium + r-spelling + r-testthat + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-googlesheets4/lilac.py b/prepare/r-googlesheets4/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-googlesheets4/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-googlesheets4/lilac.yaml b/prepare/r-googlesheets4/lilac.yaml new file mode 100644 index 0000000000..eadf86297f --- /dev/null +++ b/prepare/r-googlesheets4/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cellranger +- r-cli +- r-curl +- r-gargle +- r-glue +- r-googledrive +- r-httr +- r-ids +- r-magrittr +- r-purrr +- r-rematch2 +- r-rlang +- r-tibble +- r-vctrs +update_on: +- regex: googlesheets4_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=googlesheets4 diff --git a/prepare/r-googlevis/PKGBUILD b/prepare/r-googlevis/PKGBUILD new file mode 100644 index 0000000000..da78b8b656 --- /dev/null +++ b/prepare/r-googlevis/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=googleVis +_pkgver=0.6.10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Interface to Google Charts' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-jsonlite +) +optdepends=( + r-data.table + r-httpuv + r-knitr + r-markdown + r-rmarkdown + r-shiny +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-googlevis/lilac.py b/prepare/r-googlevis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-googlevis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-googlevis/lilac.yaml b/prepare/r-googlevis/lilac.yaml new file mode 100644 index 0000000000..2e9f878c5a --- /dev/null +++ b/prepare/r-googlevis/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-jsonlite +update_on: +- regex: googleVis_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=googleVis diff --git a/prepare/r-gopro/PKGBUILD b/prepare/r-gopro/PKGBUILD new file mode 100644 index 0000000000..712a660409 --- /dev/null +++ b/prepare/r-gopro/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GOpro +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Find the most characteristic gene ontology terms for groups of human genes' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-bh + r-dendextend + r-doparallel + r-foreach + r-go.db + r-iranges + r-multiassayexperiment + r-org.hs.eg.db + r-rcpp + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-rtcga.pancan12 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gopro/lilac.py b/prepare/r-gopro/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gopro/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gopro/lilac.yaml b/prepare/r-gopro/lilac.yaml new file mode 100644 index 0000000000..13024645c6 --- /dev/null +++ b/prepare/r-gopro/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-bh +- r-dendextend +- r-doparallel +- r-foreach +- r-go.db +- r-iranges +- r-multiassayexperiment +- r-org.hs.eg.db +- r-rcpp +- r-s4vectors +update_on: +- regex: GOpro_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GOpro diff --git a/prepare/r-goprofiles/PKGBUILD b/prepare/r-goprofiles/PKGBUILD new file mode 100644 index 0000000000..d6a99f96b6 --- /dev/null +++ b/prepare/r-goprofiles/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=goProfiles +_pkgver=1.56.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='goProfiles: an R package for the statistical analysis of functional profiles' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biobase + r-compquadform + r-go.db + r-stringr +) +optdepends=( + r-org.hs.eg.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-goprofiles/lilac.py b/prepare/r-goprofiles/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-goprofiles/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-goprofiles/lilac.yaml b/prepare/r-goprofiles/lilac.yaml new file mode 100644 index 0000000000..f930b4ba44 --- /dev/null +++ b/prepare/r-goprofiles/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-compquadform +- r-go.db +- r-stringr +update_on: +- regex: goProfiles_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/goProfiles diff --git a/prepare/r-goric/PKGBUILD b/prepare/r-goric/PKGBUILD new file mode 100644 index 0000000000..e0f1974afa --- /dev/null +++ b/prepare/r-goric/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=goric +_pkgver=1.1-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generalized Order-Restricted Information Criterion' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mvtnorm + r-quadprog +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-goric/lilac.py b/prepare/r-goric/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-goric/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-goric/lilac.yaml b/prepare/r-goric/lilac.yaml new file mode 100644 index 0000000000..810854787d --- /dev/null +++ b/prepare/r-goric/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mvtnorm +- r-quadprog +update_on: +- regex: goric_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=goric diff --git a/prepare/r-gosemsim/PKGBUILD b/prepare/r-gosemsim/PKGBUILD new file mode 100644 index 0000000000..05fd948031 --- /dev/null +++ b/prepare/r-gosemsim/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GOSemSim +_pkgver=2.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GO-terms Semantic Similarity Measures' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-go.db + r-rcpp +) +optdepends=( + r-annotationhub + r-biocmanager + r-clusterprofiler + r-dose + r-knitr + r-org.hs.eg.db + r-prettydoc + r-rmarkdown + r-rocr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gosemsim/lilac.py b/prepare/r-gosemsim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gosemsim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gosemsim/lilac.yaml b/prepare/r-gosemsim/lilac.yaml new file mode 100644 index 0000000000..9767505402 --- /dev/null +++ b/prepare/r-gosemsim/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-go.db +- r-rcpp +update_on: +- regex: GOSemSim_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GOSemSim diff --git a/prepare/r-goseq/PKGBUILD b/prepare/r-goseq/PKGBUILD new file mode 100644 index 0000000000..81d88dd683 --- /dev/null +++ b/prepare/r-goseq/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=goseq +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Ontology analyser for RNA-seq and other length biased data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-annotationdbi + r-biasedurn + r-biocgenerics + r-genelendatabase + r-go.db +) +optdepends=( + r-edger + r-org.hs.eg.db + r-rtracklayer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-goseq/lilac.py b/prepare/r-goseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-goseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-goseq/lilac.yaml b/prepare/r-goseq/lilac.yaml new file mode 100644 index 0000000000..78212120fb --- /dev/null +++ b/prepare/r-goseq/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biasedurn +- r-biocgenerics +- r-genelendatabase +- r-go.db +update_on: +- regex: goseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/goseq diff --git a/prepare/r-gosim/PKGBUILD b/prepare/r-gosim/PKGBUILD new file mode 100644 index 0000000000..1f5852031b --- /dev/null +++ b/prepare/r-gosim/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GOSim +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Computation of functional similarities between GO terms and gene products; GO enrichment analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotate + r-annotationdbi + r-corpcor + r-flexmix + r-go.db + r-graph + r-org.hs.eg.db + r-rbgl + r-rcpp + r-topgo +) +optdepends=( + r-igraph +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gosim/lilac.py b/prepare/r-gosim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gosim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gosim/lilac.yaml b/prepare/r-gosim/lilac.yaml new file mode 100644 index 0000000000..2c9ba7bd37 --- /dev/null +++ b/prepare/r-gosim/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-corpcor +- r-flexmix +- r-go.db +- r-graph +- r-org.hs.eg.db +- r-rbgl +- r-rcpp +- r-topgo +update_on: +- regex: GOSim_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GOSim diff --git a/prepare/r-gostag/PKGBUILD b/prepare/r-gostag/PKGBUILD new file mode 100644 index 0000000000..79f9f02c0f --- /dev/null +++ b/prepare/r-gostag/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=goSTAG +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A tool to use GO Subtrees to Tag and Annotate Genes within a set' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biomart + r-go.db + r-memoise +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gostag/lilac.py b/prepare/r-gostag/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gostag/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gostag/lilac.yaml b/prepare/r-gostag/lilac.yaml new file mode 100644 index 0000000000..8d0f020e60 --- /dev/null +++ b/prepare/r-gostag/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biomart +- r-go.db +- r-memoise +update_on: +- regex: goSTAG_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/goSTAG diff --git a/prepare/r-gostats/PKGBUILD b/prepare/r-gostats/PKGBUILD new file mode 100644 index 0000000000..975ef2d25c --- /dev/null +++ b/prepare/r-gostats/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GOstats +_pkgver=2.60.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for manipulating GO and microarrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotate + r-annotationdbi + r-annotationforge + r-biobase + r-category + r-go.db + r-graph + r-rbgl + r-rgraphviz +) +optdepends=( + r-all + r-biocgenerics + r-genefilter + r-geneplotter + r-gseabase + r-hgu95av2.db + r-multtest + r-org.hs.eg.db + r-rcolorbrewer + r-runit + r-sparsem + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gostats/lilac.py b/prepare/r-gostats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gostats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gostats/lilac.yaml b/prepare/r-gostats/lilac.yaml new file mode 100644 index 0000000000..ad739ae73c --- /dev/null +++ b/prepare/r-gostats/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-annotationforge +- r-biobase +- r-category +- r-go.db +- r-graph +- r-rbgl +- r-rgraphviz +update_on: +- regex: GOstats_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GOstats diff --git a/prepare/r-gosummaries/PKGBUILD b/prepare/r-gosummaries/PKGBUILD new file mode 100644 index 0000000000..3b5cfeaa46 --- /dev/null +++ b/prepare/r-gosummaries/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GOsummaries +_pkgver=2.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Word cloud summaries of GO enrichment analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-gprofiler + r-gtable + r-limma + r-plyr + r-rcpp + r-reshape2 +) +optdepends=( + r-vegan +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gosummaries/lilac.py b/prepare/r-gosummaries/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gosummaries/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gosummaries/lilac.yaml b/prepare/r-gosummaries/lilac.yaml new file mode 100644 index 0000000000..90e12d5958 --- /dev/null +++ b/prepare/r-gosummaries/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gprofiler +- r-gtable +- r-limma +- r-plyr +- r-rcpp +- r-reshape2 +update_on: +- regex: GOsummaries_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GOsummaries diff --git a/prepare/r-gothic/PKGBUILD b/prepare/r-gothic/PKGBUILD new file mode 100644 index 0000000000..9c555d4435 --- /dev/null +++ b/prepare/r-gothic/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GOTHiC +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Binomial test for Hi-C data analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocmanager + r-biostrings + r-bsgenome + r-data.table + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-rsamtools + r-rtracklayer + r-s4vectors + r-shortread +) +optdepends=( + r-hicdatalymphoblast + r-parallel +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gothic/lilac.py b/prepare/r-gothic/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gothic/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gothic/lilac.yaml b/prepare/r-gothic/lilac.yaml new file mode 100644 index 0000000000..10672e7879 --- /dev/null +++ b/prepare/r-gothic/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocmanager +- r-biostrings +- r-bsgenome +- r-data.table +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-shortread +update_on: +- regex: GOTHiC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GOTHiC diff --git a/prepare/r-gotools/PKGBUILD b/prepare/r-gotools/PKGBUILD new file mode 100644 index 0000000000..5751b6f9d9 --- /dev/null +++ b/prepare/r-gotools/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=goTools +_pkgver=1.68.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for Gene Ontology database' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-go.db +) +optdepends=( + r-hgu133a.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gotools/lilac.py b/prepare/r-gotools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gotools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gotools/lilac.yaml b/prepare/r-gotools/lilac.yaml new file mode 100644 index 0000000000..203b77b382 --- /dev/null +++ b/prepare/r-gotools/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-go.db +update_on: +- regex: goTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/goTools diff --git a/prepare/r-gower/PKGBUILD b/prepare/r-gower/PKGBUILD new file mode 100644 index 0000000000..838bdb5f6b --- /dev/null +++ b/prepare/r-gower/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gower +_pkgver=0.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Gower's Distance" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gower/lilac.py b/prepare/r-gower/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gower/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gower/lilac.yaml b/prepare/r-gower/lilac.yaml new file mode 100644 index 0000000000..24753f8236 --- /dev/null +++ b/prepare/r-gower/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gower_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gower diff --git a/prepare/r-gpa/PKGBUILD b/prepare/r-gpa/PKGBUILD new file mode 100644 index 0000000000..becceb6bf0 --- /dev/null +++ b/prepare/r-gpa/PKGBUILD @@ -0,0 +1,38 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=GPA +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GPA (Genetic analysis incorporating Pleiotropy and Annotation)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dt + r-ggplot2 + r-ggrepel + r-plyr + r-rcpp + r-shiny + r-shinybs + r-vegan +) +optdepends=( + r-gpaexample +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gpa/lilac.py b/prepare/r-gpa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gpa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gpa/lilac.yaml b/prepare/r-gpa/lilac.yaml new file mode 100644 index 0000000000..6a7e8716d9 --- /dev/null +++ b/prepare/r-gpa/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dt +- r-ggplot2 +- r-ggrepel +- r-plyr +- r-rcpp +- r-shiny +- r-shinybs +- r-vegan +update_on: +- regex: GPA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GPA diff --git a/prepare/r-gpart/PKGBUILD b/prepare/r-gpart/PKGBUILD new file mode 100644 index 0000000000..b28a0171e6 --- /dev/null +++ b/prepare/r-gpart/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gpart +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Human genome partitioning of dense sequencing data by identifying haplotype blocks' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-biomart + r-data.table + r-genomicranges + r-homo.sapiens + r-igraph + r-iranges + r-organismdbi + r-rcpp + r-txdb.hsapiens.ucsc.hg38.knowngene +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gpart/lilac.py b/prepare/r-gpart/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gpart/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gpart/lilac.yaml b/prepare/r-gpart/lilac.yaml new file mode 100644 index 0000000000..7e39eab51a --- /dev/null +++ b/prepare/r-gpart/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biomart +- r-data.table +- r-genomicranges +- r-homo.sapiens +- r-igraph +- r-iranges +- r-organismdbi +- r-rcpp +- r-txdb.hsapiens.ucsc.hg38.knowngene +update_on: +- regex: gpart_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gpart diff --git a/prepare/r-gplots/PKGBUILD b/prepare/r-gplots/PKGBUILD new file mode 100644 index 0000000000..5004613d54 --- /dev/null +++ b/prepare/r-gplots/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gplots +_pkgver=3.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Various R Programming Tools for Plotting Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-catools + r-gtools +) +optdepends=( + r-grid + r-knitr + r-mass +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gplots/lilac.py b/prepare/r-gplots/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gplots/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gplots/lilac.yaml b/prepare/r-gplots/lilac.yaml new file mode 100644 index 0000000000..7912f8c282 --- /dev/null +++ b/prepare/r-gplots/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-catools +- r-gtools +update_on: +- regex: gplots_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gplots diff --git a/prepare/r-gpls/PKGBUILD b/prepare/r-gpls/PKGBUILD new file mode 100644 index 0000000000..5d916e96a8 --- /dev/null +++ b/prepare/r-gpls/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gpls +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Classification using generalized partial least squares' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-mass +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gpls/lilac.py b/prepare/r-gpls/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gpls/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gpls/lilac.yaml b/prepare/r-gpls/lilac.yaml new file mode 100644 index 0000000000..5824855930 --- /dev/null +++ b/prepare/r-gpls/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gpls_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gpls diff --git a/prepare/r-gprege/PKGBUILD b/prepare/r-gprege/PKGBUILD new file mode 100644 index 0000000000..f6b895138b --- /dev/null +++ b/prepare/r-gprege/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gprege +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gaussian Process Ranking and Estimation of Gene Expression time-series' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-gptk +) +optdepends=( + r-spam +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gprege/lilac.py b/prepare/r-gprege/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gprege/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gprege/lilac.yaml b/prepare/r-gprege/lilac.yaml new file mode 100644 index 0000000000..f224e367ac --- /dev/null +++ b/prepare/r-gprege/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gptk +update_on: +- regex: gprege_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gprege diff --git a/prepare/r-gprofiler/PKGBUILD b/prepare/r-gprofiler/PKGBUILD new file mode 100644 index 0000000000..151d0a0847 --- /dev/null +++ b/prepare/r-gprofiler/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gProfileR +_pkgver=0.7.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Interface to the 'g:Profiler' Toolkit" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-plyr + r-rcurl +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gprofiler/lilac.py b/prepare/r-gprofiler/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gprofiler/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gprofiler/lilac.yaml b/prepare/r-gprofiler/lilac.yaml new file mode 100644 index 0000000000..9b5cd38e45 --- /dev/null +++ b/prepare/r-gprofiler/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-plyr +- r-rcurl +update_on: +- regex: gProfileR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gProfileR diff --git a/prepare/r-gprofiler2/PKGBUILD b/prepare/r-gprofiler2/PKGBUILD new file mode 100644 index 0000000000..83c8e85129 --- /dev/null +++ b/prepare/r-gprofiler2/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gprofiler2 +_pkgver=0.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Interface to the 'g:Profiler' Toolset" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-crosstalk + r-dplyr + r-ggplot2 + r-gridextra + r-jsonlite + r-plotly + r-rcurl + r-tidyr + r-viridislite +) +optdepends=( + r-knitr + r-prettydoc + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gprofiler2/lilac.py b/prepare/r-gprofiler2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gprofiler2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gprofiler2/lilac.yaml b/prepare/r-gprofiler2/lilac.yaml new file mode 100644 index 0000000000..6c40033aac --- /dev/null +++ b/prepare/r-gprofiler2/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-crosstalk +- r-dplyr +- r-ggplot2 +- r-gridextra +- r-jsonlite +- r-plotly +- r-rcurl +- r-tidyr +- r-viridislite +update_on: +- regex: gprofiler2_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gprofiler2 diff --git a/prepare/r-gptk/PKGBUILD b/prepare/r-gptk/PKGBUILD new file mode 100644 index 0000000000..9dc73ca89b --- /dev/null +++ b/prepare/r-gptk/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gptk +_pkgver=1.08 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gaussian Processes Tool-Kit' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-fields +) +optdepends=( + r-spam +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gptk/lilac.py b/prepare/r-gptk/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gptk/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gptk/lilac.yaml b/prepare/r-gptk/lilac.yaml new file mode 100644 index 0000000000..9b8dcc64ec --- /dev/null +++ b/prepare/r-gptk/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fields +update_on: +- regex: gptk_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gptk diff --git a/prepare/r-gpumagic/PKGBUILD b/prepare/r-gpumagic/PKGBUILD new file mode 100644 index 0000000000..dd1cece786 --- /dev/null +++ b/prepare/r-gpumagic/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: 1. C++11, 2. a graphic driver or a CPU SDK. 3. ICDloader For Windows user, an ICD loader is required atC:/windows/system32/OpenCL.dll (Usually it is installed by thegraphic driver). For Linux user (Except mac):ocl-icd-opencl-dev package is required. For Mac user, no actionis needed for the system has installed the dependency. 4. GNUmake +# Maintainer: Guoyi Zhang + +_pkgname=gpuMagic +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An openCL compiler with the capacity to compile R functions and run the code on GPU' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-deriv + r-desctools + r-digest + r-pryr + r-rcpp + r-stringr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gpumagic/lilac.py b/prepare/r-gpumagic/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gpumagic/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gpumagic/lilac.yaml b/prepare/r-gpumagic/lilac.yaml new file mode 100644 index 0000000000..7f116d22e8 --- /dev/null +++ b/prepare/r-gpumagic/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-deriv +- r-desctools +- r-digest +- r-pryr +- r-rcpp +- r-stringr +update_on: +- regex: gpuMagic_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gpuMagic diff --git a/prepare/r-graddescent/PKGBUILD b/prepare/r-graddescent/PKGBUILD new file mode 100644 index 0000000000..a9f15dc6bb --- /dev/null +++ b/prepare/r-graddescent/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gradDescent +_pkgver=3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gradient Descent for Regression Tasks' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-graddescent/lilac.py b/prepare/r-graddescent/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-graddescent/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-graddescent/lilac.yaml b/prepare/r-graddescent/lilac.yaml new file mode 100644 index 0000000000..1b8d4470b5 --- /dev/null +++ b/prepare/r-graddescent/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gradDescent_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gradDescent diff --git a/prepare/r-grain/PKGBUILD b/prepare/r-grain/PKGBUILD new file mode 100644 index 0000000000..89fb2098a0 --- /dev/null +++ b/prepare/r-grain/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gRain +_pkgver=1.3-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Graphical Independence Networks' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-graph + r-grbase + r-igraph + r-magrittr + r-rcpp + r-rcpparmadillo + r-rcppeigen + r-rgraphviz +) +optdepends=( + r-knitr + r-microbenchmark + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-grain/lilac.py b/prepare/r-grain/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-grain/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-grain/lilac.yaml b/prepare/r-grain/lilac.yaml new file mode 100644 index 0000000000..69a89a81eb --- /dev/null +++ b/prepare/r-grain/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +- r-grbase +- r-igraph +- r-magrittr +- r-rcpp +- r-rcpparmadillo +- r-rcppeigen +- r-rgraphviz +update_on: +- regex: gRain_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gRain diff --git a/prepare/r-gramm4r/PKGBUILD b/prepare/r-gramm4r/PKGBUILD new file mode 100644 index 0000000000..cce41b4e19 --- /dev/null +++ b/prepare/r-gramm4r/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gramm4R +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generalized correlation analysis and model construction strategy for metabolome and microbiome' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-basictrendline + r-investr + r-minerva + r-psych + r-delayedarray + r-summarizedexperiment + r-phyloseq + +) +makedepends=( + git + tar +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("git+https://git.bioconductor.org/packages/${_pkgname}.git") +sha256sums=('SKIP') + +build() { + tar -zcvf ${_pkgname}.tar.gz ${_pkgname} + R CMD INSTALL ${_pkgname}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: + diff --git a/prepare/r-gramm4r/lilac.py b/prepare/r-gramm4r/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gramm4r/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gramm4r/lilac.yaml b/prepare/r-gramm4r/lilac.yaml new file mode 100644 index 0000000000..94c01eabe4 --- /dev/null +++ b/prepare/r-gramm4r/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-basictrendline +- r-investr +- r-minerva +- r-psych +- r-delayedarray +- r-summarizedexperiment +- r-phyloseq +update_on: +- regex: Version(\d+.\d+.\d+) + source: regex + url: https://bioconductor.org/packages/gramm4R diff --git a/prepare/r-granulator/PKGBUILD b/prepare/r-granulator/PKGBUILD new file mode 100644 index 0000000000..787ee1fcbb --- /dev/null +++ b/prepare/r-granulator/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=granulator +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cowplot + r-dplyr + r-dtangle + r-e1071 + r-epir + r-ggplot2 + r-ggplotify + r-limsolve + r-magrittr + r-nnls + r-pheatmap + r-purrr + r-rlang + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-granulator/lilac.py b/prepare/r-granulator/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-granulator/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-granulator/lilac.yaml b/prepare/r-granulator/lilac.yaml new file mode 100644 index 0000000000..48bde91092 --- /dev/null +++ b/prepare/r-granulator/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cowplot +- r-dplyr +- r-dtangle +- r-e1071 +- r-epir +- r-ggplot2 +- r-ggplotify +- r-limsolve +- r-magrittr +- r-nnls +- r-pheatmap +- r-purrr +- r-rlang +- r-tibble +- r-tidyr +update_on: +- regex: granulator_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/granulator diff --git a/prepare/r-graper/PKGBUILD b/prepare/r-graper/PKGBUILD new file mode 100644 index 0000000000..df0c3b6752 --- /dev/null +++ b/prepare/r-graper/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=graper +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bh + r-cowplot + r-ggplot2 + r-matrixstats + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-graper/lilac.py b/prepare/r-graper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-graper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-graper/lilac.yaml b/prepare/r-graper/lilac.yaml new file mode 100644 index 0000000000..331f02f7b7 --- /dev/null +++ b/prepare/r-graper/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-cowplot +- r-ggplot2 +- r-matrixstats +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: graper_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/graper diff --git a/prepare/r-graph/PKGBUILD b/prepare/r-graph/PKGBUILD new file mode 100644 index 0000000000..c09f33cfbd --- /dev/null +++ b/prepare/r-graph/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=graph +_pkgver=1.72.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='graph: A package to handle graph data structures' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics +) +optdepends=( + r-cluster + r-rbgl + r-rgraphviz + r-runit + r-sparsem + r-xml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-graph/lilac.py b/prepare/r-graph/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-graph/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-graph/lilac.yaml b/prepare/r-graph/lilac.yaml new file mode 100644 index 0000000000..2ba5ac6d05 --- /dev/null +++ b/prepare/r-graph/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +update_on: +- regex: graph_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/graph diff --git a/prepare/r-graphalignment/PKGBUILD b/prepare/r-graphalignment/PKGBUILD new file mode 100644 index 0000000000..17dbf1b76e --- /dev/null +++ b/prepare/r-graphalignment/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GraphAlignment +_pkgver=1.58.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GraphAlignment' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-graphalignment/lilac.py b/prepare/r-graphalignment/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-graphalignment/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-graphalignment/lilac.yaml b/prepare/r-graphalignment/lilac.yaml new file mode 100644 index 0000000000..6f0041e81d --- /dev/null +++ b/prepare/r-graphalignment/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: GraphAlignment_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GraphAlignment diff --git a/prepare/r-graphat/PKGBUILD b/prepare/r-graphat/PKGBUILD new file mode 100644 index 0000000000..d4a1181a9e --- /dev/null +++ b/prepare/r-graphat/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GraphAT +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Graph Theoretic Association Tests' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-graph + r-mcmcpack +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-graphat/lilac.py b/prepare/r-graphat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-graphat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-graphat/lilac.yaml b/prepare/r-graphat/lilac.yaml new file mode 100644 index 0000000000..be4c4089d8 --- /dev/null +++ b/prepare/r-graphat/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +- r-mcmcpack +update_on: +- regex: GraphAT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GraphAT diff --git a/prepare/r-graphite/PKGBUILD b/prepare/r-graphite/PKGBUILD new file mode 100644 index 0000000000..cd6bf7313a --- /dev/null +++ b/prepare/r-graphite/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=graphite +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GRAPH Interaction from pathway Topological Environment' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-annotationdbi + r-checkmate + r-graph + r-httr + r-rappdirs +) +optdepends=( + r-a4preproc + r-all + r-biocstyle + r-clipper + r-codetools + r-hgu133plus2.db + r-hgu95av2.db + r-impute + r-knitr + r-org.hs.eg.db + r-parallel + r-r.rsp + r-rcy3 + r-rmarkdown + r-spia + r-testthat + r-topologygsa +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-graphite/lilac.py b/prepare/r-graphite/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-graphite/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-graphite/lilac.yaml b/prepare/r-graphite/lilac.yaml new file mode 100644 index 0000000000..f970a69d71 --- /dev/null +++ b/prepare/r-graphite/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-checkmate +- r-graph +- r-httr +- r-rappdirs +update_on: +- regex: graphite_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/graphite diff --git a/prepare/r-graphlayouts/PKGBUILD b/prepare/r-graphlayouts/PKGBUILD new file mode 100644 index 0000000000..905b7067f5 --- /dev/null +++ b/prepare/r-graphlayouts/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=graphlayouts +_pkgver=0.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Additional Layout Algorithms for Network Visualizations' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-igraph + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-ggplot2 + r-ggraph + r-knitr + r-oaqc + r-rmarkdown + r-testthat + r-uwot +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-graphlayouts/lilac.py b/prepare/r-graphlayouts/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-graphlayouts/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-graphlayouts/lilac.yaml b/prepare/r-graphlayouts/lilac.yaml new file mode 100644 index 0000000000..25200d1c91 --- /dev/null +++ b/prepare/r-graphlayouts/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: graphlayouts_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=graphlayouts diff --git a/prepare/r-graphpac/PKGBUILD b/prepare/r-graphpac/PKGBUILD new file mode 100644 index 0000000000..6c60ade3e6 --- /dev/null +++ b/prepare/r-graphpac/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GraphPAC +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-igraph + r-ipac + r-rmallow + r-tsp +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-graphpac/lilac.py b/prepare/r-graphpac/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-graphpac/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-graphpac/lilac.yaml b/prepare/r-graphpac/lilac.yaml new file mode 100644 index 0000000000..003f7c7ddc --- /dev/null +++ b/prepare/r-graphpac/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +- r-ipac +- r-rmallow +- r-tsp +update_on: +- regex: GraphPAC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GraphPAC diff --git a/prepare/r-grbase/PKGBUILD b/prepare/r-grbase/PKGBUILD new file mode 100644 index 0000000000..a593c23195 --- /dev/null +++ b/prepare/r-grbase/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gRbase +_pkgver=1.8-6.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Package for Graphical Modelling in R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-graph + r-igraph + r-magrittr + r-rbgl + r-rcpp + r-rcpparmadillo + r-rcppeigen + r-rgraphviz +) +optdepends=( + r-knitr + r-microbenchmark + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-grbase/lilac.py b/prepare/r-grbase/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-grbase/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-grbase/lilac.yaml b/prepare/r-grbase/lilac.yaml new file mode 100644 index 0000000000..b6791d9d4d --- /dev/null +++ b/prepare/r-grbase/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +- r-igraph +- r-magrittr +- r-rbgl +- r-rcpp +- r-rcpparmadillo +- r-rcppeigen +- r-rgraphviz +update_on: +- regex: gRbase_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gRbase diff --git a/prepare/r-grenits/PKGBUILD b/prepare/r-grenits/PKGBUILD new file mode 100644 index 0000000000..bdbcbd9809 --- /dev/null +++ b/prepare/r-grenits/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GRENITS +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Regulatory Network Inference Using Time Series' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-rcpp + r-rcpparmadillo + r-reshape2 +) +optdepends=( + r-network +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-grenits/lilac.py b/prepare/r-grenits/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-grenits/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-grenits/lilac.yaml b/prepare/r-grenits/lilac.yaml new file mode 100644 index 0000000000..31d7037a25 --- /dev/null +++ b/prepare/r-grenits/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-rcpp +- r-rcpparmadillo +- r-reshape2 +update_on: +- regex: GRENITS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GRENITS diff --git a/prepare/r-greylistchip/PKGBUILD b/prepare/r-greylistchip/PKGBUILD new file mode 100644 index 0000000000..4f49f8e46f --- /dev/null +++ b/prepare/r-greylistchip/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GreyListChIP +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Grey Lists -- Mask Artefact Regions Based on ChIP Inputs' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bsgenome + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-rsamtools + r-rtracklayer + r-summarizedexperiment +) +optdepends=( + r-biocgenerics + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-greylistchip/lilac.py b/prepare/r-greylistchip/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-greylistchip/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-greylistchip/lilac.yaml b/prepare/r-greylistchip/lilac.yaml new file mode 100644 index 0000000000..2024693e57 --- /dev/null +++ b/prepare/r-greylistchip/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-rsamtools +- r-rtracklayer +- r-summarizedexperiment +update_on: +- regex: GreyListChIP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GreyListChIP diff --git a/prepare/r-gridbase/PKGBUILD b/prepare/r-gridbase/PKGBUILD new file mode 100644 index 0000000000..1d80730883 --- /dev/null +++ b/prepare/r-gridbase/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gridBase +_pkgver=0.4-7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integration of base and grid graphics' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-lattice +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gridbase/lilac.py b/prepare/r-gridbase/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gridbase/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gridbase/lilac.yaml b/prepare/r-gridbase/lilac.yaml new file mode 100644 index 0000000000..125e7dde18 --- /dev/null +++ b/prepare/r-gridbase/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gridBase_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gridBase diff --git a/prepare/r-gridextra/PKGBUILD b/prepare/r-gridextra/PKGBUILD new file mode 100644 index 0000000000..22dde60168 --- /dev/null +++ b/prepare/r-gridextra/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gridExtra +_pkgver=2.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Miscellaneous Functions for "Grid" Graphics' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-gtable +) +optdepends=( + r-egg + r-ggplot2 + r-knitr + r-lattice + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gridextra/lilac.py b/prepare/r-gridextra/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gridextra/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gridextra/lilac.yaml b/prepare/r-gridextra/lilac.yaml new file mode 100644 index 0000000000..2f79bdb437 --- /dev/null +++ b/prepare/r-gridextra/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gtable +update_on: +- regex: gridExtra_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gridExtra diff --git a/prepare/r-gridgraphics/PKGBUILD b/prepare/r-gridgraphics/PKGBUILD new file mode 100644 index 0000000000..710d213e58 --- /dev/null +++ b/prepare/r-gridgraphics/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gridGraphics +_pkgver=0.5-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Redraw Base Graphics Using 'grid' Graphics" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-magick + r-pdftools +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gridgraphics/lilac.py b/prepare/r-gridgraphics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gridgraphics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gridgraphics/lilac.yaml b/prepare/r-gridgraphics/lilac.yaml new file mode 100644 index 0000000000..55e9140ca1 --- /dev/null +++ b/prepare/r-gridgraphics/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gridGraphics_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gridGraphics diff --git a/prepare/r-gridsvg/PKGBUILD b/prepare/r-gridsvg/PKGBUILD new file mode 100644 index 0000000000..0f6bc65117 --- /dev/null +++ b/prepare/r-gridsvg/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gridSVG +_pkgver=1.7-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Export 'grid' Graphics as SVG" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-jsonlite + r-xml +) +optdepends=( + r-lattice +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gridsvg/lilac.py b/prepare/r-gridsvg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gridsvg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gridsvg/lilac.yaml b/prepare/r-gridsvg/lilac.yaml new file mode 100644 index 0000000000..d4be235f38 --- /dev/null +++ b/prepare/r-gridsvg/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-jsonlite +- r-xml +update_on: +- regex: gridSVG_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gridSVG diff --git a/prepare/r-gridtext/PKGBUILD b/prepare/r-gridtext/PKGBUILD new file mode 100644 index 0000000000..ced3551b7d --- /dev/null +++ b/prepare/r-gridtext/PKGBUILD @@ -0,0 +1,43 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=gridtext +_pkgver=0.1.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Improved Text Rendering Support for 'Grid' Graphics" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-jpeg + r-markdown + r-png + r-rcpp + r-rcurl + r-rlang + r-stringr + r-xml2 +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-testthat + r-vdiffr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gridtext/lilac.py b/prepare/r-gridtext/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gridtext/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gridtext/lilac.yaml b/prepare/r-gridtext/lilac.yaml new file mode 100644 index 0000000000..696db6cd6d --- /dev/null +++ b/prepare/r-gridtext/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-jpeg +- r-markdown +- r-png +- r-rcpp +- r-rcurl +- r-rlang +- r-stringr +- r-xml2 +update_on: +- regex: gridtext_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gridtext diff --git a/prepare/r-grimport/PKGBUILD b/prepare/r-grimport/PKGBUILD new file mode 100644 index 0000000000..dd0186972b --- /dev/null +++ b/prepare/r-grimport/PKGBUILD @@ -0,0 +1,34 @@ +# system requirements: ghostscript +# Maintainer: Guoyi Zhang + +_pkgname=grImport +_pkgver=0.9-5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Importing Vector Graphics' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-xml +) +optdepends=( + r-cluster + r-colorspace + r-lattice + r-survival +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-grimport/lilac.py b/prepare/r-grimport/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-grimport/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-grimport/lilac.yaml b/prepare/r-grimport/lilac.yaml new file mode 100644 index 0000000000..be945795fb --- /dev/null +++ b/prepare/r-grimport/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-xml +update_on: +- regex: grImport_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=grImport diff --git a/prepare/r-grmetrics/PKGBUILD b/prepare/r-grmetrics/PKGBUILD new file mode 100644 index 0000000000..091038723a --- /dev/null +++ b/prepare/r-grmetrics/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GRmetrics +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Calculate growth-rate inhibition (GR) metrics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-drc + r-ggplot2 + r-plotly + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-tinytex +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-grmetrics/lilac.py b/prepare/r-grmetrics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-grmetrics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-grmetrics/lilac.yaml b/prepare/r-grmetrics/lilac.yaml new file mode 100644 index 0000000000..76dcc8379f --- /dev/null +++ b/prepare/r-grmetrics/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-drc +- r-ggplot2 +- r-plotly +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: GRmetrics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GRmetrics diff --git a/prepare/r-grohmm/PKGBUILD b/prepare/r-grohmm/PKGBUILD new file mode 100644 index 0000000000..9200ccf9fb --- /dev/null +++ b/prepare/r-grohmm/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=groHMM +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GRO-seq Analysis Pipeline' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocstyle + r-edger + r-genomicfeatures + r-org.hs.eg.db + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-grohmm/lilac.py b/prepare/r-grohmm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-grohmm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-grohmm/lilac.yaml b/prepare/r-grohmm/lilac.yaml new file mode 100644 index 0000000000..22fe4cd7e0 --- /dev/null +++ b/prepare/r-grohmm/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-rtracklayer +- r-s4vectors +update_on: +- regex: groHMM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/groHMM diff --git a/prepare/r-grr/PKGBUILD b/prepare/r-grr/PKGBUILD new file mode 100644 index 0000000000..a788566ee3 --- /dev/null +++ b/prepare/r-grr/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=grr +_pkgver=0.9.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Alternative Implementations of Base R Functions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-grr/lilac.py b/prepare/r-grr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-grr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-grr/lilac.yaml b/prepare/r-grr/lilac.yaml new file mode 100644 index 0000000000..5e871bd6a9 --- /dev/null +++ b/prepare/r-grr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: grr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=grr diff --git a/prepare/r-grridge/PKGBUILD b/prepare/r-grridge/PKGBUILD new file mode 100644 index 0000000000..1fe8ae01d3 --- /dev/null +++ b/prepare/r-grridge/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GRridge +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Better prediction by use of co-data: Adaptive group-regularized ridge regression' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-glmnet + r-graph + r-iso + r-mvtnorm + r-penalized +) +optdepends=( + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-grridge/lilac.py b/prepare/r-grridge/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-grridge/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-grridge/lilac.yaml b/prepare/r-grridge/lilac.yaml new file mode 100644 index 0000000000..6cf1b1fa5e --- /dev/null +++ b/prepare/r-grridge/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-glmnet +- r-graph +- r-iso +- r-mvtnorm +- r-penalized +update_on: +- regex: GRridge_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GRridge diff --git a/prepare/r-gsa/PKGBUILD b/prepare/r-gsa/PKGBUILD new file mode 100644 index 0000000000..eb0fa22f11 --- /dev/null +++ b/prepare/r-gsa/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GSA +_pkgver=1.03.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Set Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +optdepends=( + r-impute +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gsa/lilac.py b/prepare/r-gsa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gsa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gsa/lilac.yaml b/prepare/r-gsa/lilac.yaml new file mode 100644 index 0000000000..5ae5a7af73 --- /dev/null +++ b/prepare/r-gsa/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: GSA_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=GSA diff --git a/prepare/r-gsalightning/PKGBUILD b/prepare/r-gsalightning/PKGBUILD new file mode 100644 index 0000000000..a0d4f29e0d --- /dev/null +++ b/prepare/r-gsalightning/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GSALightning +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast Permutation-based Gene Set Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gsalightning/lilac.py b/prepare/r-gsalightning/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gsalightning/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gsalightning/lilac.yaml b/prepare/r-gsalightning/lilac.yaml new file mode 100644 index 0000000000..2937a8755a --- /dev/null +++ b/prepare/r-gsalightning/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +update_on: +- regex: GSALightning_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GSALightning diff --git a/prepare/r-gsar/PKGBUILD b/prepare/r-gsar/PKGBUILD new file mode 100644 index 0000000000..2774ca62ba --- /dev/null +++ b/prepare/r-gsar/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GSAR +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Set Analysis in R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-igraph +) +optdepends=( + r-all + r-annotate + r-biobase + r-biocstyle + r-edger + r-genefilter + r-gseabase + r-gsvadata + r-hgu95av2.db + r-mass + r-org.hs.eg.db + r-tweedeseqcountdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gsar/lilac.py b/prepare/r-gsar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gsar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gsar/lilac.yaml b/prepare/r-gsar/lilac.yaml new file mode 100644 index 0000000000..f27c755d53 --- /dev/null +++ b/prepare/r-gsar/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +update_on: +- regex: GSAR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GSAR diff --git a/prepare/r-gsca/PKGBUILD b/prepare/r-gsca/PKGBUILD new file mode 100644 index 0000000000..e230ffbe10 --- /dev/null +++ b/prepare/r-gsca/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GSCA +_pkgver=2.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GSCA: Gene Set Context Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-gplots + r-rcolorbrewer + r-reshape2 + r-rhdf5 + r-shiny + r-sp +) +optdepends=( + r-affyhgu133a2expr + r-affyhgu133aexpr + r-affyhgu133plus2expr + r-affymoe4302expr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gsca/lilac.py b/prepare/r-gsca/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gsca/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gsca/lilac.yaml b/prepare/r-gsca/lilac.yaml new file mode 100644 index 0000000000..b07d931519 --- /dev/null +++ b/prepare/r-gsca/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gplots +- r-rcolorbrewer +- r-reshape2 +- r-rhdf5 +- r-shiny +- r-sp +update_on: +- regex: GSCA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GSCA diff --git a/prepare/r-gscreend/PKGBUILD b/prepare/r-gscreend/PKGBUILD new file mode 100644 index 0000000000..eb7692eec4 --- /dev/null +++ b/prepare/r-gscreend/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gscreend +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of pooled genetic screens' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-fgarch + r-nloptr + r-summarizedexperiment +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gscreend/lilac.py b/prepare/r-gscreend/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gscreend/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gscreend/lilac.yaml b/prepare/r-gscreend/lilac.yaml new file mode 100644 index 0000000000..742c10ab30 --- /dev/null +++ b/prepare/r-gscreend/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-fgarch +- r-nloptr +- r-summarizedexperiment +update_on: +- regex: gscreend_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gscreend diff --git a/prepare/r-gseabase/PKGBUILD b/prepare/r-gseabase/PKGBUILD new file mode 100644 index 0000000000..78ed7b5f51 --- /dev/null +++ b/prepare/r-gseabase/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GSEABase +_pkgver=1.56.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene set enrichment data structures and methods' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-graph + r-xml +) +optdepends=( + r-biocstyle + r-go.db + r-hgu95av2.db + r-knitr + r-org.hs.eg.db + r-reportingtools + r-rgraphviz + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gseabase/lilac.py b/prepare/r-gseabase/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gseabase/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gseabase/lilac.yaml b/prepare/r-gseabase/lilac.yaml new file mode 100644 index 0000000000..e6ccf68727 --- /dev/null +++ b/prepare/r-gseabase/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-graph +- r-xml +update_on: +- regex: GSEABase_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GSEABase diff --git a/prepare/r-gseabenchmarker/PKGBUILD b/prepare/r-gseabenchmarker/PKGBUILD new file mode 100644 index 0000000000..0534f90833 --- /dev/null +++ b/prepare/r-gseabenchmarker/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GSEABenchmarkeR +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Reproducible GSEA Benchmarking' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-annotationhub + r-biobase + r-biocfilecache + r-biocparallel + r-edger + r-enrichmentbrowser + r-experimenthub + r-keggandmetacoredzpathwaysgeo + r-keggdzpathwaysgeo + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-gse62944 + r-knitr + r-rappdirs + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gseabenchmarker/lilac.py b/prepare/r-gseabenchmarker/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gseabenchmarker/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gseabenchmarker/lilac.yaml b/prepare/r-gseabenchmarker/lilac.yaml new file mode 100644 index 0000000000..6ab06253b9 --- /dev/null +++ b/prepare/r-gseabenchmarker/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-biobase +- r-biocfilecache +- r-biocparallel +- r-edger +- r-enrichmentbrowser +- r-experimenthub +- r-keggandmetacoredzpathwaysgeo +- r-keggdzpathwaysgeo +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: GSEABenchmarkeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GSEABenchmarkeR diff --git a/prepare/r-gsealm/PKGBUILD b/prepare/r-gsealm/PKGBUILD new file mode 100644 index 0000000000..eba2a68566 --- /dev/null +++ b/prepare/r-gsealm/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GSEAlm +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Linear Model Toolset for Gene Set Enrichment Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase +) +optdepends=( + r-all + r-annotate + r-category + r-genefilter + r-gostats + r-gseabase + r-hgu95av2.db + r-multtest + r-rcolorbrewer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gsealm/lilac.py b/prepare/r-gsealm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gsealm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gsealm/lilac.yaml b/prepare/r-gsealm/lilac.yaml new file mode 100644 index 0000000000..df98378018 --- /dev/null +++ b/prepare/r-gsealm/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: GSEAlm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GSEAlm diff --git a/prepare/r-gseamining/PKGBUILD b/prepare/r-gseamining/PKGBUILD new file mode 100644 index 0000000000..14799492da --- /dev/null +++ b/prepare/r-gseamining/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GSEAmining +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Make Biological Sense of Gene Set Enrichment Analysis Outputs' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dendextend + r-dplyr + r-ggplot2 + r-ggwordcloud + r-gridextra + r-rlang + r-stringr + r-tibble + r-tidytext +) +optdepends=( + r-biocstyle + r-clusterprofiler + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gseamining/lilac.py b/prepare/r-gseamining/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gseamining/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gseamining/lilac.yaml b/prepare/r-gseamining/lilac.yaml new file mode 100644 index 0000000000..fccb947a0a --- /dev/null +++ b/prepare/r-gseamining/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dendextend +- r-dplyr +- r-ggplot2 +- r-ggwordcloud +- r-gridextra +- r-rlang +- r-stringr +- r-tibble +- r-tidytext +update_on: +- regex: GSEAmining_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GSEAmining diff --git a/prepare/r-gsean/PKGBUILD b/prepare/r-gsean/PKGBUILD new file mode 100644 index 0000000000..f82bd4b357 --- /dev/null +++ b/prepare/r-gsean/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gsean +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Set Enrichment Analysis with Networks' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-fgsea + r-ppinfer +) +optdepends=( + r-knitr + r-plotly + r-ranks + r-rmarkdown + r-summarizedexperiment + r-wgcna +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gsean/lilac.py b/prepare/r-gsean/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gsean/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gsean/lilac.yaml b/prepare/r-gsean/lilac.yaml new file mode 100644 index 0000000000..a5eb74ede7 --- /dev/null +++ b/prepare/r-gsean/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fgsea +- r-ppinfer +update_on: +- regex: gsean_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gsean diff --git a/prepare/r-gsgalgor/PKGBUILD b/prepare/r-gsgalgor/PKGBUILD new file mode 100644 index 0000000000..f14d14566b --- /dev/null +++ b/prepare/r-gsgalgor/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GSgalgoR +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Evolutionary Framework for the Identification and Study of Prognostic Gene Expression Signatures in Cancer' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-doparallel + r-foreach + r-matchingr + r-nsga2r + r-proxy +) +optdepends=( + r-biobase + r-biocstyle + r-breastcancertransbig + r-breastcancerupp + r-genefu + r-ggplot2 + r-ic10trainingdata + r-knitr + r-pamr + r-rmarkdown + r-survcomp + r-survminer + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gsgalgor/lilac.py b/prepare/r-gsgalgor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gsgalgor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gsgalgor/lilac.yaml b/prepare/r-gsgalgor/lilac.yaml new file mode 100644 index 0000000000..56b11c0372 --- /dev/null +++ b/prepare/r-gsgalgor/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-foreach +- r-matchingr +- r-nsga2r +- r-proxy +update_on: +- regex: GSgalgoR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GSgalgoR diff --git a/prepare/r-gsl/PKGBUILD b/prepare/r-gsl/PKGBUILD new file mode 100644 index 0000000000..b20b006cf4 --- /dev/null +++ b/prepare/r-gsl/PKGBUILD @@ -0,0 +1,27 @@ +# system requirements: Gnu Scientific Library version >= 2.1 +# Maintainer: Guoyi Zhang + +_pkgname=gsl +_pkgver=2.1-7.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Wrapper for the Gnu Scientific Library' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gsl/lilac.py b/prepare/r-gsl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gsl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gsl/lilac.yaml b/prepare/r-gsl/lilac.yaml new file mode 100644 index 0000000000..81fc02f02d --- /dev/null +++ b/prepare/r-gsl/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gsl_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gsl diff --git a/prepare/r-gsmoothr/PKGBUILD b/prepare/r-gsmoothr/PKGBUILD new file mode 100644 index 0000000000..80942cb5db --- /dev/null +++ b/prepare/r-gsmoothr/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gsmoothr +_pkgver=0.1.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Smoothing tools' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gsmoothr/lilac.py b/prepare/r-gsmoothr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gsmoothr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gsmoothr/lilac.yaml b/prepare/r-gsmoothr/lilac.yaml new file mode 100644 index 0000000000..55c391cac3 --- /dev/null +++ b/prepare/r-gsmoothr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gsmoothr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gsmoothr diff --git a/prepare/r-gsreg/PKGBUILD b/prepare/r-gsreg/PKGBUILD new file mode 100644 index 0000000000..047022ef4d --- /dev/null +++ b/prepare/r-gsreg/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GSReg +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Set Regulation (GS-Reg)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-genomicfeatures + r-homo.sapiens + r-org.hs.eg.db +) +optdepends=( + r-genomicranges + r-gsbenchmark +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gsreg/lilac.py b/prepare/r-gsreg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gsreg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gsreg/lilac.yaml b/prepare/r-gsreg/lilac.yaml new file mode 100644 index 0000000000..d7af9c0beb --- /dev/null +++ b/prepare/r-gsreg/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-genomicfeatures +- r-homo.sapiens +- r-org.hs.eg.db +update_on: +- regex: GSReg_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GSReg diff --git a/prepare/r-gsri/PKGBUILD b/prepare/r-gsri/PKGBUILD new file mode 100644 index 0000000000..e2c7fa5dff --- /dev/null +++ b/prepare/r-gsri/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GSRI +_pkgver=2.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Set Regulation Index' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-fdrtool + r-genefilter + r-gseabase + r-les +) +optdepends=( + r-hgu95av2.db + r-limma + r-parallel +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gsri/lilac.py b/prepare/r-gsri/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gsri/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gsri/lilac.yaml b/prepare/r-gsri/lilac.yaml new file mode 100644 index 0000000000..b9a5b1db8e --- /dev/null +++ b/prepare/r-gsri/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-fdrtool +- r-genefilter +- r-gseabase +- r-les +update_on: +- regex: GSRI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GSRI diff --git a/prepare/r-gss/PKGBUILD b/prepare/r-gss/PKGBUILD new file mode 100644 index 0000000000..665148dcf0 --- /dev/null +++ b/prepare/r-gss/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gss +_pkgver=2.2-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='General Smoothing Splines' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gss/lilac.py b/prepare/r-gss/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gss/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gss/lilac.yaml b/prepare/r-gss/lilac.yaml new file mode 100644 index 0000000000..9cd6a6adc8 --- /dev/null +++ b/prepare/r-gss/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gss_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gss diff --git a/prepare/r-gstat/PKGBUILD b/prepare/r-gstat/PKGBUILD new file mode 100644 index 0000000000..943972b8e8 --- /dev/null +++ b/prepare/r-gstat/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gstat +_pkgver=2.0-8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Spatial and Spatio-Temporal Geostatistical Modelling, Prediction and Simulation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-fnn + r-sp + r-spacetime + r-zoo +) +optdepends=( + r-fields + r-future + r-future.apply + r-mapdata + r-maps + r-maptools + r-raster + r-rgdal + r-rgeos + r-sf + r-stars + r-xts +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gstat/lilac.py b/prepare/r-gstat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gstat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gstat/lilac.yaml b/prepare/r-gstat/lilac.yaml new file mode 100644 index 0000000000..a6926c05a8 --- /dev/null +++ b/prepare/r-gstat/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fnn +- r-sp +- r-spacetime +- r-zoo +update_on: +- regex: gstat_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gstat diff --git a/prepare/r-gsubfn/PKGBUILD b/prepare/r-gsubfn/PKGBUILD new file mode 100644 index 0000000000..e271be390e --- /dev/null +++ b/prepare/r-gsubfn/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gsubfn +_pkgver=0.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities for Strings and Function Arguments' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-proto +) +optdepends=( + r-boot + r-chron + r-grid + r-lattice + r-quantreg + r-svunit + r-tcltk + r-zoo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gsubfn/lilac.py b/prepare/r-gsubfn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gsubfn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gsubfn/lilac.yaml b/prepare/r-gsubfn/lilac.yaml new file mode 100644 index 0000000000..7439be808a --- /dev/null +++ b/prepare/r-gsubfn/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-proto +update_on: +- regex: gsubfn_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gsubfn diff --git a/prepare/r-gsva/PKGBUILD b/prepare/r-gsva/PKGBUILD new file mode 100644 index 0000000000..cf256cffa0 --- /dev/null +++ b/prepare/r-gsva/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GSVA +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Set Variation Analysis for microarray and RNA-seq data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocparallel + r-biocsingular + r-delayedarray + r-delayedmatrixstats + r-gseabase + r-hdf5array + r-iranges + r-s4vectors + r-singlecellexperiment + r-sparsematrixstats + r-summarizedexperiment +) +optdepends=( + r-biocgenerics + r-biocstyle + r-data.table + r-edger + r-future + r-genefilter + r-ggplot2 + r-gsvadata + r-knitr + r-limma + r-org.hs.eg.db + r-plotly + r-promises + r-rcolorbrewer + r-rmarkdown + r-runit + r-shiny + r-shinybusy + r-shinydashboard + r-shinyjs +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gsva/lilac.py b/prepare/r-gsva/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gsva/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gsva/lilac.yaml b/prepare/r-gsva/lilac.yaml new file mode 100644 index 0000000000..0038c03934 --- /dev/null +++ b/prepare/r-gsva/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocparallel +- r-biocsingular +- r-delayedarray +- r-delayedmatrixstats +- r-gseabase +- r-hdf5array +- r-iranges +- r-s4vectors +- r-singlecellexperiment +- r-sparsematrixstats +- r-summarizedexperiment +update_on: +- regex: GSVA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GSVA diff --git a/prepare/r-gsvadata/PKGBUILD b/prepare/r-gsvadata/PKGBUILD new file mode 100644 index 0000000000..0c4880630b --- /dev/null +++ b/prepare/r-gsvadata/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GSVAdata +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data employed in the vignette of the GSVA package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-gseabase + r-hgu95a.db +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gsvadata/lilac.py b/prepare/r-gsvadata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gsvadata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gsvadata/lilac.yaml b/prepare/r-gsvadata/lilac.yaml new file mode 100644 index 0000000000..ed395f89b1 --- /dev/null +++ b/prepare/r-gsvadata/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-gseabase +- r-hgu95a.db +update_on: +- regex: GSVAdata_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GSVAdata diff --git a/prepare/r-gtable/PKGBUILD b/prepare/r-gtable/PKGBUILD new file mode 100644 index 0000000000..c30a5ce7a3 --- /dev/null +++ b/prepare/r-gtable/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gtable +_pkgver=0.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Arrange 'Grobs' in Tables" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-covr + r-ggplot2 + r-knitr + r-profvis + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gtable/lilac.yaml b/prepare/r-gtable/lilac.yaml new file mode 100644 index 0000000000..b45b2ec6ab --- /dev/null +++ b/prepare/r-gtable/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gtable_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gtable diff --git a/prepare/r-gtools/PKGBUILD b/prepare/r-gtools/PKGBUILD new file mode 100644 index 0000000000..ec1f9aea6b --- /dev/null +++ b/prepare/r-gtools/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gtools +_pkgver=3.9.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Various R Programming Tools' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-car + r-gplots + r-knitr + r-rstudioapi + r-sgp + r-taxize +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gtools/lilac.py b/prepare/r-gtools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gtools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gtools/lilac.yaml b/prepare/r-gtools/lilac.yaml new file mode 100644 index 0000000000..7b83028cbc --- /dev/null +++ b/prepare/r-gtools/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: gtools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=gtools diff --git a/prepare/r-gtrellis/PKGBUILD b/prepare/r-gtrellis/PKGBUILD new file mode 100644 index 0000000000..96f8ec754b --- /dev/null +++ b/prepare/r-gtrellis/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gtrellis +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genome Level Trellis Layout' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-circlize + r-genomicranges + r-getoptlong + r-iranges +) +optdepends=( + r-cairo + r-complexheatmap + r-jpeg + r-knitr + r-markdown + r-png + r-rcolorbrewer + r-rmarkdown + r-testthat + r-tiff +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gtrellis/lilac.py b/prepare/r-gtrellis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gtrellis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gtrellis/lilac.yaml b/prepare/r-gtrellis/lilac.yaml new file mode 100644 index 0000000000..78f0de437e --- /dev/null +++ b/prepare/r-gtrellis/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circlize +- r-genomicranges +- r-getoptlong +- r-iranges +update_on: +- regex: gtrellis_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gtrellis diff --git a/prepare/r-guideseq/PKGBUILD b/prepare/r-guideseq/PKGBUILD new file mode 100644 index 0000000000..092d0934d1 --- /dev/null +++ b/prepare/r-guideseq/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GUIDEseq +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GUIDE-seq analysis pipeline' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-chippeakanno + r-crisprseek + r-data.table + r-dplyr + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-hash + r-iranges + r-limma + r-matrixstats + r-rsamtools + r-s4vectors +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-knitr + r-org.hs.eg.db + r-runit + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-guideseq/lilac.py b/prepare/r-guideseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-guideseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-guideseq/lilac.yaml b/prepare/r-guideseq/lilac.yaml new file mode 100644 index 0000000000..7f50e3047d --- /dev/null +++ b/prepare/r-guideseq/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-chippeakanno +- r-crisprseek +- r-data.table +- r-dplyr +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-hash +- r-iranges +- r-limma +- r-matrixstats +- r-rsamtools +- r-s4vectors +update_on: +- regex: GUIDEseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GUIDEseq diff --git a/prepare/r-guitar/PKGBUILD b/prepare/r-guitar/PKGBUILD new file mode 100644 index 0000000000..32c8984b55 --- /dev/null +++ b/prepare/r-guitar/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Guitar +_pkgver=2.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Guitar' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-dplyr + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-knitr + r-magrittr + r-rtracklayer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-guitar/lilac.py b/prepare/r-guitar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-guitar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-guitar/lilac.yaml b/prepare/r-guitar/lilac.yaml new file mode 100644 index 0000000000..0ab01dd8ee --- /dev/null +++ b/prepare/r-guitar/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-dplyr +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-knitr +- r-magrittr +- r-rtracklayer +update_on: +- regex: Guitar_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Guitar diff --git a/prepare/r-gunifrac/PKGBUILD b/prepare/r-gunifrac/PKGBUILD new file mode 100644 index 0000000000..02fde334b4 --- /dev/null +++ b/prepare/r-gunifrac/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GUniFrac +_pkgver=1.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate Methods for Microbiome Data Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-dirmult + r-foreach + r-ggplot2 + r-ggrepel + r-lmertest + r-matrixstats + r-modeest + r-rcpp + r-rmutil + r-statmod + r-vegan +) +optdepends=( + r-ade4 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gunifrac/lilac.py b/prepare/r-gunifrac/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gunifrac/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gunifrac/lilac.yaml b/prepare/r-gunifrac/lilac.yaml new file mode 100644 index 0000000000..b7d3181c13 --- /dev/null +++ b/prepare/r-gunifrac/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-dirmult +- r-foreach +- r-ggplot2 +- r-ggrepel +- r-lmertest +- r-matrixstats +- r-modeest +- r-rcpp +- r-rmutil +- r-statmod +- r-vegan +update_on: +- regex: GUniFrac_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=GUniFrac diff --git a/prepare/r-gviz/PKGBUILD b/prepare/r-gviz/PKGBUILD new file mode 100644 index 0000000000..05854d9be5 --- /dev/null +++ b/prepare/r-gviz/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Gviz +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Plotting data and annotation information along genomic coordinates' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biobase + r-biocgenerics + r-biomart + r-biostrings + r-biovizbase + r-bsgenome + r-digest + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-latticeextra + r-matrixstats + r-rcolorbrewer + r-rsamtools + r-rtracklayer + r-s4vectors + r-xvector +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-knitr + r-rmarkdown + r-testthat + r-xml2 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gviz/lilac.py b/prepare/r-gviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gviz/lilac.yaml b/prepare/r-gviz/lilac.yaml new file mode 100644 index 0000000000..63fbf58eda --- /dev/null +++ b/prepare/r-gviz/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-biomart +- r-biostrings +- r-biovizbase +- r-bsgenome +- r-digest +- r-ensembldb +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-latticeextra +- r-matrixstats +- r-rcolorbrewer +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-xvector +update_on: +- regex: Gviz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Gviz diff --git a/prepare/r-gwas.bayes/PKGBUILD b/prepare/r-gwas.bayes/PKGBUILD new file mode 100644 index 0000000000..3fbbcd95a8 --- /dev/null +++ b/prepare/r-gwas.bayes/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GWAS.BAYES +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GWAS for Selfing Species' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-caret + r-doparallel + r-ga + r-ggplot2 + r-memoise + r-rcpp + r-rcppeigen + r-reshape2 +) +optdepends=( + r-biocstyle + r-formatr + r-knitr + r-qqman + r-rmarkdown + r-rrblup +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gwas.bayes/lilac.py b/prepare/r-gwas.bayes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gwas.bayes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gwas.bayes/lilac.yaml b/prepare/r-gwas.bayes/lilac.yaml new file mode 100644 index 0000000000..53685a0d55 --- /dev/null +++ b/prepare/r-gwas.bayes/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-caret +- r-doparallel +- r-ga +- r-ggplot2 +- r-memoise +- r-rcpp +- r-rcppeigen +- r-reshape2 +update_on: +- regex: GWAS.BAYES_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GWAS.BAYES diff --git a/prepare/r-gwascat/PKGBUILD b/prepare/r-gwascat/PKGBUILD new file mode 100644 index 0000000000..b321185157 --- /dev/null +++ b/prepare/r-gwascat/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gwascat +_pkgver=2.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='representing and modeling data in the EMBL-EBI GWAS catalog' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-annotationhub + r-biocfilecache + r-biostrings + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-readr + r-s4vectors + r-snpstats + r-variantannotation +) +optdepends=( + r-biocstyle + r-delayedarray + r-do.db + r-dt + r-ggbio + r-graph + r-gviz + r-iranges + r-knitr + r-org.hs.eg.db + r-rbgl + r-rmarkdown + r-rsamtools + r-rtracklayer + r-snplocs.hsapiens.dbsnp144.grch37 + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gwascat/lilac.py b/prepare/r-gwascat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gwascat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gwascat/lilac.yaml b/prepare/r-gwascat/lilac.yaml new file mode 100644 index 0000000000..656ff89acd --- /dev/null +++ b/prepare/r-gwascat/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-biocfilecache +- r-biostrings +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-readr +- r-s4vectors +- r-snpstats +- r-variantannotation +update_on: +- regex: gwascat_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gwascat diff --git a/prepare/r-gwasexacthw/PKGBUILD b/prepare/r-gwasexacthw/PKGBUILD new file mode 100644 index 0000000000..788af418ae --- /dev/null +++ b/prepare/r-gwasexacthw/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GWASExactHW +_pkgver=1.01 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Exact Hardy-Weinburg testing for Genome Wide Association Studies' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gwasexacthw/lilac.py b/prepare/r-gwasexacthw/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gwasexacthw/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gwasexacthw/lilac.yaml b/prepare/r-gwasexacthw/lilac.yaml new file mode 100644 index 0000000000..63287e3790 --- /dev/null +++ b/prepare/r-gwasexacthw/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: GWASExactHW_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=GWASExactHW diff --git a/prepare/r-gwastools/PKGBUILD b/prepare/r-gwastools/PKGBUILD new file mode 100644 index 0000000000..22baba114b --- /dev/null +++ b/prepare/r-gwastools/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GWASTools +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Genome Wide Association Studies' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-data.table + r-dbi + r-dnacopy + r-gdsfmt + r-gwasexacthw + r-lmtest + r-logistf + r-quantsmooth + r-rsqlite + r-sandwich +) +optdepends=( + r-biocgenerics + r-biostrings + r-genomicranges + r-gwasdata + r-iranges + r-ncdf4 + r-parallel + r-runit + r-s4vectors + r-snprelate + r-snpstats + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gwastools/lilac.py b/prepare/r-gwastools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gwastools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gwastools/lilac.yaml b/prepare/r-gwastools/lilac.yaml new file mode 100644 index 0000000000..10679dce84 --- /dev/null +++ b/prepare/r-gwastools/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-data.table +- r-dbi +- r-dnacopy +- r-gdsfmt +- r-gwasexacthw +- r-lmtest +- r-logistf +- r-quantsmooth +- r-rsqlite +- r-sandwich +update_on: +- regex: GWASTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GWASTools diff --git a/prepare/r-gwasurvivr/PKGBUILD b/prepare/r-gwasurvivr/PKGBUILD new file mode 100644 index 0000000000..40de1fb9b9 --- /dev/null +++ b/prepare/r-gwasurvivr/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=gwasurvivr +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='gwasurvivr: an R package for genome wide survival analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-gwastools + r-matrixstats + r-snprelate + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gwasurvivr/lilac.py b/prepare/r-gwasurvivr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gwasurvivr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gwasurvivr/lilac.yaml b/prepare/r-gwasurvivr/lilac.yaml new file mode 100644 index 0000000000..30a9275227 --- /dev/null +++ b/prepare/r-gwasurvivr/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gwastools +- r-matrixstats +- r-snprelate +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: gwasurvivr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/gwasurvivr diff --git a/prepare/r-gwena/PKGBUILD b/prepare/r-gwena/PKGBUILD new file mode 100644 index 0000000000..b5a8b08c2a --- /dev/null +++ b/prepare/r-gwena/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=GWENA +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pipeline for augmented co-expression analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-dynamictreecut + r-ggplot2 + r-gprofiler2 + r-igraph + r-magrittr + r-matrixstats + r-netrep + r-purrr + r-rcolorbrewer + r-rlist + r-stringr + r-summarizedexperiment + r-tibble + r-tidyr + r-wgcna +) +optdepends=( + r-biocstyle + r-httr + r-knitr + r-prettydoc + r-rmarkdown + r-s4vectors + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-gwena/lilac.py b/prepare/r-gwena/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-gwena/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-gwena/lilac.yaml b/prepare/r-gwena/lilac.yaml new file mode 100644 index 0000000000..0f36af436e --- /dev/null +++ b/prepare/r-gwena/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-dynamictreecut +- r-ggplot2 +- r-gprofiler2 +- r-igraph +- r-magrittr +- r-matrixstats +- r-netrep +- r-purrr +- r-rcolorbrewer +- r-rlist +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-tidyr +- r-wgcna +update_on: +- regex: GWENA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/GWENA diff --git a/prepare/r-h5vc/PKGBUILD b/prepare/r-h5vc/PKGBUILD new file mode 100644 index 0000000000..33a2670ba1 --- /dev/null +++ b/prepare/r-h5vc/PKGBUILD @@ -0,0 +1,52 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=h5vc +_pkgver=2.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Managing alignment tallies using a hdf5 backend' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-batchjobs + r-biocparallel + r-biostrings + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gridextra + r-h5vcdata + r-iranges + r-reshape + r-rhdf5 + r-rhtslib + r-rsamtools + r-s4vectors +) +optdepends=( + r-biocgenerics + r-biomart + r-bsgenome.hsapiens.ncbi.grch38 + r-bsgenome.hsapiens.ucsc.hg19 + r-knitr + r-locfit + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-h5vc/lilac.py b/prepare/r-h5vc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-h5vc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-h5vc/lilac.yaml b/prepare/r-h5vc/lilac.yaml new file mode 100644 index 0000000000..000d647918 --- /dev/null +++ b/prepare/r-h5vc/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-batchjobs +- r-biocparallel +- r-biostrings +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-gridextra +- r-h5vcdata +- r-iranges +- r-reshape +- r-rhdf5 +- r-rhtslib +- r-rsamtools +- r-s4vectors +update_on: +- regex: h5vc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/h5vc diff --git a/prepare/r-h5vcdata/PKGBUILD b/prepare/r-h5vcdata/PKGBUILD new file mode 100644 index 0000000000..5861ca4332 --- /dev/null +++ b/prepare/r-h5vcdata/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=h5vcData +_pkgver=2.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Example data for the h5vc package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-h5vc +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-h5vcdata/lilac.py b/prepare/r-h5vcdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-h5vcdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-h5vcdata/lilac.yaml b/prepare/r-h5vcdata/lilac.yaml new file mode 100644 index 0000000000..9ae751694e --- /dev/null +++ b/prepare/r-h5vcdata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: h5vcData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/h5vcData diff --git a/prepare/r-hapfabia/PKGBUILD b/prepare/r-hapfabia/PKGBUILD new file mode 100644 index 0000000000..046e635dee --- /dev/null +++ b/prepare/r-hapfabia/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hapFabia +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-fabia +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hapfabia/lilac.py b/prepare/r-hapfabia/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hapfabia/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hapfabia/lilac.yaml b/prepare/r-hapfabia/lilac.yaml new file mode 100644 index 0000000000..c657c305b4 --- /dev/null +++ b/prepare/r-hapfabia/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-fabia +update_on: +- regex: hapFabia_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hapFabia diff --git a/prepare/r-haplo.stats/PKGBUILD b/prepare/r-haplo.stats/PKGBUILD new file mode 100644 index 0000000000..9ca52d1da9 --- /dev/null +++ b/prepare/r-haplo.stats/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=haplo.stats +_pkgver=1.8.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-arsenal + r-rms +) +optdepends=( + r-r.rsp + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-haplo.stats/lilac.py b/prepare/r-haplo.stats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-haplo.stats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-haplo.stats/lilac.yaml b/prepare/r-haplo.stats/lilac.yaml new file mode 100644 index 0000000000..7526063932 --- /dev/null +++ b/prepare/r-haplo.stats/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-arsenal +- r-rms +update_on: +- regex: haplo.stats_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=haplo.stats diff --git a/prepare/r-hardyweinberg/PKGBUILD b/prepare/r-hardyweinberg/PKGBUILD new file mode 100644 index 0000000000..d1f8448917 --- /dev/null +++ b/prepare/r-hardyweinberg/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HardyWeinberg +_pkgver=1.7.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Tests and Graphics for Hardy-Weinberg Equilibrium' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mice + r-rcpp + r-rsolnp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hardyweinberg/lilac.py b/prepare/r-hardyweinberg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hardyweinberg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hardyweinberg/lilac.yaml b/prepare/r-hardyweinberg/lilac.yaml new file mode 100644 index 0000000000..bd29b0a35d --- /dev/null +++ b/prepare/r-hardyweinberg/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mice +- r-rcpp +- r-rsolnp +update_on: +- regex: HardyWeinberg_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=HardyWeinberg diff --git a/prepare/r-harman/PKGBUILD b/prepare/r-harman/PKGBUILD new file mode 100644 index 0000000000..657bafe106 --- /dev/null +++ b/prepare/r-harman/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Harman +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The removal of batch effects from datasets using a PCA and constrained optimisation based technique' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-affydata + r-biocgenerics + r-biocstyle + r-bladderbatch + r-harmandata + r-knitr + r-limma + r-lumi + r-minfi + r-minfidata + r-msmseda + r-rcolorbrewer + r-rmarkdown + r-runit + r-sva +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-harman/lilac.py b/prepare/r-harman/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-harman/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-harman/lilac.yaml b/prepare/r-harman/lilac.yaml new file mode 100644 index 0000000000..df80bd742b --- /dev/null +++ b/prepare/r-harman/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: Harman_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Harman diff --git a/prepare/r-harmonicmeanp/PKGBUILD b/prepare/r-harmonicmeanp/PKGBUILD new file mode 100644 index 0000000000..f597d79912 --- /dev/null +++ b/prepare/r-harmonicmeanp/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=harmonicmeanp +_pkgver=3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Harmonic Mean p-Values and Model Averaging by Mean Maximum Likelihood' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-fmstable +) +optdepends=( + r-ape + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-harmonicmeanp/lilac.py b/prepare/r-harmonicmeanp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-harmonicmeanp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-harmonicmeanp/lilac.yaml b/prepare/r-harmonicmeanp/lilac.yaml new file mode 100644 index 0000000000..0954e041a4 --- /dev/null +++ b/prepare/r-harmonicmeanp/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fmstable +update_on: +- regex: harmonicmeanp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=harmonicmeanp diff --git a/prepare/r-harshlight/PKGBUILD b/prepare/r-harshlight/PKGBUILD new file mode 100644 index 0000000000..e9a9c17c45 --- /dev/null +++ b/prepare/r-harshlight/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Harshlight +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A "corrective make-up" program for microarray chips' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-altcdfenvs + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-harshlight/lilac.py b/prepare/r-harshlight/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-harshlight/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-harshlight/lilac.yaml b/prepare/r-harshlight/lilac.yaml new file mode 100644 index 0000000000..b816e212f9 --- /dev/null +++ b/prepare/r-harshlight/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-altcdfenvs +- r-biobase +update_on: +- regex: Harshlight_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Harshlight diff --git a/prepare/r-hash/PKGBUILD b/prepare/r-hash/PKGBUILD new file mode 100644 index 0000000000..3737ed9f56 --- /dev/null +++ b/prepare/r-hash/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hash +_pkgver=2.2.6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Full Feature Implementation of Hash/Associated Arrays/Dictionaries' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hash/lilac.py b/prepare/r-hash/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hash/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hash/lilac.yaml b/prepare/r-hash/lilac.yaml new file mode 100644 index 0000000000..f49e71552d --- /dev/null +++ b/prepare/r-hash/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: hash_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=hash diff --git a/prepare/r-haven/PKGBUILD b/prepare/r-haven/PKGBUILD new file mode 100644 index 0000000000..f5acbfe369 --- /dev/null +++ b/prepare/r-haven/PKGBUILD @@ -0,0 +1,46 @@ +# system requirements: GNU make, C++11, zlib +# Maintainer: Guoyi Zhang + +_pkgname=haven +_pkgver=2.4.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Import and Export 'SPSS', 'Stata' and 'SAS' Files" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-cpp11 + r-forcats + r-hms + r-readr + r-rlang + r-tibble + r-tidyselect + r-vctrs +) +optdepends=( + r-cli + r-covr + r-crayon + r-fs + r-knitr + r-pillar + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-haven/lilac.py b/prepare/r-haven/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-haven/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-haven/lilac.yaml b/prepare/r-haven/lilac.yaml new file mode 100644 index 0000000000..63f9d0ff2d --- /dev/null +++ b/prepare/r-haven/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cpp11 +- r-forcats +- r-hms +- r-readr +- r-rlang +- r-tibble +- r-tidyselect +- r-vctrs +update_on: +- regex: haven_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=haven diff --git a/prepare/r-hca/PKGBUILD b/prepare/r-hca/PKGBUILD new file mode 100644 index 0000000000..e27b739163 --- /dev/null +++ b/prepare/r-hca/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hca +_pkgver=1.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Exploring the Human Cell Atlas Data Coordinating Platform' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocfilecache + r-digest + r-dplyr + r-httr + r-jsonlite + r-readr + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-futile.logger + r-knitr + r-loomexperiment + r-methods + r-rmarkdown + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hca/lilac.py b/prepare/r-hca/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hca/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hca/lilac.yaml b/prepare/r-hca/lilac.yaml new file mode 100644 index 0000000000..6d10cfedba --- /dev/null +++ b/prepare/r-hca/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-digest +- r-dplyr +- r-httr +- r-jsonlite +- r-readr +- r-tibble +- r-tidyr +update_on: +- regex: hca_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hca diff --git a/prepare/r-hdf5array/PKGBUILD b/prepare/r-hdf5array/PKGBUILD new file mode 100644 index 0000000000..ddc0c194ee --- /dev/null +++ b/prepare/r-hdf5array/PKGBUILD @@ -0,0 +1,46 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=HDF5Array +_pkgver=1.22.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='HDF5 backend for DelayedArray objects' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-delayedarray + r-iranges + r-rhdf5 + r-rhdf5filters + r-rhdf5lib + r-s4vectors +) +optdepends=( + r-biocparallel + r-experimenthub + r-genomicfeatures + r-genomicranges + r-h5vcdata + r-runit + r-singlecellexperiment + r-summarizedexperiment + r-tenxbraindata + r-zellkonverter +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hdf5array/lilac.py b/prepare/r-hdf5array/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hdf5array/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hdf5array/lilac.yaml b/prepare/r-hdf5array/lilac.yaml new file mode 100644 index 0000000000..50f2895ca2 --- /dev/null +++ b/prepare/r-hdf5array/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-delayedarray +- r-iranges +- r-rhdf5 +- r-rhdf5filters +- r-rhdf5lib +- r-s4vectors +update_on: +- regex: HDF5Array_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HDF5Array diff --git a/prepare/r-hdinterval/PKGBUILD b/prepare/r-hdinterval/PKGBUILD new file mode 100644 index 0000000000..6c5f365791 --- /dev/null +++ b/prepare/r-hdinterval/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HDInterval +_pkgver=0.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Highest (Posterior) Density Intervals' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-coda +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hdinterval/lilac.py b/prepare/r-hdinterval/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hdinterval/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hdinterval/lilac.yaml b/prepare/r-hdinterval/lilac.yaml new file mode 100644 index 0000000000..2c41fe1f94 --- /dev/null +++ b/prepare/r-hdinterval/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: HDInterval_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=HDInterval diff --git a/prepare/r-hdrcde/PKGBUILD b/prepare/r-hdrcde/PKGBUILD new file mode 100644 index 0000000000..0d9181cccd --- /dev/null +++ b/prepare/r-hdrcde/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hdrcde +_pkgver=3.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Highest Density Regions and Conditional Density Estimation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ash + r-ggplot2 + r-ks + r-locfit + r-rcolorbrewer +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hdrcde/lilac.py b/prepare/r-hdrcde/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hdrcde/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hdrcde/lilac.yaml b/prepare/r-hdrcde/lilac.yaml new file mode 100644 index 0000000000..aeb2def2f4 --- /dev/null +++ b/prepare/r-hdrcde/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ash +- r-ggplot2 +- r-ks +- r-locfit +- r-rcolorbrewer +update_on: +- regex: hdrcde_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=hdrcde diff --git a/prepare/r-hdtd/PKGBUILD b/prepare/r-hdtd/PKGBUILD new file mode 100644 index 0000000000..924175026f --- /dev/null +++ b/prepare/r-hdtd/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HDTD +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hdtd/lilac.py b/prepare/r-hdtd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hdtd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hdtd/lilac.yaml b/prepare/r-hdtd/lilac.yaml new file mode 100644 index 0000000000..df6e7cb6f4 --- /dev/null +++ b/prepare/r-hdtd/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: HDTD_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HDTD diff --git a/prepare/r-heatmap3/PKGBUILD b/prepare/r-heatmap3/PKGBUILD new file mode 100644 index 0000000000..5287cd0b50 --- /dev/null +++ b/prepare/r-heatmap3/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=heatmap3 +_pkgver=1.1.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Improved Heatmap Package' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-fastcluster +) +optdepends=( + r-knitr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-heatmap3/lilac.py b/prepare/r-heatmap3/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-heatmap3/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-heatmap3/lilac.yaml b/prepare/r-heatmap3/lilac.yaml new file mode 100644 index 0000000000..7e5472ad5e --- /dev/null +++ b/prepare/r-heatmap3/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fastcluster +update_on: +- regex: heatmap3_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=heatmap3 diff --git a/prepare/r-heatmaply/PKGBUILD b/prepare/r-heatmaply/PKGBUILD new file mode 100644 index 0000000000..daedbfb717 --- /dev/null +++ b/prepare/r-heatmaply/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=heatmaply +_pkgver=1.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Interactive Cluster Heat Maps Using 'plotly' and 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-colorspace + r-dendextend + r-egg + r-ggplot2 + r-htmlwidgets + r-magrittr + r-plotly + r-rcolorbrewer + r-reshape2 + r-scales + r-seriation + r-viridis + r-webshot +) +optdepends=( + r-covr + r-gplots + r-knitr + r-rmarkdown + r-testthat + r-tidyselect +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-heatmaply/lilac.py b/prepare/r-heatmaply/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-heatmaply/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-heatmaply/lilac.yaml b/prepare/r-heatmaply/lilac.yaml new file mode 100644 index 0000000000..a7fd80ba5f --- /dev/null +++ b/prepare/r-heatmaply/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-colorspace +- r-dendextend +- r-egg +- r-ggplot2 +- r-htmlwidgets +- r-magrittr +- r-plotly +- r-rcolorbrewer +- r-reshape2 +- r-scales +- r-seriation +- r-viridis +- r-webshot +update_on: +- regex: heatmaply_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=heatmaply diff --git a/prepare/r-heatmaps/PKGBUILD b/prepare/r-heatmaps/PKGBUILD new file mode 100644 index 0000000000..1e7d17f456 --- /dev/null +++ b/prepare/r-heatmaps/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=heatmaps +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Flexible Heatmaps for Functional Genomics and Sequence Features' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biostrings + r-ebimage + r-genomeinfodb + r-genomicranges + r-iranges + r-plotrix + r-rcolorbrewer +) +optdepends=( + r-bsgenome.drerio.ucsc.danrer7 + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-heatmaps/lilac.py b/prepare/r-heatmaps/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-heatmaps/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-heatmaps/lilac.yaml b/prepare/r-heatmaps/lilac.yaml new file mode 100644 index 0000000000..0f29fab007 --- /dev/null +++ b/prepare/r-heatmaps/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-ebimage +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-plotrix +- r-rcolorbrewer +update_on: +- regex: heatmaps_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/heatmaps diff --git a/prepare/r-heatplus/PKGBUILD b/prepare/r-heatplus/PKGBUILD new file mode 100644 index 0000000000..82a5bec5b2 --- /dev/null +++ b/prepare/r-heatplus/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Heatplus +_pkgver=3.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Heatmaps with row and/or column covariates and colored clusters' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rcolorbrewer +) +optdepends=( + r-biobase + r-hgu95av2.db + r-limma +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-heatplus/lilac.py b/prepare/r-heatplus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-heatplus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-heatplus/lilac.yaml b/prepare/r-heatplus/lilac.yaml new file mode 100644 index 0000000000..30bd0cc37b --- /dev/null +++ b/prepare/r-heatplus/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcolorbrewer +update_on: +- regex: Heatplus_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Heatplus diff --git a/prepare/r-helloranges/PKGBUILD b/prepare/r-helloranges/PKGBUILD new file mode 100644 index 0000000000..8bd1ff2a51 --- /dev/null +++ b/prepare/r-helloranges/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HelloRanges +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Introduce *Ranges to bedtools users' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-bsgenome + r-docopt + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-biocstyle + r-hellorangesdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-helloranges/lilac.py b/prepare/r-helloranges/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-helloranges/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-helloranges/lilac.yaml b/prepare/r-helloranges/lilac.yaml new file mode 100644 index 0000000000..3bfb896b9e --- /dev/null +++ b/prepare/r-helloranges/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-docopt +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: HelloRanges_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HelloRanges diff --git a/prepare/r-help/PKGBUILD b/prepare/r-help/PKGBUILD new file mode 100644 index 0000000000..c6283de679 --- /dev/null +++ b/prepare/r-help/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HELP +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for HELP data analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-help/lilac.py b/prepare/r-help/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-help/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-help/lilac.yaml b/prepare/r-help/lilac.yaml new file mode 100644 index 0000000000..4f6284073c --- /dev/null +++ b/prepare/r-help/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: HELP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HELP diff --git a/prepare/r-hem/PKGBUILD b/prepare/r-hem/PKGBUILD new file mode 100644 index 0000000000..13cdf20848 --- /dev/null +++ b/prepare/r-hem/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HEM +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Heterogeneous error model for identification of differentially expressed genes under multiple conditions' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hem/lilac.py b/prepare/r-hem/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hem/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hem/lilac.yaml b/prepare/r-hem/lilac.yaml new file mode 100644 index 0000000000..fea7faa42e --- /dev/null +++ b/prepare/r-hem/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: HEM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HEM diff --git a/prepare/r-here/PKGBUILD b/prepare/r-here/PKGBUILD new file mode 100644 index 0000000000..2409ec2d06 --- /dev/null +++ b/prepare/r-here/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=here +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Simpler Way to Find Your Files' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-rprojroot +) +optdepends=( + r-conflicted + r-covr + r-fs + r-knitr + r-palmerpenguins + r-plyr + r-readr + r-rlang + r-rmarkdown + r-testthat + r-uuid + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-here/lilac.py b/prepare/r-here/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-here/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-here/lilac.yaml b/prepare/r-here/lilac.yaml new file mode 100644 index 0000000000..9e2311875b --- /dev/null +++ b/prepare/r-here/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rprojroot +update_on: +- regex: here_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=here diff --git a/prepare/r-herper/PKGBUILD b/prepare/r-herper/PKGBUILD new file mode 100644 index 0000000000..5322df8fa3 --- /dev/null +++ b/prepare/r-herper/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Herper +_pkgver=1.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The Herper package is a simple toolset to install and manage conda packages and environments from R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-reticulate + r-rjson + r-withr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-seqcna + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-herper/lilac.py b/prepare/r-herper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-herper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-herper/lilac.yaml b/prepare/r-herper/lilac.yaml new file mode 100644 index 0000000000..278281d31d --- /dev/null +++ b/prepare/r-herper/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-reticulate +- r-rjson +- r-withr +update_on: +- regex: Herper_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Herper diff --git a/prepare/r-hexbin/PKGBUILD b/prepare/r-hexbin/PKGBUILD new file mode 100644 index 0000000000..1ae8b78cb2 --- /dev/null +++ b/prepare/r-hexbin/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hexbin +_pkgver=1.28.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Hexagonal Binning Routines' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-affy + r-biobase + r-knitr + r-limma + r-marray +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hexbin/lilac.py b/prepare/r-hexbin/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hexbin/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hexbin/lilac.yaml b/prepare/r-hexbin/lilac.yaml new file mode 100644 index 0000000000..9ccc08b880 --- /dev/null +++ b/prepare/r-hexbin/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: hexbin_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=hexbin diff --git a/prepare/r-hgc/PKGBUILD b/prepare/r-hgc/PKGBUILD new file mode 100644 index 0000000000..649cb5ffc3 --- /dev/null +++ b/prepare/r-hgc/PKGBUILD @@ -0,0 +1,42 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=HGC +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A fast hierarchical graph-based clustering method' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-dendextend + r-dplyr + r-ggplot2 + r-mclust + r-patchwork + r-rann + r-rcpp + r-rcppeigen +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hgc/lilac.py b/prepare/r-hgc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hgc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hgc/lilac.yaml b/prepare/r-hgc/lilac.yaml new file mode 100644 index 0000000000..921ae90d74 --- /dev/null +++ b/prepare/r-hgc/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-dendextend +- r-dplyr +- r-ggplot2 +- r-mclust +- r-patchwork +- r-rann +- r-rcpp +- r-rcppeigen +update_on: +- regex: HGC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HGC diff --git a/prepare/r-hgnchelper/PKGBUILD b/prepare/r-hgnchelper/PKGBUILD new file mode 100644 index 0000000000..507abaab92 --- /dev/null +++ b/prepare/r-hgnchelper/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HGNChelper +_pkgver=0.8.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hgnchelper/lilac.py b/prepare/r-hgnchelper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hgnchelper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hgnchelper/lilac.yaml b/prepare/r-hgnchelper/lilac.yaml new file mode 100644 index 0000000000..00c360768f --- /dev/null +++ b/prepare/r-hgnchelper/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: HGNChelper_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=HGNChelper diff --git a/prepare/r-hgu133a.db/PKGBUILD b/prepare/r-hgu133a.db/PKGBUILD new file mode 100644 index 0000000000..3dad84a298 --- /dev/null +++ b/prepare/r-hgu133a.db/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hgu133a.db +_pkgver=3.13.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Affymetrix Affymetrix HG-U133A Array annotation data (chip hgu133a)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-org.hs.eg.db +) +optdepends=( + r-annotate + r-dbi + r-runit +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hgu133a.db/lilac.py b/prepare/r-hgu133a.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hgu133a.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hgu133a.db/lilac.yaml b/prepare/r-hgu133a.db/lilac.yaml new file mode 100644 index 0000000000..718a75a5ce --- /dev/null +++ b/prepare/r-hgu133a.db/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-org.hs.eg.db +update_on: +- regex: hgu133a.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hgu133a.db diff --git a/prepare/r-hgu133a2.db/PKGBUILD b/prepare/r-hgu133a2.db/PKGBUILD new file mode 100644 index 0000000000..75c305267e --- /dev/null +++ b/prepare/r-hgu133a2.db/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hgu133a2.db +_pkgver=3.13.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Affymetrix Affymetrix HG-U133A_2 Array annotation data (chip hgu133a2)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-org.hs.eg.db +) +optdepends=( + r-annotate + r-dbi + r-runit +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hgu133a2.db/lilac.py b/prepare/r-hgu133a2.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hgu133a2.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hgu133a2.db/lilac.yaml b/prepare/r-hgu133a2.db/lilac.yaml new file mode 100644 index 0000000000..00237637f8 --- /dev/null +++ b/prepare/r-hgu133a2.db/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-org.hs.eg.db +update_on: +- regex: hgu133a2.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hgu133a2.db diff --git a/prepare/r-hgu133plus2.db/PKGBUILD b/prepare/r-hgu133plus2.db/PKGBUILD new file mode 100644 index 0000000000..18947b3154 --- /dev/null +++ b/prepare/r-hgu133plus2.db/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hgu133plus2.db +_pkgver=3.13.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-org.hs.eg.db +) +optdepends=( + r-annotate + r-dbi + r-runit +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hgu133plus2.db/lilac.py b/prepare/r-hgu133plus2.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hgu133plus2.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hgu133plus2.db/lilac.yaml b/prepare/r-hgu133plus2.db/lilac.yaml new file mode 100644 index 0000000000..83a2141d42 --- /dev/null +++ b/prepare/r-hgu133plus2.db/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-org.hs.eg.db +update_on: +- regex: hgu133plus2.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hgu133plus2.db diff --git a/prepare/r-hgu95a.db/PKGBUILD b/prepare/r-hgu95a.db/PKGBUILD new file mode 100644 index 0000000000..61ee18ec7f --- /dev/null +++ b/prepare/r-hgu95a.db/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hgu95a.db +_pkgver=3.13.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Affymetrix Affymetrix HG_U95A Array annotation data (chip hgu95a)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-org.hs.eg.db +) +optdepends=( + r-annotate + r-dbi + r-runit +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hgu95a.db/lilac.py b/prepare/r-hgu95a.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hgu95a.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hgu95a.db/lilac.yaml b/prepare/r-hgu95a.db/lilac.yaml new file mode 100644 index 0000000000..f14fca210c --- /dev/null +++ b/prepare/r-hgu95a.db/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-org.hs.eg.db +update_on: +- regex: hgu95a.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hgu95a.db diff --git a/prepare/r-hgu95av2.db/PKGBUILD b/prepare/r-hgu95av2.db/PKGBUILD new file mode 100644 index 0000000000..b4fad66a75 --- /dev/null +++ b/prepare/r-hgu95av2.db/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hgu95av2.db +_pkgver=3.13.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Affymetrix Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-org.hs.eg.db +) +optdepends=( + r-annotate + r-dbi + r-runit +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hgu95av2.db/lilac.py b/prepare/r-hgu95av2.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hgu95av2.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hgu95av2.db/lilac.yaml b/prepare/r-hgu95av2.db/lilac.yaml new file mode 100644 index 0000000000..d600baeab4 --- /dev/null +++ b/prepare/r-hgu95av2.db/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-org.hs.eg.db +update_on: +- regex: hgu95av2.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hgu95av2.db diff --git a/prepare/r-hh/PKGBUILD b/prepare/r-hh/PKGBUILD new file mode 100644 index 0000000000..de49d5d815 --- /dev/null +++ b/prepare/r-hh/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HH +_pkgver=3.1-43 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Analysis and Data Display: Heiberger and Holland' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-colorspace + r-gridextra + r-hmisc + r-latticeextra + r-leaps + r-multcomp + r-rcolorbrewer + r-reshape2 + r-rmpfr + r-shiny + r-vcd +) +optdepends=( + r-car + r-microplot + r-mvtnorm + r-rcmdr + r-rcmdrplugin.hh + r-teachingdemos +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hh/lilac.py b/prepare/r-hh/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hh/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hh/lilac.yaml b/prepare/r-hh/lilac.yaml new file mode 100644 index 0000000000..2a10d94372 --- /dev/null +++ b/prepare/r-hh/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-colorspace +- r-gridextra +- r-hmisc +- r-latticeextra +- r-leaps +- r-multcomp +- r-rcolorbrewer +- r-reshape2 +- r-rmpfr +- r-shiny +- r-vcd +update_on: +- regex: HH_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=HH diff --git a/prepare/r-hiannotator/PKGBUILD b/prepare/r-hiannotator/PKGBUILD new file mode 100644 index 0000000000..e540e49793 --- /dev/null +++ b/prepare/r-hiannotator/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hiAnnotator +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for annotating GRanges objects' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bsgenome + r-dplyr + r-foreach + r-genomicranges + r-ggplot2 + r-iterators + r-rtracklayer + r-scales +) +optdepends=( + r-biocgenerics + r-doparallel + r-knitr + r-markdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hiannotator/lilac.py b/prepare/r-hiannotator/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hiannotator/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hiannotator/lilac.yaml b/prepare/r-hiannotator/lilac.yaml new file mode 100644 index 0000000000..44117bde79 --- /dev/null +++ b/prepare/r-hiannotator/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +- r-dplyr +- r-foreach +- r-genomicranges +- r-ggplot2 +- r-iterators +- r-rtracklayer +- r-scales +update_on: +- regex: hiAnnotator_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hiAnnotator diff --git a/prepare/r-hibag/PKGBUILD b/prepare/r-hibag/PKGBUILD new file mode 100644 index 0000000000..99d4fc6044 --- /dev/null +++ b/prepare/r-hibag/PKGBUILD @@ -0,0 +1,39 @@ +# system requirements: C++11, GNU make +# Maintainer: Guoyi Zhang + +_pkgname=HIBAG +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='HLA Genotype Imputation with Attribute Bagging' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rcppparallel +) +optdepends=( + r-gdsfmt + r-ggplot2 + r-knitr + r-markdown + r-parallel + r-reshape2 + r-rmarkdown + r-seqarray + r-snprelate +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hibag/lilac.py b/prepare/r-hibag/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hibag/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hibag/lilac.yaml b/prepare/r-hibag/lilac.yaml new file mode 100644 index 0000000000..b6e4dfc630 --- /dev/null +++ b/prepare/r-hibag/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcppparallel +update_on: +- regex: HIBAG_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HIBAG diff --git a/prepare/r-hicbricks/PKGBUILD b/prepare/r-hicbricks/PKGBUILD new file mode 100644 index 0000000000..26218f64a9 --- /dev/null +++ b/prepare/r-hicbricks/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HiCBricks +_pkgver=1.11.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Framework for Storing and Accessing Hi-C Data Through HDF Files' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocparallel + r-curl + r-data.table + r-digest + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-jsonlite + r-r.utils + r-r6 + r-rcolorbrewer + r-readr + r-reshape2 + r-rhdf5 + r-s4vectors + r-scales + r-stringr + r-tibble + r-viridis +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hicbricks/lilac.py b/prepare/r-hicbricks/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hicbricks/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hicbricks/lilac.yaml b/prepare/r-hicbricks/lilac.yaml new file mode 100644 index 0000000000..1f079e1457 --- /dev/null +++ b/prepare/r-hicbricks/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-curl +- r-data.table +- r-digest +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-jsonlite +- r-r.utils +- r-r6 +- r-rcolorbrewer +- r-readr +- r-reshape2 +- r-rhdf5 +- r-s4vectors +- r-scales +- r-stringr +- r-tibble +- r-viridis +update_on: +- regex: HiCBricks_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HiCBricks diff --git a/prepare/r-hiccompare/PKGBUILD b/prepare/r-hiccompare/PKGBUILD new file mode 100644 index 0000000000..f5043276c5 --- /dev/null +++ b/prepare/r-hiccompare/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HiCcompare +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocparallel + r-data.table + r-dplyr + r-genomicranges + r-ggplot2 + r-gridextra + r-gtools + r-interactionset + r-iranges + r-pheatmap + r-qdnaseq + r-rhdf5 + r-s4vectors +) +optdepends=( + r-knitr + r-multihiccompare + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hiccompare/lilac.py b/prepare/r-hiccompare/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hiccompare/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hiccompare/lilac.yaml b/prepare/r-hiccompare/lilac.yaml new file mode 100644 index 0000000000..65f9c333c3 --- /dev/null +++ b/prepare/r-hiccompare/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-data.table +- r-dplyr +- r-genomicranges +- r-ggplot2 +- r-gridextra +- r-gtools +- r-interactionset +- r-iranges +- r-pheatmap +- r-qdnaseq +- r-rhdf5 +- r-s4vectors +update_on: +- regex: HiCcompare_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HiCcompare diff --git a/prepare/r-hicdcplus/PKGBUILD b/prepare/r-hicdcplus/PKGBUILD new file mode 100644 index 0000000000..9138a617e6 --- /dev/null +++ b/prepare/r-hicdcplus/PKGBUILD @@ -0,0 +1,61 @@ +# system requirements: JRE 8+ +# Maintainer: Guoyi Zhang + +_pkgname=HiCDCPlus +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Hi-C Direct Caller Plus' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bbmle + r-biostrings + r-bsgenome + r-data.table + r-dplyr + r-genomeinfodb + r-genomicinteractions + r-genomicranges + r-interactionset + r-iranges + r-pscl + r-r.utils + r-rcpp + r-rlang + r-rtracklayer + r-s4vectors + r-tibble + r-tidyr +) +optdepends=( + r-biocfilecache + r-biocgenerics + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.hsapiens.ucsc.hg38 + r-bsgenome.mmusculus.ucsc.mm10 + r-bsgenome.mmusculus.ucsc.mm9 + r-deseq2 + r-hitc + r-knitr + r-matrix + r-parallel + r-rappdirs + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hicdcplus/lilac.py b/prepare/r-hicdcplus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hicdcplus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hicdcplus/lilac.yaml b/prepare/r-hicdcplus/lilac.yaml new file mode 100644 index 0000000000..d87b0bec11 --- /dev/null +++ b/prepare/r-hicdcplus/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bbmle +- r-biostrings +- r-bsgenome +- r-data.table +- r-dplyr +- r-genomeinfodb +- r-genomicinteractions +- r-genomicranges +- r-interactionset +- r-iranges +- r-pscl +- r-r.utils +- r-rcpp +- r-rlang +- r-rtracklayer +- r-s4vectors +- r-tibble +- r-tidyr +update_on: +- regex: HiCDCPlus_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HiCDCPlus diff --git a/prepare/r-hiddenmarkov/PKGBUILD b/prepare/r-hiddenmarkov/PKGBUILD new file mode 100644 index 0000000000..bb33308cd6 --- /dev/null +++ b/prepare/r-hiddenmarkov/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HiddenMarkov +_pkgver=1.8-13 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Hidden Markov Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-parallel +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hiddenmarkov/lilac.py b/prepare/r-hiddenmarkov/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hiddenmarkov/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hiddenmarkov/lilac.yaml b/prepare/r-hiddenmarkov/lilac.yaml new file mode 100644 index 0000000000..eb86639875 --- /dev/null +++ b/prepare/r-hiddenmarkov/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: HiddenMarkov_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=HiddenMarkov diff --git a/prepare/r-hiergwas/PKGBUILD b/prepare/r-hiergwas/PKGBUILD new file mode 100644 index 0000000000..6a24314625 --- /dev/null +++ b/prepare/r-hiergwas/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hierGWAS +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Asessing statistical significance in predictive GWA studies' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-fastcluster + r-fmsb + r-glmnet +) +optdepends=( + r-biocgenerics + r-mass + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hiergwas/lilac.py b/prepare/r-hiergwas/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hiergwas/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hiergwas/lilac.yaml b/prepare/r-hiergwas/lilac.yaml new file mode 100644 index 0000000000..e72728c189 --- /dev/null +++ b/prepare/r-hiergwas/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fastcluster +- r-fmsb +- r-glmnet +update_on: +- regex: hierGWAS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hierGWAS diff --git a/prepare/r-hierinf/PKGBUILD b/prepare/r-hierinf/PKGBUILD new file mode 100644 index 0000000000..00f322723a --- /dev/null +++ b/prepare/r-hierinf/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hierinf +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Hierarchical Inference' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-fmsb + r-glmnet +) +optdepends=( + r-knitr + r-mass + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hierinf/lilac.py b/prepare/r-hierinf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hierinf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hierinf/lilac.yaml b/prepare/r-hierinf/lilac.yaml new file mode 100644 index 0000000000..07686a1b53 --- /dev/null +++ b/prepare/r-hierinf/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fmsb +- r-glmnet +update_on: +- regex: hierinf_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hierinf diff --git a/prepare/r-highcharter/PKGBUILD b/prepare/r-highcharter/PKGBUILD new file mode 100644 index 0000000000..fbb8b795c4 --- /dev/null +++ b/prepare/r-highcharter/PKGBUILD @@ -0,0 +1,63 @@ +# Maintainer: Guoyi Zhang + +_pkgname=highcharter +_pkgver=0.9.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="A Wrapper for the 'Highcharts' Library" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-assertthat + r-broom + r-dplyr + r-htmltools + r-htmlwidgets + r-igraph + r-jsonlite + r-lubridate + r-magrittr + r-purrr + r-quantmod + r-rjson + r-rlang + r-rlist + r-stringr + r-tibble + r-tidyr + r-xts + r-yaml + r-zoo +) +optdepends=( + r-covr + r-forecast + r-gapminder + r-geojsonio + r-ggplot2 + r-httr + r-knitr + r-mass + r-rmarkdown + r-shiny + r-spelling + r-survival + r-testthat + r-viridislite +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-highcharter/lilac.py b/prepare/r-highcharter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-highcharter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-highcharter/lilac.yaml b/prepare/r-highcharter/lilac.yaml new file mode 100644 index 0000000000..6bb2caf6be --- /dev/null +++ b/prepare/r-highcharter/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-broom +- r-dplyr +- r-htmltools +- r-htmlwidgets +- r-igraph +- r-jsonlite +- r-lubridate +- r-magrittr +- r-purrr +- r-quantmod +- r-rjson +- r-rlang +- r-rlist +- r-stringr +- r-tibble +- r-tidyr +- r-xts +- r-yaml +- r-zoo +update_on: +- regex: highcharter_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=highcharter diff --git a/prepare/r-highr/PKGBUILD b/prepare/r-highr/PKGBUILD new file mode 100644 index 0000000000..aa84d5a3b4 --- /dev/null +++ b/prepare/r-highr/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=highr +_pkgver=0.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Syntax Highlighting for R Source Code' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-xfun +) +optdepends=( + r-knitr + r-markdown + r-testit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-highr/lilac.py b/prepare/r-highr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-highr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-highr/lilac.yaml b/prepare/r-highr/lilac.yaml new file mode 100644 index 0000000000..9c1bfb41c2 --- /dev/null +++ b/prepare/r-highr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-xfun +update_on: +- regex: highr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=highr diff --git a/prepare/r-hilbertcurve/PKGBUILD b/prepare/r-hilbertcurve/PKGBUILD new file mode 100644 index 0000000000..fe1a9b2be6 --- /dev/null +++ b/prepare/r-hilbertcurve/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HilbertCurve +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Making 2D Hilbert Curve' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-circlize + r-genomicranges + r-hilbertvis + r-iranges + r-png + r-polylabelr +) +optdepends=( + r-complexheatmap + r-getoptlong + r-knitr + r-markdown + r-rcolorbrewer + r-rcurl + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hilbertcurve/lilac.py b/prepare/r-hilbertcurve/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hilbertcurve/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hilbertcurve/lilac.yaml b/prepare/r-hilbertcurve/lilac.yaml new file mode 100644 index 0000000000..44ff05f25d --- /dev/null +++ b/prepare/r-hilbertcurve/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circlize +- r-genomicranges +- r-hilbertvis +- r-iranges +- r-png +- r-polylabelr +update_on: +- regex: HilbertCurve_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HilbertCurve diff --git a/prepare/r-hilbertvis/PKGBUILD b/prepare/r-hilbertvis/PKGBUILD new file mode 100644 index 0000000000..dcb789ece8 --- /dev/null +++ b/prepare/r-hilbertvis/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HilbertVis +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Hilbert curve visualization' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-ebimage + r-iranges +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hilbertvis/lilac.py b/prepare/r-hilbertvis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hilbertvis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hilbertvis/lilac.yaml b/prepare/r-hilbertvis/lilac.yaml new file mode 100644 index 0000000000..85ef74ccb6 --- /dev/null +++ b/prepare/r-hilbertvis/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: HilbertVis_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HilbertVis diff --git a/prepare/r-hilbertvisgui/PKGBUILD b/prepare/r-hilbertvisgui/PKGBUILD new file mode 100644 index 0000000000..25f94a2454 --- /dev/null +++ b/prepare/r-hilbertvisgui/PKGBUILD @@ -0,0 +1,32 @@ +# system requirements: gtkmm-2.4, GNU make +# Maintainer: Guoyi Zhang + +_pkgname=HilbertVisGUI +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='HilbertVisGUI' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-hilbertvis +) +optdepends=( + r-iranges + r-lattice +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hilbertvisgui/lilac.py b/prepare/r-hilbertvisgui/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hilbertvisgui/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hilbertvisgui/lilac.yaml b/prepare/r-hilbertvisgui/lilac.yaml new file mode 100644 index 0000000000..3f5a3f4876 --- /dev/null +++ b/prepare/r-hilbertvisgui/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-hilbertvis +update_on: +- regex: HilbertVisGUI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HilbertVisGUI diff --git a/prepare/r-hilda/PKGBUILD b/prepare/r-hilda/PKGBUILD new file mode 100644 index 0000000000..6e2ad2a637 --- /dev/null +++ b/prepare/r-hilda/PKGBUILD @@ -0,0 +1,49 @@ +# system requirements: JAGS 4.0.0 +# Maintainer: Guoyi Zhang + +_pkgname=HiLDA +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-biocgenerics + r-biostrings + r-bsgenome.hsapiens.ucsc.hg19 + r-cowplot + r-forcats + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-r2jags + r-rcpp + r-s4vectors + r-stringr + r-tidyr + r-txdb.hsapiens.ucsc.hg19.knowngene + r-xvector +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hilda/lilac.py b/prepare/r-hilda/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hilda/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hilda/lilac.yaml b/prepare/r-hilda/lilac.yaml new file mode 100644 index 0000000000..7395474b00 --- /dev/null +++ b/prepare/r-hilda/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-biocgenerics +- r-biostrings +- r-bsgenome.hsapiens.ucsc.hg19 +- r-cowplot +- r-forcats +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-r2jags +- r-rcpp +- r-s4vectors +- r-stringr +- r-tidyr +- r-txdb.hsapiens.ucsc.hg19.knowngene +- r-xvector +update_on: +- regex: HiLDA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HiLDA diff --git a/prepare/r-hipathia/PKGBUILD b/prepare/r-hipathia/PKGBUILD new file mode 100644 index 0000000000..1ccb5e41a5 --- /dev/null +++ b/prepare/r-hipathia/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hipathia +_pkgver=2.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='HiPathia: High-throughput Pathway Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationhub + r-coin + r-delayedarray + r-igraph + r-limma + r-matrixstats + r-multiassayexperiment + r-preprocesscore + r-s4vectors + r-servr + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hipathia/lilac.py b/prepare/r-hipathia/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hipathia/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hipathia/lilac.yaml b/prepare/r-hipathia/lilac.yaml new file mode 100644 index 0000000000..c8389ab536 --- /dev/null +++ b/prepare/r-hipathia/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-coin +- r-delayedarray +- r-igraph +- r-limma +- r-matrixstats +- r-multiassayexperiment +- r-preprocesscore +- r-s4vectors +- r-servr +- r-summarizedexperiment +update_on: +- regex: hipathia_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hipathia diff --git a/prepare/r-hippo/PKGBUILD b/prepare/r-hippo/PKGBUILD new file mode 100644 index 0000000000..0388da6dc4 --- /dev/null +++ b/prepare/r-hippo/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HIPPO +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Heterogeneity-Induced Pre-Processing tOol' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-ggplot2 + r-ggrepel + r-gridextra + r-irlba + r-magrittr + r-reshape2 + r-rlang + r-rtsne + r-singlecellexperiment + r-umap +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hippo/lilac.py b/prepare/r-hippo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hippo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hippo/lilac.yaml b/prepare/r-hippo/lilac.yaml new file mode 100644 index 0000000000..08d0720c09 --- /dev/null +++ b/prepare/r-hippo/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-ggrepel +- r-gridextra +- r-irlba +- r-magrittr +- r-reshape2 +- r-rlang +- r-rtsne +- r-singlecellexperiment +- r-umap +update_on: +- regex: HIPPO_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HIPPO diff --git a/prepare/r-hireadsprocessor/PKGBUILD b/prepare/r-hireadsprocessor/PKGBUILD new file mode 100644 index 0000000000..07395604f4 --- /dev/null +++ b/prepare/r-hireadsprocessor/PKGBUILD @@ -0,0 +1,41 @@ +# system requirements: BLAT, UCSC hg18 in 2bit format for BLAT +# Maintainer: Guoyi Zhang + +_pkgname=hiReadsProcessor +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions to process LM-PCR reads from 454/Illumina data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-dplyr + r-genomicalignments + r-genomicranges + r-hiannotator + r-readxl + r-soniclength +) +optdepends=( + r-knitr + r-markdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hireadsprocessor/lilac.py b/prepare/r-hireadsprocessor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hireadsprocessor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hireadsprocessor/lilac.yaml b/prepare/r-hireadsprocessor/lilac.yaml new file mode 100644 index 0000000000..c8eea98147 --- /dev/null +++ b/prepare/r-hireadsprocessor/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-dplyr +- r-genomicalignments +- r-genomicranges +- r-hiannotator +- r-readxl +- r-soniclength +update_on: +- regex: hiReadsProcessor_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hiReadsProcessor diff --git a/prepare/r-hireewas/PKGBUILD b/prepare/r-hireewas/PKGBUILD new file mode 100644 index 0000000000..e095dd1175 --- /dev/null +++ b/prepare/r-hireewas/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HIREewas +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-gplots + r-quadprog +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hireewas/lilac.py b/prepare/r-hireewas/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hireewas/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hireewas/lilac.yaml b/prepare/r-hireewas/lilac.yaml new file mode 100644 index 0000000000..865153ea71 --- /dev/null +++ b/prepare/r-hireewas/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gplots +- r-quadprog +update_on: +- regex: HIREewas_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HIREewas diff --git a/prepare/r-hitc/PKGBUILD b/prepare/r-hitc/PKGBUILD new file mode 100644 index 0000000000..44142b77ba --- /dev/null +++ b/prepare/r-hitc/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HiTC +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='High Throughput Chromosome Conformation Capture analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-genomeinfodb + r-genomicranges + r-iranges + r-rcolorbrewer + r-rtracklayer +) +optdepends=( + r-biocstyle + r-hicdatahumanimr90 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hitc/lilac.py b/prepare/r-hitc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hitc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hitc/lilac.yaml b/prepare/r-hitc/lilac.yaml new file mode 100644 index 0000000000..133a11e143 --- /dev/null +++ b/prepare/r-hitc/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rcolorbrewer +- r-rtracklayer +update_on: +- regex: HiTC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HiTC diff --git a/prepare/r-hiver/PKGBUILD b/prepare/r-hiver/PKGBUILD new file mode 100644 index 0000000000..9d1ca0574f --- /dev/null +++ b/prepare/r-hiver/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HiveR +_pkgver=0.3.63 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='2D and 3D Hive Plots for R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-jpeg + r-plyr + r-png + r-rcolorbrewer + r-rgl +) +optdepends=( + r-bipartite + r-funcmap + r-knitr + r-rmarkdown + r-sna + r-tint + r-xtable +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hiver/lilac.py b/prepare/r-hiver/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hiver/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hiver/lilac.yaml b/prepare/r-hiver/lilac.yaml new file mode 100644 index 0000000000..052ebe9dd6 --- /dev/null +++ b/prepare/r-hiver/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-jpeg +- r-plyr +- r-png +- r-rcolorbrewer +- r-rgl +update_on: +- regex: HiveR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=HiveR diff --git a/prepare/r-hmdbquery/PKGBUILD b/prepare/r-hmdbquery/PKGBUILD new file mode 100644 index 0000000000..9361b1231a --- /dev/null +++ b/prepare/r-hmdbquery/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hmdbQuery +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='utilities for exploration of human metabolome database' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-s4vectors + r-xml +) +optdepends=( + r-annotate + r-gwascat + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hmdbquery/lilac.py b/prepare/r-hmdbquery/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hmdbquery/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hmdbquery/lilac.yaml b/prepare/r-hmdbquery/lilac.yaml new file mode 100644 index 0000000000..08375e8dcc --- /dev/null +++ b/prepare/r-hmdbquery/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-s4vectors +- r-xml +update_on: +- regex: hmdbQuery_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hmdbQuery diff --git a/prepare/r-hmisc/PKGBUILD b/prepare/r-hmisc/PKGBUILD new file mode 100644 index 0000000000..50d58c4372 --- /dev/null +++ b/prepare/r-hmisc/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Hmisc +_pkgver=4.6-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Harrell Miscellaneous' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-base64enc + r-data.table + r-formula + r-ggplot2 + r-gridextra + r-gtable + r-htmltable + r-htmltools + r-latticeextra + r-viridis +) +optdepends=( + r-acepack + r-chron + r-knitr + r-mice + r-plotly + r-plyr + r-rlang + r-rms + r-tables + r-vgam +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hmisc/lilac.py b/prepare/r-hmisc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hmisc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hmisc/lilac.yaml b/prepare/r-hmisc/lilac.yaml new file mode 100644 index 0000000000..ec166bb225 --- /dev/null +++ b/prepare/r-hmisc/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-data.table +- r-formula +- r-ggplot2 +- r-gridextra +- r-gtable +- r-htmltable +- r-htmltools +- r-latticeextra +- r-viridis +update_on: +- regex: Hmisc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Hmisc diff --git a/prepare/r-hmmcopy/PKGBUILD b/prepare/r-hmmcopy/PKGBUILD new file mode 100644 index 0000000000..8cde83b220 --- /dev/null +++ b/prepare/r-hmmcopy/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HMMcopy +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Copy number prediction with correction for GC and mappability bias for HTS data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hmmcopy/lilac.py b/prepare/r-hmmcopy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hmmcopy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hmmcopy/lilac.yaml b/prepare/r-hmmcopy/lilac.yaml new file mode 100644 index 0000000000..15b0a0ae98 --- /dev/null +++ b/prepare/r-hmmcopy/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +update_on: +- regex: HMMcopy_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HMMcopy diff --git a/prepare/r-homo.sapiens/PKGBUILD b/prepare/r-homo.sapiens/PKGBUILD new file mode 100644 index 0000000000..64caec9535 --- /dev/null +++ b/prepare/r-homo.sapiens/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Homo.sapiens +_pkgver=1.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation package for the Homo.sapiens object' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-genomicfeatures + r-go.db + r-org.hs.eg.db + r-organismdbi + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-homo.sapiens/lilac.py b/prepare/r-homo.sapiens/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-homo.sapiens/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-homo.sapiens/lilac.yaml b/prepare/r-homo.sapiens/lilac.yaml new file mode 100644 index 0000000000..93318ce329 --- /dev/null +++ b/prepare/r-homo.sapiens/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-genomicfeatures +- r-go.db +- r-org.hs.eg.db +- r-organismdbi +- r-txdb.hsapiens.ucsc.hg19.knowngene +update_on: +- regex: Homo.sapiens_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Homo.sapiens diff --git a/prepare/r-homologene/PKGBUILD b/prepare/r-homologene/PKGBUILD new file mode 100644 index 0000000000..3e2ead3f00 --- /dev/null +++ b/prepare/r-homologene/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=homologene +_pkgver=1.4.68.19.3.27 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quick Access to Homologene and Gene Annotation Updates' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-magrittr + r-purrr + r-r.utils + r-readr +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-homologene/lilac.py b/prepare/r-homologene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-homologene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-homologene/lilac.yaml b/prepare/r-homologene/lilac.yaml new file mode 100644 index 0000000000..f7d819b917 --- /dev/null +++ b/prepare/r-homologene/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-magrittr +- r-purrr +- r-r.utils +- r-readr +update_on: +- regex: homologene_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=homologene diff --git a/prepare/r-hopach/PKGBUILD b/prepare/r-hopach/PKGBUILD new file mode 100644 index 0000000000..1898121386 --- /dev/null +++ b/prepare/r-hopach/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hopach +_pkgver=2.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hopach/lilac.py b/prepare/r-hopach/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hopach/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hopach/lilac.yaml b/prepare/r-hopach/lilac.yaml new file mode 100644 index 0000000000..7716c9bf07 --- /dev/null +++ b/prepare/r-hopach/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +update_on: +- regex: hopach_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hopach diff --git a/prepare/r-howmany/PKGBUILD b/prepare/r-howmany/PKGBUILD new file mode 100644 index 0000000000..dcd6c8b0a9 --- /dev/null +++ b/prepare/r-howmany/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=howmany +_pkgver=0.3-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A lower bound for the number of correct rejections' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-howmany/lilac.py b/prepare/r-howmany/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-howmany/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-howmany/lilac.yaml b/prepare/r-howmany/lilac.yaml new file mode 100644 index 0000000000..7411b16e21 --- /dev/null +++ b/prepare/r-howmany/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: howmany_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=howmany diff --git a/prepare/r-hpaanalyze/PKGBUILD b/prepare/r-hpaanalyze/PKGBUILD new file mode 100644 index 0000000000..d9d1ed8431 --- /dev/null +++ b/prepare/r-hpaanalyze/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HPAanalyze +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Retrieve and analyze data from the Human Protein Atlas' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-ggplot2 + r-gridextra + r-openxlsx + r-tibble + r-xml2 +) +optdepends=( + r-biocstyle + r-devtools + r-knitr + r-markdown + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hpaanalyze/lilac.py b/prepare/r-hpaanalyze/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hpaanalyze/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hpaanalyze/lilac.yaml b/prepare/r-hpaanalyze/lilac.yaml new file mode 100644 index 0000000000..5f2357d545 --- /dev/null +++ b/prepare/r-hpaanalyze/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-gridextra +- r-openxlsx +- r-tibble +- r-xml2 +update_on: +- regex: HPAanalyze_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HPAanalyze diff --git a/prepare/r-hpar/PKGBUILD b/prepare/r-hpar/PKGBUILD new file mode 100644 index 0000000000..8c37feff00 --- /dev/null +++ b/prepare/r-hpar/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hpar +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Human Protein Atlas in R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-biocstyle + r-go.db + r-knitr + r-org.hs.eg.db + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hpar/lilac.py b/prepare/r-hpar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hpar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hpar/lilac.yaml b/prepare/r-hpar/lilac.yaml new file mode 100644 index 0000000000..35d4cd022e --- /dev/null +++ b/prepare/r-hpar/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: hpar_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hpar diff --git a/prepare/r-hpastainr/PKGBUILD b/prepare/r-hpastainr/PKGBUILD new file mode 100644 index 0000000000..440f5a862a --- /dev/null +++ b/prepare/r-hpastainr/PKGBUILD @@ -0,0 +1,42 @@ +# system requirements: 4GB of RAM +# Maintainer: Guoyi Zhang + +_pkgname=HPAStainR +_pkgver=1.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Queries the Human Protein Atlas Staining Data for Multiple Proteins and Genes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-data.table + r-dplyr + r-scales + r-shiny + r-stringr + r-tibble + r-tidyr +) +optdepends=( + r-biocmanager + r-hpar + r-knitr + r-qpdf + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hpastainr/lilac.py b/prepare/r-hpastainr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hpastainr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hpastainr/lilac.yaml b/prepare/r-hpastainr/lilac.yaml new file mode 100644 index 0000000000..358960a218 --- /dev/null +++ b/prepare/r-hpastainr/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-dplyr +- r-scales +- r-shiny +- r-stringr +- r-tibble +- r-tidyr +update_on: +- regex: HPAStainR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HPAStainR diff --git a/prepare/r-hpip/PKGBUILD b/prepare/r-hpip/PKGBUILD new file mode 100644 index 0000000000..f2ab6c601f --- /dev/null +++ b/prepare/r-hpip/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HPiP +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Host-Pathogen Interaction Prediction' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-caret + r-corrplot + r-dplyr + r-ggplot2 + r-httr + r-igraph + r-magrittr + r-proc + r-protr + r-prroc + r-purrr + r-readr + r-stringr + r-tibble + r-tidyr +) +optdepends=( + r-biocgenerics + r-biocstyle + r-biostrings + r-colorspace + r-e1071 + r-ggthemes + r-gprofiler2 + r-gridextra + r-kernlab + r-knitr + r-randomforest + r-ranger + r-rmarkdown + r-runit + r-summarizedexperiment + r-tools +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hpip/lilac.py b/prepare/r-hpip/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hpip/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hpip/lilac.yaml b/prepare/r-hpip/lilac.yaml new file mode 100644 index 0000000000..6c475ed7e1 --- /dev/null +++ b/prepare/r-hpip/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-caret +- r-corrplot +- r-dplyr +- r-ggplot2 +- r-httr +- r-igraph +- r-magrittr +- r-proc +- r-protr +- r-prroc +- r-purrr +- r-readr +- r-stringr +- r-tibble +- r-tidyr +update_on: +- regex: HPiP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HPiP diff --git a/prepare/r-hsmmsinglecell/PKGBUILD b/prepare/r-hsmmsinglecell/PKGBUILD new file mode 100644 index 0000000000..197cf2bc37 --- /dev/null +++ b/prepare/r-hsmmsinglecell/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HSMMSingleCell +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hsmmsinglecell/lilac.py b/prepare/r-hsmmsinglecell/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hsmmsinglecell/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hsmmsinglecell/lilac.yaml b/prepare/r-hsmmsinglecell/lilac.yaml new file mode 100644 index 0000000000..7cff4ba541 --- /dev/null +++ b/prepare/r-hsmmsinglecell/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: HSMMSingleCell_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HSMMSingleCell diff --git a/prepare/r-htm2txt/PKGBUILD b/prepare/r-htm2txt/PKGBUILD new file mode 100644 index 0000000000..b3b66ef9ef --- /dev/null +++ b/prepare/r-htm2txt/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=htm2txt +_pkgver=2.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Convert Html into Text' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-htm2txt/lilac.py b/prepare/r-htm2txt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-htm2txt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-htm2txt/lilac.yaml b/prepare/r-htm2txt/lilac.yaml new file mode 100644 index 0000000000..d749404007 --- /dev/null +++ b/prepare/r-htm2txt/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: htm2txt_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=htm2txt diff --git a/prepare/r-htmltable/PKGBUILD b/prepare/r-htmltable/PKGBUILD new file mode 100644 index 0000000000..8c6b5fe8cc --- /dev/null +++ b/prepare/r-htmltable/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=htmlTable +_pkgver=2.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Advanced Tables for Markdown/HTML' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-checkmate + r-htmltools + r-htmlwidgets + r-knitr + r-magrittr + r-rstudioapi + r-stringr +) +optdepends=( + r-chron + r-dplyr + r-glue + r-hmisc + r-lubridate + r-purrr + r-reshape + r-rlang + r-rmarkdown + r-testthat + r-tibble + r-tidyr + r-tidyselect + r-xml + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-htmltable/lilac.py b/prepare/r-htmltable/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-htmltable/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-htmltable/lilac.yaml b/prepare/r-htmltable/lilac.yaml new file mode 100644 index 0000000000..3bfd1419ae --- /dev/null +++ b/prepare/r-htmltable/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-checkmate +- r-htmltools +- r-htmlwidgets +- r-knitr +- r-magrittr +- r-rstudioapi +- r-stringr +update_on: +- regex: htmlTable_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=htmlTable diff --git a/prepare/r-htmltools/PKGBUILD b/prepare/r-htmltools/PKGBUILD new file mode 100644 index 0000000000..42e3051ff0 --- /dev/null +++ b/prepare/r-htmltools/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=htmltools +_pkgver=0.5.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for HTML' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-base64enc + r-digest + r-fastmap + r-rlang +) +optdepends=( + r-cairo + r-knitr + r-markdown + r-ragg + r-shiny + r-testthat + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-htmltools/lilac.py b/prepare/r-htmltools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-htmltools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-htmltools/lilac.yaml b/prepare/r-htmltools/lilac.yaml new file mode 100644 index 0000000000..873931695e --- /dev/null +++ b/prepare/r-htmltools/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-digest +- r-fastmap +- r-rlang +update_on: +- regex: htmltools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=htmltools diff --git a/prepare/r-htmlutils/PKGBUILD b/prepare/r-htmlutils/PKGBUILD new file mode 100644 index 0000000000..b6df8d92bd --- /dev/null +++ b/prepare/r-htmlutils/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HTMLUtils +_pkgver=0.1.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Facilitates Automated HTML Report Creation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-r2html +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-htmlutils/lilac.py b/prepare/r-htmlutils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-htmlutils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-htmlutils/lilac.yaml b/prepare/r-htmlutils/lilac.yaml new file mode 100644 index 0000000000..bf05bedd76 --- /dev/null +++ b/prepare/r-htmlutils/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-r2html +update_on: +- regex: HTMLUtils_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=HTMLUtils diff --git a/prepare/r-htmlwidgets/PKGBUILD b/prepare/r-htmlwidgets/PKGBUILD new file mode 100644 index 0000000000..544c0a8b77 --- /dev/null +++ b/prepare/r-htmlwidgets/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=htmlwidgets +_pkgver=1.5.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='HTML Widgets for R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmltools + r-jsonlite + r-yaml +) +optdepends=( + r-knitr + r-rmarkdown + r-shiny + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-htmlwidgets/lilac.py b/prepare/r-htmlwidgets/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-htmlwidgets/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-htmlwidgets/lilac.yaml b/prepare/r-htmlwidgets/lilac.yaml new file mode 100644 index 0000000000..38d869e99d --- /dev/null +++ b/prepare/r-htmlwidgets/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-jsonlite +- r-yaml +update_on: +- regex: htmlwidgets_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=htmlwidgets diff --git a/prepare/r-htqpcr/PKGBUILD b/prepare/r-htqpcr/PKGBUILD new file mode 100644 index 0000000000..5db3bdeeac --- /dev/null +++ b/prepare/r-htqpcr/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HTqPCR +_pkgver=1.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automated analysis of high-throughput qPCR data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-affy + r-biobase + r-gplots + r-limma + r-rcolorbrewer +) +optdepends=( + r-statmod +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-htqpcr/lilac.py b/prepare/r-htqpcr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-htqpcr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-htqpcr/lilac.yaml b/prepare/r-htqpcr/lilac.yaml new file mode 100644 index 0000000000..360de60798 --- /dev/null +++ b/prepare/r-htqpcr/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +- r-gplots +- r-limma +- r-rcolorbrewer +update_on: +- regex: HTqPCR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HTqPCR diff --git a/prepare/r-htscluster/PKGBUILD b/prepare/r-htscluster/PKGBUILD new file mode 100644 index 0000000000..15f235522e --- /dev/null +++ b/prepare/r-htscluster/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HTSCluster +_pkgver=2.0.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clustering High-Throughput Transcriptome Sequencing (HTS) Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-capushe + r-edger + r-plotrix +) +optdepends=( + r-biobase + r-htsfilter +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-htscluster/lilac.py b/prepare/r-htscluster/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-htscluster/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-htscluster/lilac.yaml b/prepare/r-htscluster/lilac.yaml new file mode 100644 index 0000000000..f21896724d --- /dev/null +++ b/prepare/r-htscluster/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-capushe +- r-edger +- r-plotrix +update_on: +- regex: HTSCluster_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=HTSCluster diff --git a/prepare/r-htseqgenie/PKGBUILD b/prepare/r-htseqgenie/PKGBUILD new file mode 100644 index 0000000000..de2710db29 --- /dev/null +++ b/prepare/r-htseqgenie/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HTSeqGenie +_pkgver=4.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A NGS analysis pipeline.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-cairo + r-chipseq + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-gmapr + r-hwriter + r-iranges + r-rsamtools + r-rtracklayer + r-s4vectors + r-shortread + r-summarizedexperiment + r-variantannotation + r-varianttools +) +optdepends=( + r-lungcancerlines + r-org.hs.eg.db + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-htseqgenie/lilac.py b/prepare/r-htseqgenie/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-htseqgenie/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-htseqgenie/lilac.yaml b/prepare/r-htseqgenie/lilac.yaml new file mode 100644 index 0000000000..3ea1f6e567 --- /dev/null +++ b/prepare/r-htseqgenie/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-cairo +- r-chipseq +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-gmapr +- r-hwriter +- r-iranges +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-shortread +- r-summarizedexperiment +- r-variantannotation +- r-varianttools +update_on: +- regex: HTSeqGenie_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HTSeqGenie diff --git a/prepare/r-htsfilter/PKGBUILD b/prepare/r-htsfilter/PKGBUILD new file mode 100644 index 0000000000..f1f205b450 --- /dev/null +++ b/prepare/r-htsfilter/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HTSFilter +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Filter replicated high-throughput transcriptome sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocparallel + r-deseq2 + r-edger +) +optdepends=( + r-biocstyle + r-edaseq + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-htsfilter/lilac.py b/prepare/r-htsfilter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-htsfilter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-htsfilter/lilac.yaml b/prepare/r-htsfilter/lilac.yaml new file mode 100644 index 0000000000..c9f6811d94 --- /dev/null +++ b/prepare/r-htsfilter/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocparallel +- r-deseq2 +- r-edger +update_on: +- regex: HTSFilter_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HTSFilter diff --git a/prepare/r-httpcode/PKGBUILD b/prepare/r-httpcode/PKGBUILD new file mode 100644 index 0000000000..6bd95ea7cd --- /dev/null +++ b/prepare/r-httpcode/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=httpcode +_pkgver=0.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'HTTP' Status Code Helper" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-httpcode/lilac.py b/prepare/r-httpcode/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-httpcode/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-httpcode/lilac.yaml b/prepare/r-httpcode/lilac.yaml new file mode 100644 index 0000000000..917e5509d8 --- /dev/null +++ b/prepare/r-httpcode/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: httpcode_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=httpcode diff --git a/prepare/r-httpuv/PKGBUILD b/prepare/r-httpuv/PKGBUILD new file mode 100644 index 0000000000..08957f0bf2 --- /dev/null +++ b/prepare/r-httpuv/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: GNU make, C++11, zlib +# Maintainer: Guoyi Zhang + +_pkgname=httpuv +_pkgver=1.6.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='HTTP and WebSocket Server Library' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-later + r-promises + r-r6 + r-rcpp +) +optdepends=( + r-callr + r-curl + r-testthat + r-websocket +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-httpuv/lilac.py b/prepare/r-httpuv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-httpuv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-httpuv/lilac.yaml b/prepare/r-httpuv/lilac.yaml new file mode 100644 index 0000000000..cec31662fd --- /dev/null +++ b/prepare/r-httpuv/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-later +- r-promises +- r-r6 +- r-rcpp +update_on: +- regex: httpuv_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=httpuv diff --git a/prepare/r-hubpub/PKGBUILD b/prepare/r-hubpub/PKGBUILD new file mode 100644 index 0000000000..712a19979f --- /dev/null +++ b/prepare/r-hubpub/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HubPub +_pkgver=1.2.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities to create and use Bioconductor Hubs' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-available + r-aws.s3 + r-biocmanager + r-biocthis + r-dplyr + r-fs + r-usethis +) +optdepends=( + r-annotationhubdata + r-biocstyle + r-experimenthubdata + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hubpub/lilac.py b/prepare/r-hubpub/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hubpub/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hubpub/lilac.yaml b/prepare/r-hubpub/lilac.yaml new file mode 100644 index 0000000000..943ef9f4c9 --- /dev/null +++ b/prepare/r-hubpub/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-available +- r-aws.s3 +- r-biocmanager +- r-biocthis +- r-dplyr +- r-fs +- r-usethis +update_on: +- regex: HubPub_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HubPub diff --git a/prepare/r-huge/PKGBUILD b/prepare/r-huge/PKGBUILD new file mode 100644 index 0000000000..7fe49f0a29 --- /dev/null +++ b/prepare/r-huge/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=huge +_pkgver=1.3.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='High-Dimensional Undirected Graph Estimation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-igraph + r-rcpp + r-rcppeigen +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-huge/lilac.py b/prepare/r-huge/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-huge/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-huge/lilac.yaml b/prepare/r-huge/lilac.yaml new file mode 100644 index 0000000000..2ae35b85fc --- /dev/null +++ b/prepare/r-huge/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +- r-rcpp +- r-rcppeigen +update_on: +- regex: huge_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=huge diff --git a/prepare/r-humantranscriptomecompendium/PKGBUILD b/prepare/r-humantranscriptomecompendium/PKGBUILD new file mode 100644 index 0000000000..17fad88591 --- /dev/null +++ b/prepare/r-humantranscriptomecompendium/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HumanTranscriptomeCompendium +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools to work with a Compendium of 181000 human transcriptome sequencing studies' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-s4vectors + r-shiny + r-ssrch + r-summarizedexperiment +) +optdepends=( + r-beeswarm + r-biocfilecache + r-biocstyle + r-dplyr + r-dt + r-knitr + r-magrittr + r-rhdf5client + r-rmarkdown + r-testthat + r-tximport + r-tximportdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-humantranscriptomecompendium/lilac.py b/prepare/r-humantranscriptomecompendium/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-humantranscriptomecompendium/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-humantranscriptomecompendium/lilac.yaml b/prepare/r-humantranscriptomecompendium/lilac.yaml new file mode 100644 index 0000000000..52b2bc20c8 --- /dev/null +++ b/prepare/r-humantranscriptomecompendium/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-s4vectors +- r-shiny +- r-ssrch +- r-summarizedexperiment +update_on: +- regex: HumanTranscriptomeCompendium_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HumanTranscriptomeCompendium diff --git a/prepare/r-hummingbird/PKGBUILD b/prepare/r-hummingbird/PKGBUILD new file mode 100644 index 0000000000..5f5055e036 --- /dev/null +++ b/prepare/r-hummingbird/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hummingbird +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian Hidden Markov Model for the detection of differentially methylated regions' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicranges + r-iranges + r-rcpp + r-summarizedexperiment +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hummingbird/lilac.py b/prepare/r-hummingbird/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hummingbird/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hummingbird/lilac.yaml b/prepare/r-hummingbird/lilac.yaml new file mode 100644 index 0000000000..141366e21e --- /dev/null +++ b/prepare/r-hummingbird/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-iranges +- r-rcpp +- r-summarizedexperiment +update_on: +- regex: hummingbird_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hummingbird diff --git a/prepare/r-hunspell/PKGBUILD b/prepare/r-hunspell/PKGBUILD new file mode 100644 index 0000000000..dfc2ced5e3 --- /dev/null +++ b/prepare/r-hunspell/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hunspell +_pkgver=3.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='High-Performance Stemmer, Tokenizer, and Spell Checker' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-digest + r-rcpp +) +optdepends=( + r-janeaustenr + r-knitr + r-pdftools + r-rmarkdown + r-spelling + r-stopwords + r-testthat + r-wordcloud2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hunspell/lilac.py b/prepare/r-hunspell/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hunspell/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hunspell/lilac.yaml b/prepare/r-hunspell/lilac.yaml new file mode 100644 index 0000000000..52b727a976 --- /dev/null +++ b/prepare/r-hunspell/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-rcpp +update_on: +- regex: hunspell_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=hunspell diff --git a/prepare/r-hwriter/PKGBUILD b/prepare/r-hwriter/PKGBUILD new file mode 100644 index 0000000000..cead6b20cd --- /dev/null +++ b/prepare/r-hwriter/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hwriter +_pkgver=1.3.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='HTML Writer - Outputs R objects in HTML format' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hwriter/lilac.py b/prepare/r-hwriter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hwriter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hwriter/lilac.yaml b/prepare/r-hwriter/lilac.yaml new file mode 100644 index 0000000000..5b3a10b8f2 --- /dev/null +++ b/prepare/r-hwriter/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: hwriter_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=hwriter diff --git a/prepare/r-hybridmtest/PKGBUILD b/prepare/r-hybridmtest/PKGBUILD new file mode 100644 index 0000000000..cdcdffaa25 --- /dev/null +++ b/prepare/r-hybridmtest/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=HybridMTest +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Hybrid Multiple Testing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-fdrtool +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hybridmtest/lilac.py b/prepare/r-hybridmtest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hybridmtest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hybridmtest/lilac.yaml b/prepare/r-hybridmtest/lilac.yaml new file mode 100644 index 0000000000..0781c18275 --- /dev/null +++ b/prepare/r-hybridmtest/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-fdrtool +update_on: +- regex: HybridMTest_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/HybridMTest diff --git a/prepare/r-hyper/PKGBUILD b/prepare/r-hyper/PKGBUILD new file mode 100644 index 0000000000..400b34778b --- /dev/null +++ b/prepare/r-hyper/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hypeR +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R Package For Geneset Enrichment Workflows' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-ggforce + r-ggplot2 + r-htmltools + r-httr + r-igraph + r-kableextra + r-magrittr + r-msigdbr + r-openxlsx + r-purrr + r-r6 + r-reactable + r-reshape2 + r-rlang + r-rmarkdown + r-scales + r-shiny + r-stringr + r-visnetwork +) +optdepends=( + r-devtools + r-knitr + r-testthat + r-tidyverse +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hyper/lilac.py b/prepare/r-hyper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hyper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hyper/lilac.yaml b/prepare/r-hyper/lilac.yaml new file mode 100644 index 0000000000..c282ac72e8 --- /dev/null +++ b/prepare/r-hyper/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggforce +- r-ggplot2 +- r-htmltools +- r-httr +- r-igraph +- r-kableextra +- r-magrittr +- r-msigdbr +- r-openxlsx +- r-purrr +- r-r6 +- r-reactable +- r-reshape2 +- r-rlang +- r-rmarkdown +- r-scales +- r-shiny +- r-stringr +- r-visnetwork +update_on: +- regex: hypeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hypeR diff --git a/prepare/r-hyperdraw/PKGBUILD b/prepare/r-hyperdraw/PKGBUILD new file mode 100644 index 0000000000..d849e09c19 --- /dev/null +++ b/prepare/r-hyperdraw/PKGBUILD @@ -0,0 +1,30 @@ +# system requirements: graphviz +# Maintainer: Guoyi Zhang + +_pkgname=hyperdraw +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualizing Hypergaphs' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-graph + r-hypergraph + r-rgraphviz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hyperdraw/lilac.py b/prepare/r-hyperdraw/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hyperdraw/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hyperdraw/lilac.yaml b/prepare/r-hyperdraw/lilac.yaml new file mode 100644 index 0000000000..0d3f7f6e64 --- /dev/null +++ b/prepare/r-hyperdraw/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +- r-hypergraph +- r-rgraphviz +update_on: +- regex: hyperdraw_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hyperdraw diff --git a/prepare/r-hypergraph/PKGBUILD b/prepare/r-hypergraph/PKGBUILD new file mode 100644 index 0000000000..01265da551 --- /dev/null +++ b/prepare/r-hypergraph/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=hypergraph +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A package providing hypergraph data structures' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-graph +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-hypergraph/lilac.py b/prepare/r-hypergraph/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-hypergraph/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-hypergraph/lilac.yaml b/prepare/r-hypergraph/lilac.yaml new file mode 100644 index 0000000000..eb62df6db3 --- /dev/null +++ b/prepare/r-hypergraph/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +update_on: +- regex: hypergraph_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/hypergraph diff --git a/prepare/r-iaseq/PKGBUILD b/prepare/r-iaseq/PKGBUILD new file mode 100644 index 0000000000..095c01152f --- /dev/null +++ b/prepare/r-iaseq/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iASeq +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='iASeq: integrating multiple sequencing datasets for detecting allele-specific events' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-iaseq/lilac.py b/prepare/r-iaseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-iaseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-iaseq/lilac.yaml b/prepare/r-iaseq/lilac.yaml new file mode 100644 index 0000000000..26dbefc9a4 --- /dev/null +++ b/prepare/r-iaseq/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: iASeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iASeq diff --git a/prepare/r-iasva/PKGBUILD b/prepare/r-iasva/PKGBUILD new file mode 100644 index 0000000000..7d9aa8ff7a --- /dev/null +++ b/prepare/r-iasva/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iasva +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Iteratively Adjusted Surrogate Variable Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-irlba + r-summarizedexperiment +) +optdepends=( + r-corrplot + r-desctools + r-knitr + r-pheatmap + r-rcolorbrewer + r-rmarkdown + r-rtsne + r-sva + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-iasva/lilac.py b/prepare/r-iasva/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-iasva/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-iasva/lilac.yaml b/prepare/r-iasva/lilac.yaml new file mode 100644 index 0000000000..267073d71f --- /dev/null +++ b/prepare/r-iasva/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-irlba +- r-summarizedexperiment +update_on: +- regex: iasva_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iasva diff --git a/prepare/r-ibbig/PKGBUILD b/prepare/r-ibbig/PKGBUILD new file mode 100644 index 0000000000..ab8062dcc5 --- /dev/null +++ b/prepare/r-ibbig/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iBBiG +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Iterative Binary Biclustering of Genesets' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ade4 + r-biclust + r-xtable +) +optdepends=( + r-methods +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ibbig/lilac.py b/prepare/r-ibbig/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ibbig/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ibbig/lilac.yaml b/prepare/r-ibbig/lilac.yaml new file mode 100644 index 0000000000..ce232ed20d --- /dev/null +++ b/prepare/r-ibbig/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ade4 +- r-biclust +- r-xtable +update_on: +- regex: iBBiG_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iBBiG diff --git a/prepare/r-ibh/PKGBUILD b/prepare/r-ibh/PKGBUILD new file mode 100644 index 0000000000..558509de82 --- /dev/null +++ b/prepare/r-ibh/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ibh +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interaction Based Homogeneity for Evaluating Gene Lists' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-simpintlists +) +optdepends=( + r-stats + r-yeastcc +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ibh/lilac.py b/prepare/r-ibh/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ibh/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ibh/lilac.yaml b/prepare/r-ibh/lilac.yaml new file mode 100644 index 0000000000..e08b60c2f7 --- /dev/null +++ b/prepare/r-ibh/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-simpintlists +update_on: +- regex: ibh_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ibh diff --git a/prepare/r-ibmq/PKGBUILD b/prepare/r-ibmq/PKGBUILD new file mode 100644 index 0000000000..25ff017dab --- /dev/null +++ b/prepare/r-ibmq/PKGBUILD @@ -0,0 +1,29 @@ +# system requirements: GSL and OpenMP +# Maintainer: Guoyi Zhang + +_pkgname=iBMQ +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='integrated Bayesian Modeling of eQTL data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-ggplot2 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ibmq/lilac.py b/prepare/r-ibmq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ibmq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ibmq/lilac.yaml b/prepare/r-ibmq/lilac.yaml new file mode 100644 index 0000000000..fd3e66a52e --- /dev/null +++ b/prepare/r-ibmq/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-ggplot2 +update_on: +- regex: iBMQ_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iBMQ diff --git a/prepare/r-ic10/PKGBUILD b/prepare/r-ic10/PKGBUILD new file mode 100644 index 0000000000..17a9ba699b --- /dev/null +++ b/prepare/r-ic10/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iC10 +_pkgver=1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Copy Number and Expression-Based Classifier for Breast Tumours' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ic10trainingdata + r-impute + r-pamr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ic10/lilac.py b/prepare/r-ic10/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ic10/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ic10/lilac.yaml b/prepare/r-ic10/lilac.yaml new file mode 100644 index 0000000000..20168362f9 --- /dev/null +++ b/prepare/r-ic10/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ic10trainingdata +- r-impute +- r-pamr +update_on: +- regex: iC10_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=iC10 diff --git a/prepare/r-ic10trainingdata/PKGBUILD b/prepare/r-ic10trainingdata/PKGBUILD new file mode 100644 index 0000000000..c3ded40d46 --- /dev/null +++ b/prepare/r-ic10trainingdata/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iC10TrainingData +_pkgver=1.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Training Datasets for iC10 Package' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ic10trainingdata/lilac.py b/prepare/r-ic10trainingdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ic10trainingdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ic10trainingdata/lilac.yaml b/prepare/r-ic10trainingdata/lilac.yaml new file mode 100644 index 0000000000..21af4da88d --- /dev/null +++ b/prepare/r-ic10trainingdata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: iC10TrainingData_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=iC10TrainingData diff --git a/prepare/r-ica/PKGBUILD b/prepare/r-ica/PKGBUILD new file mode 100644 index 0000000000..98dac9809c --- /dev/null +++ b/prepare/r-ica/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ica +_pkgver=1.0-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Independent Component Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ica/lilac.py b/prepare/r-ica/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ica/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ica/lilac.yaml b/prepare/r-ica/lilac.yaml new file mode 100644 index 0000000000..75545cd46c --- /dev/null +++ b/prepare/r-ica/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ica_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ica diff --git a/prepare/r-icare/PKGBUILD b/prepare/r-icare/PKGBUILD new file mode 100644 index 0000000000..360d46989c --- /dev/null +++ b/prepare/r-icare/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iCARE +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-gtools + r-hmisc + r-plotrix +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-icare/lilac.py b/prepare/r-icare/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-icare/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-icare/lilac.yaml b/prepare/r-icare/lilac.yaml new file mode 100644 index 0000000000..0a7c328706 --- /dev/null +++ b/prepare/r-icare/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gtools +- r-hmisc +- r-plotrix +update_on: +- regex: iCARE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iCARE diff --git a/prepare/r-icens/PKGBUILD b/prepare/r-icens/PKGBUILD new file mode 100644 index 0000000000..150b02648e --- /dev/null +++ b/prepare/r-icens/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Icens +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='NPMLE for Censored and Truncated Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-icens/lilac.py b/prepare/r-icens/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-icens/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-icens/lilac.yaml b/prepare/r-icens/lilac.yaml new file mode 100644 index 0000000000..b502bb61c7 --- /dev/null +++ b/prepare/r-icens/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Icens_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Icens diff --git a/prepare/r-icetea/PKGBUILD b/prepare/r-icetea/PKGBUILD new file mode 100644 index 0000000000..7eff2665e9 --- /dev/null +++ b/prepare/r-icetea/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=icetea +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integrating Cap Enrichment with Transcript Expression Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-csaw + r-deseq2 + r-edger + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-limma + r-rsamtools + r-rtracklayer + r-s4vectors + r-shortread + r-summarizedexperiment + r-txdb.dmelanogaster.ucsc.dm6.ensgene + r-variantannotation +) +optdepends=( + r-knitr + r-rmarkdown + r-rsubread + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-icetea/lilac.py b/prepare/r-icetea/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-icetea/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-icetea/lilac.yaml b/prepare/r-icetea/lilac.yaml new file mode 100644 index 0000000000..2607f5d5c7 --- /dev/null +++ b/prepare/r-icetea/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-csaw +- r-deseq2 +- r-edger +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-limma +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-shortread +- r-summarizedexperiment +- r-txdb.dmelanogaster.ucsc.dm6.ensgene +- r-variantannotation +update_on: +- regex: icetea_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/icetea diff --git a/prepare/r-icheck/PKGBUILD b/prepare/r-icheck/PKGBUILD new file mode 100644 index 0000000000..a0531f09ef --- /dev/null +++ b/prepare/r-icheck/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iCheck +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-biobase + r-geneselectmmd + r-gplots + r-limma + r-lmtest + r-lumi + r-preprocesscore + r-randomforest + r-rgl + r-scatterplot3d +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-icheck/lilac.py b/prepare/r-icheck/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-icheck/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-icheck/lilac.yaml b/prepare/r-icheck/lilac.yaml new file mode 100644 index 0000000000..88725f8a50 --- /dev/null +++ b/prepare/r-icheck/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +- r-geneselectmmd +- r-gplots +- r-limma +- r-lmtest +- r-lumi +- r-preprocesscore +- r-randomforest +- r-rgl +- r-scatterplot3d +update_on: +- regex: iCheck_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iCheck diff --git a/prepare/r-ichip/PKGBUILD b/prepare/r-ichip/PKGBUILD new file mode 100644 index 0000000000..d8a3d3cae6 --- /dev/null +++ b/prepare/r-ichip/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iChip +_pkgver=1.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-limma +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ichip/lilac.py b/prepare/r-ichip/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ichip/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ichip/lilac.yaml b/prepare/r-ichip/lilac.yaml new file mode 100644 index 0000000000..b78e5df82b --- /dev/null +++ b/prepare/r-ichip/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-limma +update_on: +- regex: iChip_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iChip diff --git a/prepare/r-icluster/PKGBUILD b/prepare/r-icluster/PKGBUILD new file mode 100644 index 0000000000..333cc77fea --- /dev/null +++ b/prepare/r-icluster/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iCluster +_pkgver=2.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integrative clustering of multiple genomic data types' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-catools + r-gdata + r-gplots + r-gtools +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-icluster/lilac.py b/prepare/r-icluster/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-icluster/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-icluster/lilac.yaml b/prepare/r-icluster/lilac.yaml new file mode 100644 index 0000000000..fb3a08c290 --- /dev/null +++ b/prepare/r-icluster/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-catools +- r-gdata +- r-gplots +- r-gtools +update_on: +- regex: iCluster_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=iCluster diff --git a/prepare/r-iclusterplus/PKGBUILD b/prepare/r-iclusterplus/PKGBUILD new file mode 100644 index 0000000000..df86d5d286 --- /dev/null +++ b/prepare/r-iclusterplus/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iClusterPlus +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integrative clustering of multi-type genomic data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biocgenerics + r-runit +) +makedepends=( + gcc-fortran +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-iclusterplus/lilac.py b/prepare/r-iclusterplus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-iclusterplus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-iclusterplus/lilac.yaml b/prepare/r-iclusterplus/lilac.yaml new file mode 100644 index 0000000000..fe1ef54b6e --- /dev/null +++ b/prepare/r-iclusterplus/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: iClusterPlus_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iClusterPlus diff --git a/prepare/r-icnv/PKGBUILD b/prepare/r-icnv/PKGBUILD new file mode 100644 index 0000000000..e1c4986779 --- /dev/null +++ b/prepare/r-icnv/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iCNV +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integrated Copy Number Variation detection' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-codex + r-data.table + r-dplyr + r-fields + r-ggplot2 + r-rlang + r-tidyr + r-truncnorm +) +optdepends=( + r-knitr + r-rmarkdown + r-wes.1kg.wugsc +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-icnv/lilac.py b/prepare/r-icnv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-icnv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-icnv/lilac.yaml b/prepare/r-icnv/lilac.yaml new file mode 100644 index 0000000000..1d00910060 --- /dev/null +++ b/prepare/r-icnv/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-codex +- r-data.table +- r-dplyr +- r-fields +- r-ggplot2 +- r-rlang +- r-tidyr +- r-truncnorm +update_on: +- regex: iCNV_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iCNV diff --git a/prepare/r-icobra/PKGBUILD b/prepare/r-icobra/PKGBUILD new file mode 100644 index 0000000000..5c8a7f7344 --- /dev/null +++ b/prepare/r-icobra/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iCOBRA +_pkgver=1.22.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Comparison and Visualization of Ranking and Assignment Methods' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-dt + r-ggplot2 + r-limma + r-reshape2 + r-rocr + r-scales + r-shiny + r-shinybs + r-shinydashboard + r-upsetr +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-icobra/lilac.py b/prepare/r-icobra/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-icobra/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-icobra/lilac.yaml b/prepare/r-icobra/lilac.yaml new file mode 100644 index 0000000000..357ad915cd --- /dev/null +++ b/prepare/r-icobra/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-dt +- r-ggplot2 +- r-limma +- r-reshape2 +- r-rocr +- r-scales +- r-shiny +- r-shinybs +- r-shinydashboard +- r-upsetr +update_on: +- regex: iCOBRA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iCOBRA diff --git a/prepare/r-ics/PKGBUILD b/prepare/r-ics/PKGBUILD new file mode 100644 index 0000000000..ba76a9de9a --- /dev/null +++ b/prepare/r-ics/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ICS +_pkgver=1.3-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Exploring Multivariate Data via ICS/ICA' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mvtnorm + r-survey +) +optdepends=( + r-icsnp + r-mass + r-pixmap + r-robustbase +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ics/lilac.py b/prepare/r-ics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ics/lilac.yaml b/prepare/r-ics/lilac.yaml new file mode 100644 index 0000000000..0a30890d26 --- /dev/null +++ b/prepare/r-ics/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mvtnorm +- r-survey +update_on: +- regex: ICS_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ICS diff --git a/prepare/r-icsnp/PKGBUILD b/prepare/r-icsnp/PKGBUILD new file mode 100644 index 0000000000..79740a0db2 --- /dev/null +++ b/prepare/r-icsnp/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ICSNP +_pkgver=1.1-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Multivariate Nonparametrics' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ics + r-mvtnorm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-icsnp/lilac.py b/prepare/r-icsnp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-icsnp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-icsnp/lilac.yaml b/prepare/r-icsnp/lilac.yaml new file mode 100644 index 0000000000..a3c567bff8 --- /dev/null +++ b/prepare/r-icsnp/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ics +- r-mvtnorm +update_on: +- regex: ICSNP_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ICSNP diff --git a/prepare/r-ideal/PKGBUILD b/prepare/r-ideal/PKGBUILD new file mode 100644 index 0000000000..c6cc33f471 --- /dev/null +++ b/prepare/r-ideal/PKGBUILD @@ -0,0 +1,70 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ideal +_pkgver=1.18.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive Differential Expression AnaLysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-base64enc + r-biocparallel + r-deseq2 + r-dplyr + r-dt + r-genomicranges + r-ggplot2 + r-ggrepel + r-go.db + r-goseq + r-gostats + r-gplots + r-heatmaply + r-ihw + r-iranges + r-knitr + r-limma + r-pcaexplorer + r-pheatmap + r-plotly + r-rentrez + r-rintrojs + r-rlang + r-rmarkdown + r-s4vectors + r-shiny + r-shinyace + r-shinybs + r-shinydashboard + r-stringr + r-summarizedexperiment + r-topgo + r-upsetr +) +optdepends=( + r-airway + r-biocstyle + r-deformats + r-edger + r-org.hs.eg.db + r-testthat + r-txdb.hsapiens.ucsc.hg38.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ideal/lilac.py b/prepare/r-ideal/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ideal/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ideal/lilac.yaml b/prepare/r-ideal/lilac.yaml new file mode 100644 index 0000000000..7892265667 --- /dev/null +++ b/prepare/r-ideal/lilac.yaml @@ -0,0 +1,43 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-base64enc +- r-biocparallel +- r-deseq2 +- r-dplyr +- r-dt +- r-genomicranges +- r-ggplot2 +- r-ggrepel +- r-go.db +- r-goseq +- r-gostats +- r-gplots +- r-heatmaply +- r-ihw +- r-iranges +- r-knitr +- r-limma +- r-pcaexplorer +- r-pheatmap +- r-plotly +- r-rentrez +- r-rintrojs +- r-rlang +- r-rmarkdown +- r-s4vectors +- r-shiny +- r-shinyace +- r-shinybs +- r-shinydashboard +- r-stringr +- r-summarizedexperiment +- r-topgo +- r-upsetr +update_on: +- regex: ideal_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ideal diff --git a/prepare/r-ideoviz/PKGBUILD b/prepare/r-ideoviz/PKGBUILD new file mode 100644 index 0000000000..afb6801139 --- /dev/null +++ b/prepare/r-ideoviz/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IdeoViz +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Plots data (continuous/discrete) along chromosomal ideogram' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-genomeinfodb + r-genomicranges + r-iranges + r-rcolorbrewer + r-rtracklayer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ideoviz/lilac.py b/prepare/r-ideoviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ideoviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ideoviz/lilac.yaml b/prepare/r-ideoviz/lilac.yaml new file mode 100644 index 0000000000..f887511cd6 --- /dev/null +++ b/prepare/r-ideoviz/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rcolorbrewer +- r-rtracklayer +update_on: +- regex: IdeoViz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IdeoViz diff --git a/prepare/r-idiogram/PKGBUILD b/prepare/r-idiogram/PKGBUILD new file mode 100644 index 0000000000..cf5b53c5a3 --- /dev/null +++ b/prepare/r-idiogram/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=idiogram +_pkgver=1.70.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='idiogram' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotate + r-biobase + r-plotrix +) +optdepends=( + r-golubesets + r-hgu95av2.db + r-hu6800.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-idiogram/lilac.py b/prepare/r-idiogram/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-idiogram/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-idiogram/lilac.yaml b/prepare/r-idiogram/lilac.yaml new file mode 100644 index 0000000000..cf86ca5326 --- /dev/null +++ b/prepare/r-idiogram/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-biobase +- r-plotrix +update_on: +- regex: idiogram_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/idiogram diff --git a/prepare/r-idpmisc/PKGBUILD b/prepare/r-idpmisc/PKGBUILD new file mode 100644 index 0000000000..edbb527b2a --- /dev/null +++ b/prepare/r-idpmisc/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IDPmisc +_pkgver=1.1.20 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'Utilities of Institute of Data Analyses and Process Design (www.zhaw.ch/idp)'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-swissair +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-idpmisc/lilac.py b/prepare/r-idpmisc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-idpmisc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-idpmisc/lilac.yaml b/prepare/r-idpmisc/lilac.yaml new file mode 100644 index 0000000000..98c48a08a8 --- /dev/null +++ b/prepare/r-idpmisc/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: IDPmisc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=IDPmisc diff --git a/prepare/r-idpr/PKGBUILD b/prepare/r-idpr/PKGBUILD new file mode 100644 index 0000000000..e1ef408da2 --- /dev/null +++ b/prepare/r-idpr/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=idpr +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Profiling and Analyzing Intrinsically Disordered Proteins in R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biostrings + r-dplyr + r-ggplot2 + r-jsonlite + r-magrittr + r-plyr + r-rlang +) +optdepends=( + r-ape + r-knitr + r-msa + r-rmarkdown + r-seqinr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-idpr/lilac.py b/prepare/r-idpr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-idpr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-idpr/lilac.yaml b/prepare/r-idpr/lilac.yaml new file mode 100644 index 0000000000..14f21712a3 --- /dev/null +++ b/prepare/r-idpr/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-dplyr +- r-ggplot2 +- r-jsonlite +- r-magrittr +- r-plyr +- r-rlang +update_on: +- regex: idpr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/idpr diff --git a/prepare/r-idr/PKGBUILD b/prepare/r-idr/PKGBUILD new file mode 100644 index 0000000000..1f8b5ecda1 --- /dev/null +++ b/prepare/r-idr/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=idr +_pkgver=1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Irreproducible discovery rate' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-idr/lilac.py b/prepare/r-idr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-idr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-idr/lilac.yaml b/prepare/r-idr/lilac.yaml new file mode 100644 index 0000000000..a6ad8aaf5a --- /dev/null +++ b/prepare/r-idr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: idr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=idr diff --git a/prepare/r-idr2d/PKGBUILD b/prepare/r-idr2d/PKGBUILD new file mode 100644 index 0000000000..ecefacf647 --- /dev/null +++ b/prepare/r-idr2d/PKGBUILD @@ -0,0 +1,47 @@ +# system requirements: Python (>= 3.5.0), hic-straw +# Maintainer: Guoyi Zhang + +_pkgname=idr2d +_pkgver=1.8.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Irreproducible Discovery Rate for Genomic Interactions Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-futile.logger + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-idr + r-iranges + r-magrittr + r-reticulate + r-scales + r-stringr +) +optdepends=( + r-dt + r-htmltools + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-idr2d/lilac.py b/prepare/r-idr2d/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-idr2d/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-idr2d/lilac.yaml b/prepare/r-idr2d/lilac.yaml new file mode 100644 index 0000000000..91b35972d4 --- /dev/null +++ b/prepare/r-idr2d/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-futile.logger +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-idr +- r-iranges +- r-magrittr +- r-reticulate +- r-scales +- r-stringr +update_on: +- regex: idr2d_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/idr2d diff --git a/prepare/r-ids/PKGBUILD b/prepare/r-ids/PKGBUILD new file mode 100644 index 0000000000..67293f5f55 --- /dev/null +++ b/prepare/r-ids/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ids +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generate Random Identifiers' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-openssl + r-uuid +) +optdepends=( + r-knitr + r-rcorpora + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ids/lilac.py b/prepare/r-ids/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ids/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ids/lilac.yaml b/prepare/r-ids/lilac.yaml new file mode 100644 index 0000000000..d53895aee2 --- /dev/null +++ b/prepare/r-ids/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-openssl +- r-uuid +update_on: +- regex: ids_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ids diff --git a/prepare/r-igc/PKGBUILD b/prepare/r-igc/PKGBUILD new file mode 100644 index 0000000000..c1136e0e09 --- /dev/null +++ b/prepare/r-igc/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iGC +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An integrated analysis package of Gene expression and Copy number alteration' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-plyr +) +optdepends=( + r-biocstyle + r-domc + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-igc/lilac.py b/prepare/r-igc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-igc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-igc/lilac.yaml b/prepare/r-igc/lilac.yaml new file mode 100644 index 0000000000..205a464a0a --- /dev/null +++ b/prepare/r-igc/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-plyr +update_on: +- regex: iGC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iGC diff --git a/prepare/r-iggeneusage/PKGBUILD b/prepare/r-iggeneusage/PKGBUILD new file mode 100644 index 0000000000..e64881a862 --- /dev/null +++ b/prepare/r-iggeneusage/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IgGeneUsage +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential gene usage in immune repertoires' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-rcpp + r-reshape2 + r-rstan + r-stanheaders + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-ggforce + r-ggplot2 + r-ggrepel + r-gridextra + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-iggeneusage/lilac.py b/prepare/r-iggeneusage/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-iggeneusage/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-iggeneusage/lilac.yaml b/prepare/r-iggeneusage/lilac.yaml new file mode 100644 index 0000000000..86d052f589 --- /dev/null +++ b/prepare/r-iggeneusage/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-reshape2 +- r-rstan +- r-stanheaders +- r-summarizedexperiment +update_on: +- regex: IgGeneUsage_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IgGeneUsage diff --git a/prepare/r-igraph/PKGBUILD b/prepare/r-igraph/PKGBUILD new file mode 100644 index 0000000000..55ae735f4e --- /dev/null +++ b/prepare/r-igraph/PKGBUILD @@ -0,0 +1,44 @@ +# system requirements: gmp (>= 4.38, optional), libxml2 (optional), glpk(optional) +# Maintainer: Guoyi Zhang + +_pkgname=igraph +_pkgver=1.2.11 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Network Analysis and Visualization' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-magrittr + r-pkgconfig +) +optdepends=( + r-ape + r-digest + r-graph + r-igraphdata + r-rgl + r-scales + r-stats4 + r-tcltk + r-testthat + r-withr +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-igraph/lilac.py b/prepare/r-igraph/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-igraph/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-igraph/lilac.yaml b/prepare/r-igraph/lilac.yaml new file mode 100644 index 0000000000..323828a1bb --- /dev/null +++ b/prepare/r-igraph/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-magrittr +- r-pkgconfig +update_on: +- regex: igraph_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=igraph diff --git a/prepare/r-igvr/PKGBUILD b/prepare/r-igvr/PKGBUILD new file mode 100644 index 0000000000..bf9cf99476 --- /dev/null +++ b/prepare/r-igvr/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=igvR +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='igvR: integrative genomics viewer' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-browserviz + r-genomicalignments + r-genomicranges + r-httpuv + r-motifdb + r-rcolorbrewer + r-rtracklayer + r-seqlogo + r-variantannotation +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-igvr/lilac.py b/prepare/r-igvr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-igvr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-igvr/lilac.yaml b/prepare/r-igvr/lilac.yaml new file mode 100644 index 0000000000..ff8ff45c40 --- /dev/null +++ b/prepare/r-igvr/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-browserviz +- r-genomicalignments +- r-genomicranges +- r-httpuv +- r-motifdb +- r-rcolorbrewer +- r-rtracklayer +- r-seqlogo +- r-variantannotation +update_on: +- regex: igvR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/igvR diff --git a/prepare/r-ihw/PKGBUILD b/prepare/r-ihw/PKGBUILD new file mode 100644 index 0000000000..cde379e537 --- /dev/null +++ b/prepare/r-ihw/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IHW +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Independent Hypothesis Weighting' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-fdrtool + r-lpsymphony + r-slam +) +optdepends=( + r-airway + r-biocstyle + r-deseq2 + r-devtools + r-dplyr + r-ggplot2 + r-gridextra + r-knitr + r-matrix + r-rmarkdown + r-scales + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ihw/lilac.py b/prepare/r-ihw/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ihw/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ihw/lilac.yaml b/prepare/r-ihw/lilac.yaml new file mode 100644 index 0000000000..dfce3229c8 --- /dev/null +++ b/prepare/r-ihw/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-fdrtool +- r-lpsymphony +- r-slam +update_on: +- regex: IHW_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IHW diff --git a/prepare/r-illumina450probevariants.db/PKGBUILD b/prepare/r-illumina450probevariants.db/PKGBUILD new file mode 100644 index 0000000000..14a73f870f --- /dev/null +++ b/prepare/r-illumina450probevariants.db/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Illumina450ProbeVariants.db +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-illumina450probevariants.db/lilac.py b/prepare/r-illumina450probevariants.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-illumina450probevariants.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-illumina450probevariants.db/lilac.yaml b/prepare/r-illumina450probevariants.db/lilac.yaml new file mode 100644 index 0000000000..fdab6e7dcf --- /dev/null +++ b/prepare/r-illumina450probevariants.db/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Illumina450ProbeVariants.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Illumina450ProbeVariants.db diff --git a/prepare/r-illuminahumanmethylation450kanno.ilmn12.hg19/PKGBUILD b/prepare/r-illuminahumanmethylation450kanno.ilmn12.hg19/PKGBUILD new file mode 100644 index 0000000000..93cd85e7ce --- /dev/null +++ b/prepare/r-illuminahumanmethylation450kanno.ilmn12.hg19/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IlluminaHumanMethylation450kanno.ilmn12.hg19 +_pkgver=0.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Annotation for Illumina's 450k methylation arrays" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-minfi +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-illuminahumanmethylation450kanno.ilmn12.hg19/lilac.py b/prepare/r-illuminahumanmethylation450kanno.ilmn12.hg19/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-illuminahumanmethylation450kanno.ilmn12.hg19/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-illuminahumanmethylation450kanno.ilmn12.hg19/lilac.yaml b/prepare/r-illuminahumanmethylation450kanno.ilmn12.hg19/lilac.yaml new file mode 100644 index 0000000000..3218a160b7 --- /dev/null +++ b/prepare/r-illuminahumanmethylation450kanno.ilmn12.hg19/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-minfi +update_on: +- regex: IlluminaHumanMethylation450kanno.ilmn12.hg19_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19 diff --git a/prepare/r-illuminahumanmethylation450kmanifest/PKGBUILD b/prepare/r-illuminahumanmethylation450kmanifest/PKGBUILD new file mode 100644 index 0000000000..1c13778e07 --- /dev/null +++ b/prepare/r-illuminahumanmethylation450kmanifest/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IlluminaHumanMethylation450kmanifest +_pkgver=0.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Annotation for Illumina's 450k methylation arrays" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-minfi +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-illuminahumanmethylation450kmanifest/lilac.py b/prepare/r-illuminahumanmethylation450kmanifest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-illuminahumanmethylation450kmanifest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-illuminahumanmethylation450kmanifest/lilac.yaml b/prepare/r-illuminahumanmethylation450kmanifest/lilac.yaml new file mode 100644 index 0000000000..62cd56516b --- /dev/null +++ b/prepare/r-illuminahumanmethylation450kmanifest/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-minfi +update_on: +- regex: IlluminaHumanMethylation450kmanifest_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IlluminaHumanMethylation450kmanifest diff --git a/prepare/r-illuminahumanmethylationepicanno.ilm10b2.hg19/PKGBUILD b/prepare/r-illuminahumanmethylationepicanno.ilm10b2.hg19/PKGBUILD new file mode 100644 index 0000000000..e929db2d06 --- /dev/null +++ b/prepare/r-illuminahumanmethylationepicanno.ilm10b2.hg19/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IlluminaHumanMethylationEPICanno.ilm10b2.hg19 +_pkgver=0.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Annotation for Illumina's EPIC methylation arrays" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-minfi +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-illuminahumanmethylationepicanno.ilm10b2.hg19/lilac.py b/prepare/r-illuminahumanmethylationepicanno.ilm10b2.hg19/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-illuminahumanmethylationepicanno.ilm10b2.hg19/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-illuminahumanmethylationepicanno.ilm10b2.hg19/lilac.yaml b/prepare/r-illuminahumanmethylationepicanno.ilm10b2.hg19/lilac.yaml new file mode 100644 index 0000000000..6981dcde7b --- /dev/null +++ b/prepare/r-illuminahumanmethylationepicanno.ilm10b2.hg19/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-minfi +update_on: +- regex: IlluminaHumanMethylationEPICanno.ilm10b2.hg19_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IlluminaHumanMethylationEPICanno.ilm10b2.hg19 diff --git a/prepare/r-illuminahumanmethylationepicanno.ilm10b4.hg19/PKGBUILD b/prepare/r-illuminahumanmethylationepicanno.ilm10b4.hg19/PKGBUILD new file mode 100644 index 0000000000..d0fee5feef --- /dev/null +++ b/prepare/r-illuminahumanmethylationepicanno.ilm10b4.hg19/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IlluminaHumanMethylationEPICanno.ilm10b4.hg19 +_pkgver=0.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Annotation for Illumina's EPIC methylation arrays" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-minfi +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-illuminahumanmethylationepicanno.ilm10b4.hg19/lilac.py b/prepare/r-illuminahumanmethylationepicanno.ilm10b4.hg19/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-illuminahumanmethylationepicanno.ilm10b4.hg19/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-illuminahumanmethylationepicanno.ilm10b4.hg19/lilac.yaml b/prepare/r-illuminahumanmethylationepicanno.ilm10b4.hg19/lilac.yaml new file mode 100644 index 0000000000..c563cbf774 --- /dev/null +++ b/prepare/r-illuminahumanmethylationepicanno.ilm10b4.hg19/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-minfi +update_on: +- regex: IlluminaHumanMethylationEPICanno.ilm10b4.hg19_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IlluminaHumanMethylationEPICanno.ilm10b4.hg19 diff --git a/prepare/r-illuminahumanmethylationepicmanifest/PKGBUILD b/prepare/r-illuminahumanmethylationepicmanifest/PKGBUILD new file mode 100644 index 0000000000..290d680846 --- /dev/null +++ b/prepare/r-illuminahumanmethylationepicmanifest/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IlluminaHumanMethylationEPICmanifest +_pkgver=0.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Manifest for Illumina's EPIC methylation arrays" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-minfi +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-illuminahumanmethylationepicmanifest/lilac.py b/prepare/r-illuminahumanmethylationepicmanifest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-illuminahumanmethylationepicmanifest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-illuminahumanmethylationepicmanifest/lilac.yaml b/prepare/r-illuminahumanmethylationepicmanifest/lilac.yaml new file mode 100644 index 0000000000..9ecfdf230b --- /dev/null +++ b/prepare/r-illuminahumanmethylationepicmanifest/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-minfi +update_on: +- regex: IlluminaHumanMethylationEPICmanifest_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest diff --git a/prepare/r-illuminaio/PKGBUILD b/prepare/r-illuminaio/PKGBUILD new file mode 100644 index 0000000000..9b897a48f6 --- /dev/null +++ b/prepare/r-illuminaio/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=illuminaio +_pkgver=0.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Parsing Illumina Microarray Output Files' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-base64 +) +optdepends=( + r-biocgenerics + r-biocstyle + r-illuminadatatestfiles + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-illuminaio/lilac.py b/prepare/r-illuminaio/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-illuminaio/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-illuminaio/lilac.yaml b/prepare/r-illuminaio/lilac.yaml new file mode 100644 index 0000000000..12df1c16b5 --- /dev/null +++ b/prepare/r-illuminaio/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64 +update_on: +- regex: illuminaio_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/illuminaio diff --git a/prepare/r-iloreg/PKGBUILD b/prepare/r-iloreg/PKGBUILD new file mode 100644 index 0000000000..eca4019a2e --- /dev/null +++ b/prepare/r-iloreg/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ILoReg +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-aricode + r-cowplot + r-dendextend + r-desctools + r-dorng + r-dosnow + r-dplyr + r-fastcluster + r-foreach + r-ggplot2 + r-liblinear + r-paralleldist + r-pheatmap + r-plyr + r-reshape2 + r-rspectra + r-rtsne + r-s4vectors + r-scales + r-singlecellexperiment + r-sparsem + r-summarizedexperiment + r-umap +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-iloreg/lilac.py b/prepare/r-iloreg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-iloreg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-iloreg/lilac.yaml b/prepare/r-iloreg/lilac.yaml new file mode 100644 index 0000000000..64b4e4de9b --- /dev/null +++ b/prepare/r-iloreg/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aricode +- r-cowplot +- r-dendextend +- r-desctools +- r-dorng +- r-dosnow +- r-dplyr +- r-fastcluster +- r-foreach +- r-ggplot2 +- r-liblinear +- r-paralleldist +- r-pheatmap +- r-plyr +- r-reshape2 +- r-rspectra +- r-rtsne +- r-s4vectors +- r-scales +- r-singlecellexperiment +- r-sparsem +- r-summarizedexperiment +- r-umap +update_on: +- regex: ILoReg_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ILoReg diff --git a/prepare/r-imagehts/PKGBUILD b/prepare/r-imagehts/PKGBUILD new file mode 100644 index 0000000000..ff16a7f102 --- /dev/null +++ b/prepare/r-imagehts/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=imageHTS +_pkgver=1.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of high-throughput microscopy-based screens' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-cellhts2 + r-e1071 + r-ebimage + r-hwriter + r-vsn +) +optdepends=( + r-biocstyle + r-mass +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-imagehts/lilac.py b/prepare/r-imagehts/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-imagehts/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-imagehts/lilac.yaml b/prepare/r-imagehts/lilac.yaml new file mode 100644 index 0000000000..5def51f03d --- /dev/null +++ b/prepare/r-imagehts/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-cellhts2 +- r-e1071 +- r-ebimage +- r-hwriter +- r-vsn +update_on: +- regex: imageHTS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/imageHTS diff --git a/prepare/r-imas/PKGBUILD b/prepare/r-imas/PKGBUILD new file mode 100644 index 0000000000..a16c165913 --- /dev/null +++ b/prepare/r-imas/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IMAS +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integrative analysis of Multi-omics data for Alternative Splicing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocgenerics + r-biocparallel + r-doparallel + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggfortify + r-ggplot2 + r-gridextra + r-iranges + r-ivas + r-lme4 + r-rsamtools + r-s4vectors +) +optdepends=( + r-biocstyle + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-imas/lilac.py b/prepare/r-imas/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-imas/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-imas/lilac.yaml b/prepare/r-imas/lilac.yaml new file mode 100644 index 0000000000..52bab2629b --- /dev/null +++ b/prepare/r-imas/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-biocparallel +- r-doparallel +- r-foreach +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggfortify +- r-ggplot2 +- r-gridextra +- r-iranges +- r-ivas +- r-lme4 +- r-rsamtools +- r-s4vectors +update_on: +- regex: IMAS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IMAS diff --git a/prepare/r-imcrtools/PKGBUILD b/prepare/r-imcrtools/PKGBUILD new file mode 100644 index 0000000000..caa2fc5f37 --- /dev/null +++ b/prepare/r-imcrtools/PKGBUILD @@ -0,0 +1,62 @@ +# Maintainer: Guoyi Zhang + +_pkgname=imcRtools +_pkgver=1.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methods for imaging mass cytometry data analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-biocneighbors + r-biocparallel + r-concaveman + r-cytomapper + r-data.table + r-dplyr + r-dt + r-ebimage + r-ggplot2 + r-ggraph + r-igraph + r-magrittr + r-pheatmap + r-readr + r-rtriangle + r-s4vectors + r-scuttle + r-sf + r-singlecellexperiment + r-spatialexperiment + r-stringr + r-summarizedexperiment + r-tidygraph + r-viridis + r-vroom +) +optdepends=( + r-biocstyle + r-catalyst + r-grid + r-knitr + r-markdown + r-rmarkdown + r-testthat + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-imcrtools/lilac.py b/prepare/r-imcrtools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-imcrtools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-imcrtools/lilac.yaml b/prepare/r-imcrtools/lilac.yaml new file mode 100644 index 0000000000..e4094564e9 --- /dev/null +++ b/prepare/r-imcrtools/lilac.yaml @@ -0,0 +1,35 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-biocneighbors +- r-biocparallel +- r-concaveman +- r-cytomapper +- r-data.table +- r-dplyr +- r-dt +- r-ebimage +- r-ggplot2 +- r-ggraph +- r-igraph +- r-magrittr +- r-pheatmap +- r-readr +- r-rtriangle +- r-s4vectors +- r-scuttle +- r-sf +- r-singlecellexperiment +- r-spatialexperiment +- r-stringr +- r-summarizedexperiment +- r-tidygraph +- r-viridis +- r-vroom +update_on: +- regex: imcRtools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/imcRtools diff --git a/prepare/r-imman/PKGBUILD b/prepare/r-imman/PKGBUILD new file mode 100644 index 0000000000..792e928447 --- /dev/null +++ b/prepare/r-imman/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IMMAN +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interlog protein network reconstruction by Mapping and Mining ANalysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-igraph + r-seqinr + r-stringdb +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-imman/lilac.py b/prepare/r-imman/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-imman/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-imman/lilac.yaml b/prepare/r-imman/lilac.yaml new file mode 100644 index 0000000000..aa80a19f41 --- /dev/null +++ b/prepare/r-imman/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-igraph +- r-seqinr +- r-stringdb +update_on: +- regex: IMMAN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IMMAN diff --git a/prepare/r-immunespacer/PKGBUILD b/prepare/r-immunespacer/PKGBUILD new file mode 100644 index 0000000000..5251225513 --- /dev/null +++ b/prepare/r-immunespacer/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ImmuneSpaceR +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Thin Wrapper around the ImmuneSpace Database' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-curl + r-data.table + r-digest + r-flowcore + r-flowworkspace + r-ggplot2 + r-gplots + r-heatmaply + r-httr + r-jsonlite + r-pheatmap + r-plotly + r-preprocesscore + r-r6 + r-rlabkey + r-rmarkdown + r-scales +) +optdepends=( + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-immunespacer/lilac.py b/prepare/r-immunespacer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-immunespacer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-immunespacer/lilac.yaml b/prepare/r-immunespacer/lilac.yaml new file mode 100644 index 0000000000..f9a958ca69 --- /dev/null +++ b/prepare/r-immunespacer/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-curl +- r-data.table +- r-digest +- r-flowcore +- r-flowworkspace +- r-ggplot2 +- r-gplots +- r-heatmaply +- r-httr +- r-jsonlite +- r-pheatmap +- r-plotly +- r-preprocesscore +- r-r6 +- r-rlabkey +- r-rmarkdown +- r-scales +update_on: +- regex: ImmuneSpaceR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ImmuneSpaceR diff --git a/prepare/r-immunoclust/PKGBUILD b/prepare/r-immunoclust/PKGBUILD new file mode 100644 index 0000000000..9bd9dcba1b --- /dev/null +++ b/prepare/r-immunoclust/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=immunoClust +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='immunoClust - Automated Pipeline for Population Detection in Flow Cytometry' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-flowcore +) +optdepends=( + r-biocstyle + r-testthat + r-utils +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-immunoclust/lilac.py b/prepare/r-immunoclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-immunoclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-immunoclust/lilac.yaml b/prepare/r-immunoclust/lilac.yaml new file mode 100644 index 0000000000..22eafc9500 --- /dev/null +++ b/prepare/r-immunoclust/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-flowcore +update_on: +- regex: immunoClust_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/immunoClust diff --git a/prepare/r-immunotation/PKGBUILD b/prepare/r-immunotation/PKGBUILD new file mode 100644 index 0000000000..ab44ee425e --- /dev/null +++ b/prepare/r-immunotation/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=immunotation +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for working with diverse immune genes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-curl + r-ggplot2 + r-maps + r-ontologyindex + r-readr + r-rlang + r-rvest + r-stringr + r-tidyr + r-xml2 +) +optdepends=( + r-biocgenerics + r-biocstyle + r-dt + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-immunotation/lilac.py b/prepare/r-immunotation/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-immunotation/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-immunotation/lilac.yaml b/prepare/r-immunotation/lilac.yaml new file mode 100644 index 0000000000..bac9534110 --- /dev/null +++ b/prepare/r-immunotation/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-ggplot2 +- r-maps +- r-ontologyindex +- r-readr +- r-rlang +- r-rvest +- r-stringr +- r-tidyr +- r-xml2 +update_on: +- regex: immunotation_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/immunotation diff --git a/prepare/r-imp4p/PKGBUILD b/prepare/r-imp4p/PKGBUILD new file mode 100644 index 0000000000..9c382e6ffa --- /dev/null +++ b/prepare/r-imp4p/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=imp4p +_pkgver=1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Imputation for Proteomics' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-iso + r-missforest + r-missmda + r-norm + r-rcpp + r-truncnorm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-imp4p/lilac.py b/prepare/r-imp4p/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-imp4p/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-imp4p/lilac.yaml b/prepare/r-imp4p/lilac.yaml new file mode 100644 index 0000000000..7eabc459a0 --- /dev/null +++ b/prepare/r-imp4p/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-iso +- r-missforest +- r-missmda +- r-norm +- r-rcpp +- r-truncnorm +update_on: +- regex: imp4p_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=imp4p diff --git a/prepare/r-impcdata/PKGBUILD b/prepare/r-impcdata/PKGBUILD new file mode 100644 index 0000000000..e62caf7444 --- /dev/null +++ b/prepare/r-impcdata/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IMPCdata +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Retrieves data from IMPC database' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-rjson +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-impcdata/lilac.py b/prepare/r-impcdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-impcdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-impcdata/lilac.yaml b/prepare/r-impcdata/lilac.yaml new file mode 100644 index 0000000000..cecb12ae8d --- /dev/null +++ b/prepare/r-impcdata/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rjson +update_on: +- regex: IMPCdata_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IMPCdata diff --git a/prepare/r-import/PKGBUILD b/prepare/r-import/PKGBUILD new file mode 100644 index 0000000000..404734e97f --- /dev/null +++ b/prepare/r-import/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=import +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Import Mechanism for R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-knitr + r-magrittr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-import/lilac.py b/prepare/r-import/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-import/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-import/lilac.yaml b/prepare/r-import/lilac.yaml new file mode 100644 index 0000000000..75d2f90ab3 --- /dev/null +++ b/prepare/r-import/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: import_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=import diff --git a/prepare/r-impute/PKGBUILD b/prepare/r-impute/PKGBUILD new file mode 100644 index 0000000000..1f74690c4c --- /dev/null +++ b/prepare/r-impute/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=impute +_pkgver=1.68.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='impute: Imputation for microarray data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-impute/lilac.py b/prepare/r-impute/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-impute/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-impute/lilac.yaml b/prepare/r-impute/lilac.yaml new file mode 100644 index 0000000000..4e5cc5f98b --- /dev/null +++ b/prepare/r-impute/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: impute_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/impute diff --git a/prepare/r-imputelcmd/PKGBUILD b/prepare/r-imputelcmd/PKGBUILD new file mode 100644 index 0000000000..efa1e980a6 --- /dev/null +++ b/prepare/r-imputelcmd/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=imputeLCMD +_pkgver=2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A collection of methods for left-censored missing data imputation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-impute + r-norm + r-pcamethods + r-tmvtnorm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-imputelcmd/lilac.py b/prepare/r-imputelcmd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-imputelcmd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-imputelcmd/lilac.yaml b/prepare/r-imputelcmd/lilac.yaml new file mode 100644 index 0000000000..2e99068116 --- /dev/null +++ b/prepare/r-imputelcmd/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-impute +- r-norm +- r-pcamethods +- r-tmvtnorm +update_on: +- regex: imputeLCMD_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=imputeLCMD diff --git a/prepare/r-inaparc/PKGBUILD b/prepare/r-inaparc/PKGBUILD new file mode 100644 index 0000000000..11b0d9f119 --- /dev/null +++ b/prepare/r-inaparc/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=inaparc +_pkgver=1.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Initialization Algorithms for Partitioning Cluster Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-kpeaks + r-lhs +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-inaparc/lilac.py b/prepare/r-inaparc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-inaparc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-inaparc/lilac.yaml b/prepare/r-inaparc/lilac.yaml new file mode 100644 index 0000000000..b48150c154 --- /dev/null +++ b/prepare/r-inaparc/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-kpeaks +- r-lhs +update_on: +- regex: inaparc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=inaparc diff --git a/prepare/r-indeed/PKGBUILD b/prepare/r-indeed/PKGBUILD new file mode 100644 index 0000000000..3c24e6ee04 --- /dev/null +++ b/prepare/r-indeed/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=INDEED +_pkgver=2.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-devtools + r-glasso + r-igraph + r-visnetwork +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-indeed/lilac.py b/prepare/r-indeed/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-indeed/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-indeed/lilac.yaml b/prepare/r-indeed/lilac.yaml new file mode 100644 index 0000000000..fff1ef05af --- /dev/null +++ b/prepare/r-indeed/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-devtools +- r-glasso +- r-igraph +- r-visnetwork +update_on: +- regex: INDEED_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/INDEED diff --git a/prepare/r-ineq/PKGBUILD b/prepare/r-ineq/PKGBUILD new file mode 100644 index 0000000000..83defd2c01 --- /dev/null +++ b/prepare/r-ineq/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ineq +_pkgver=0.2-13 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Measuring Inequality, Concentration, and Poverty' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ineq/lilac.py b/prepare/r-ineq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ineq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ineq/lilac.yaml b/prepare/r-ineq/lilac.yaml new file mode 100644 index 0000000000..1d18bdc2e6 --- /dev/null +++ b/prepare/r-ineq/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ineq_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ineq diff --git a/prepare/r-infercnv/PKGBUILD b/prepare/r-infercnv/PKGBUILD new file mode 100644 index 0000000000..895771d7ad --- /dev/null +++ b/prepare/r-infercnv/PKGBUILD @@ -0,0 +1,62 @@ +# system requirements: JAGS 4.x.y +# Maintainer: Guoyi Zhang + +_pkgname=infercnv +_pkgver=1.10.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Infer Copy Number Variation from Single-Cell RNA-Seq Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-ape + r-argparse + r-biocgenerics + r-catools + r-coda + r-coin + r-digest + r-doparallel + r-dplyr + r-edger + r-fastcluster + r-fitdistrplus + r-foreach + r-futile.logger + r-future + r-ggplot2 + r-gplots + r-gridextra + r-hiddenmarkov + r-leiden + r-phyclust + r-rann + r-rcolorbrewer + r-reshape + r-rjags + r-singlecellexperiment + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-infercnv/lilac.py b/prepare/r-infercnv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-infercnv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-infercnv/lilac.yaml b/prepare/r-infercnv/lilac.yaml new file mode 100644 index 0000000000..cad1fbc37a --- /dev/null +++ b/prepare/r-infercnv/lilac.yaml @@ -0,0 +1,37 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-argparse +- r-biocgenerics +- r-catools +- r-coda +- r-coin +- r-digest +- r-doparallel +- r-dplyr +- r-edger +- r-fastcluster +- r-fitdistrplus +- r-foreach +- r-futile.logger +- r-future +- r-ggplot2 +- r-gplots +- r-gridextra +- r-hiddenmarkov +- r-leiden +- r-phyclust +- r-rann +- r-rcolorbrewer +- r-reshape +- r-rjags +- r-singlecellexperiment +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: infercnv_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/infercnv diff --git a/prepare/r-infinityflow/PKGBUILD b/prepare/r-infinityflow/PKGBUILD new file mode 100644 index 0000000000..39436513fe --- /dev/null +++ b/prepare/r-infinityflow/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=infinityFlow +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-flowcore + r-generics + r-gtools + r-matlab + r-pbapply + r-png + r-raster + r-uwot + r-xgboost +) +optdepends=( + r-e1071 + r-glmnetutils + r-keras + r-knitr + r-rmarkdown + r-tensorflow +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-infinityflow/lilac.py b/prepare/r-infinityflow/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-infinityflow/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-infinityflow/lilac.yaml b/prepare/r-infinityflow/lilac.yaml new file mode 100644 index 0000000000..bc95907fbc --- /dev/null +++ b/prepare/r-infinityflow/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-flowcore +- r-generics +- r-gtools +- r-matlab +- r-pbapply +- r-png +- r-raster +- r-uwot +- r-xgboost +update_on: +- regex: infinityFlow_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/infinityFlow diff --git a/prepare/r-influencer/PKGBUILD b/prepare/r-influencer/PKGBUILD new file mode 100644 index 0000000000..e345f6e186 --- /dev/null +++ b/prepare/r-influencer/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=influenceR +_pkgver=0.1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Software Tools to Quantify Structural Importance of Nodes in a Network' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-igraph +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-influencer/lilac.py b/prepare/r-influencer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-influencer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-influencer/lilac.yaml b/prepare/r-influencer/lilac.yaml new file mode 100644 index 0000000000..d3bc1b6e2a --- /dev/null +++ b/prepare/r-influencer/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +update_on: +- regex: influenceR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=influenceR diff --git a/prepare/r-informeasure/PKGBUILD b/prepare/r-informeasure/PKGBUILD new file mode 100644 index 0000000000..563f0bed5c --- /dev/null +++ b/prepare/r-informeasure/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Informeasure +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R implementation of Information measures' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-entropy +) +optdepends=( + r-knitr + r-rmarkdown + r-summarizedexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-informeasure/lilac.py b/prepare/r-informeasure/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-informeasure/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-informeasure/lilac.yaml b/prepare/r-informeasure/lilac.yaml new file mode 100644 index 0000000000..fc75468b46 --- /dev/null +++ b/prepare/r-informeasure/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-entropy +update_on: +- regex: Informeasure_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Informeasure diff --git a/prepare/r-infotheo/PKGBUILD b/prepare/r-infotheo/PKGBUILD new file mode 100644 index 0000000000..0a7c9e2aa2 --- /dev/null +++ b/prepare/r-infotheo/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=infotheo +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Information-Theoretic Measures' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-infotheo/lilac.py b/prepare/r-infotheo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-infotheo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-infotheo/lilac.yaml b/prepare/r-infotheo/lilac.yaml new file mode 100644 index 0000000000..f302202595 --- /dev/null +++ b/prepare/r-infotheo/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: infotheo_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=infotheo diff --git a/prepare/r-ini/PKGBUILD b/prepare/r-ini/PKGBUILD new file mode 100644 index 0000000000..181d08996a --- /dev/null +++ b/prepare/r-ini/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ini +_pkgver=0.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Read and Write '.ini' Files" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ini/lilac.py b/prepare/r-ini/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ini/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ini/lilac.yaml b/prepare/r-ini/lilac.yaml new file mode 100644 index 0000000000..f7c9196254 --- /dev/null +++ b/prepare/r-ini/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ini_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ini diff --git a/prepare/r-inline/PKGBUILD b/prepare/r-inline/PKGBUILD new file mode 100644 index 0000000000..ada8cbe68b --- /dev/null +++ b/prepare/r-inline/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=inline +_pkgver=0.3.19 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions to Inline C, C++, Fortran Function Calls from R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +optdepends=( + r-rcpp + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-inline/lilac.py b/prepare/r-inline/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-inline/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-inline/lilac.yaml b/prepare/r-inline/lilac.yaml new file mode 100644 index 0000000000..119a825676 --- /dev/null +++ b/prepare/r-inline/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: inline_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=inline diff --git a/prepare/r-inpas/PKGBUILD b/prepare/r-inpas/PKGBUILD new file mode 100644 index 0000000000..e7c9b93fa2 --- /dev/null +++ b/prepare/r-inpas/PKGBUILD @@ -0,0 +1,65 @@ +# Maintainer: Guoyi Zhang + +_pkgname=InPAS +_pkgver=2.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Bioconductor package for identifying novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biobase + r-biocparallel + r-biostrings + r-bsgenome + r-cleanupdtseq + r-dbi + r-depmixs4 + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-limma + r-magrittr + r-plyranges + r-preprocesscore + r-purrr + r-readr + r-reshape2 + r-rsqlite + r-s4vectors +) +optdepends=( + r-biocgenerics + r-biocmanager + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.mmusculus.ucsc.mm10 + r-ensdb.hsapiens.v86 + r-ensdb.mmusculus.v79 + r-knitr + r-markdown + r-rmarkdown + r-rtracklayer + r-runit + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.mmusculus.ucsc.mm10.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-inpas/lilac.py b/prepare/r-inpas/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-inpas/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-inpas/lilac.yaml b/prepare/r-inpas/lilac.yaml new file mode 100644 index 0000000000..48edc2f163 --- /dev/null +++ b/prepare/r-inpas/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-cleanupdtseq +- r-dbi +- r-depmixs4 +- r-dplyr +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-limma +- r-magrittr +- r-plyranges +- r-preprocesscore +- r-purrr +- r-readr +- r-reshape2 +- r-rsqlite +- r-s4vectors +update_on: +- regex: InPAS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/InPAS diff --git a/prepare/r-inpower/PKGBUILD b/prepare/r-inpower/PKGBUILD new file mode 100644 index 0000000000..8e4f2b4205 --- /dev/null +++ b/prepare/r-inpower/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=INPower +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package for computing the number of susceptibility SNPs' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-mvtnorm +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-inpower/lilac.py b/prepare/r-inpower/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-inpower/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-inpower/lilac.yaml b/prepare/r-inpower/lilac.yaml new file mode 100644 index 0000000000..5617b00e13 --- /dev/null +++ b/prepare/r-inpower/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mvtnorm +update_on: +- regex: INPower_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/INPower diff --git a/prepare/r-insight/PKGBUILD b/prepare/r-insight/PKGBUILD new file mode 100644 index 0000000000..5e225a28e1 --- /dev/null +++ b/prepare/r-insight/PKGBUILD @@ -0,0 +1,116 @@ +# Maintainer: Guoyi Zhang + +_pkgname=insight +_pkgver=0.15.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Easy Access to Model Information for Various Model Objects' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-aer + r-afex + r-aod + r-bayesfactor + r-bayestestr + r-bbmle + r-bdsmatrix + r-betareg + r-bife + r-biglm + r-blavaan + r-blme + r-boot + r-brms + r-censreg + r-cgam + r-clubsandwich + r-coxme + r-cplm + r-crch + r-datawizard + r-effectsize + r-emmeans + r-epir + r-estimatr + r-feisr + r-fixest + r-fungible + r-gam + r-gamlss + r-gamm4 + r-gbm + r-gee + r-geepack + r-glmmadaptive + r-glmmtmb + r-gmnl + r-gt + r-httr + r-ivreg + r-jm + r-knitr + r-lavaan + r-lfe + r-lme4 + r-lmtest + r-logistf + r-mass + r-matrix + r-mclust + r-mcmcglmm + r-mertools + r-metabma + r-mgcv + r-mice + r-mlogit + r-multgee + r-nlme + r-nnet + r-nonnest2 + r-ordinal + r-panelr + r-parameters + r-parsnip + r-performance + r-plm + r-poorman + r-pscl + r-psych + r-quantreg + r-rmarkdown + r-rms + r-robustbase + r-robustlmm + r-rstanarm + r-rstantools + r-rstudioapi + r-sandwich + r-speedglm + r-spelling + r-splines + r-statmod + r-survey + r-survival + r-testthat + r-tripack + r-truncreg + r-vgam +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-insight/lilac.py b/prepare/r-insight/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-insight/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-insight/lilac.yaml b/prepare/r-insight/lilac.yaml new file mode 100644 index 0000000000..d1371432a5 --- /dev/null +++ b/prepare/r-insight/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: insight_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=insight diff --git a/prepare/r-inspect/PKGBUILD b/prepare/r-inspect/PKGBUILD new file mode 100644 index 0000000000..d619ca0bc4 --- /dev/null +++ b/prepare/r-inspect/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=INSPEcT +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Modeling RNA synthesis, processing and degradation with RNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-deseq2 + r-desolve + r-gdata + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-plgem + r-proc + r-rootsolve + r-rsamtools + r-rtracklayer + r-s4vectors + r-shiny + r-summarizedexperiment + r-txdb.mmusculus.ucsc.mm9.knowngene +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-inspect/lilac.py b/prepare/r-inspect/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-inspect/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-inspect/lilac.yaml b/prepare/r-inspect/lilac.yaml new file mode 100644 index 0000000000..2a85011616 --- /dev/null +++ b/prepare/r-inspect/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-deseq2 +- r-desolve +- r-gdata +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-plgem +- r-proc +- r-rootsolve +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-shiny +- r-summarizedexperiment +- r-txdb.mmusculus.ucsc.mm9.knowngene +update_on: +- regex: INSPEcT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/INSPEcT diff --git a/prepare/r-intad/PKGBUILD b/prepare/r-intad/PKGBUILD new file mode 100644 index 0000000000..5e0ff5349e --- /dev/null +++ b/prepare/r-intad/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=InTAD +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Search for correlation between epigenetic signals and gene expression in TADs' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-genomicranges + r-ggplot2 + r-ggpubr + r-iranges + r-mclust + r-multiassayexperiment + r-qvalue + r-rtracklayer + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-intad/lilac.py b/prepare/r-intad/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-intad/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-intad/lilac.yaml b/prepare/r-intad/lilac.yaml new file mode 100644 index 0000000000..cd3839ad93 --- /dev/null +++ b/prepare/r-intad/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-genomicranges +- r-ggplot2 +- r-ggpubr +- r-iranges +- r-mclust +- r-multiassayexperiment +- r-qvalue +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: InTAD_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/InTAD diff --git a/prepare/r-intansv/PKGBUILD b/prepare/r-intansv/PKGBUILD new file mode 100644 index 0000000000..0119469ed4 --- /dev/null +++ b/prepare/r-intansv/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=intansv +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integrative analysis of structural variations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-genomicranges + r-ggbio + r-iranges + r-plyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-intansv/lilac.py b/prepare/r-intansv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-intansv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-intansv/lilac.yaml b/prepare/r-intansv/lilac.yaml new file mode 100644 index 0000000000..9b5f21e7af --- /dev/null +++ b/prepare/r-intansv/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomicranges +- r-ggbio +- r-iranges +- r-plyr +update_on: +- regex: intansv_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/intansv diff --git a/prepare/r-interaccircos/PKGBUILD b/prepare/r-interaccircos/PKGBUILD new file mode 100644 index 0000000000..fe74f8ab6d --- /dev/null +++ b/prepare/r-interaccircos/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=interacCircos +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The Generation of Interactive Circos Plot' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-htmlwidgets + r-plyr + r-rcolorbrewer +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-interaccircos/lilac.py b/prepare/r-interaccircos/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-interaccircos/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-interaccircos/lilac.yaml b/prepare/r-interaccircos/lilac.yaml new file mode 100644 index 0000000000..340732ccc3 --- /dev/null +++ b/prepare/r-interaccircos/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmlwidgets +- r-plyr +- r-rcolorbrewer +update_on: +- regex: interacCircos_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/interacCircos diff --git a/prepare/r-interactionset/PKGBUILD b/prepare/r-interactionset/PKGBUILD new file mode 100644 index 0000000000..bf40e6237f --- /dev/null +++ b/prepare/r-interactionset/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=InteractionSet +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Base Classes for Storing Genomic Interaction Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-genomeinfodb + r-genomicranges + r-iranges + r-rcpp + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-interactionset/lilac.py b/prepare/r-interactionset/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-interactionset/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-interactionset/lilac.yaml b/prepare/r-interactionset/lilac.yaml new file mode 100644 index 0000000000..81267c2252 --- /dev/null +++ b/prepare/r-interactionset/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rcpp +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: InteractionSet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/InteractionSet diff --git a/prepare/r-interactivecomplexheatmap/PKGBUILD b/prepare/r-interactivecomplexheatmap/PKGBUILD new file mode 100644 index 0000000000..880b0268ca --- /dev/null +++ b/prepare/r-interactivecomplexheatmap/PKGBUILD @@ -0,0 +1,73 @@ +# Maintainer: Guoyi Zhang + +_pkgname=InteractiveComplexHeatmap +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Make Interactive Complex Heatmaps' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-clisymbols + r-complexheatmap + r-digest + r-fontawesome + r-getoptlong + r-htmltools + r-iranges + r-jsonlite + r-kableextra + r-rcolorbrewer + r-s4vectors + r-shiny + r-svglite +) +optdepends=( + r-airway + r-biocmanager + r-circlize + r-cluster + r-cola + r-data.table + r-deseq2 + r-dt + r-enrichedheatmap + r-genomicfeatures + r-genomicranges + r-go.db + r-goexpress + r-gplots + r-gridtext + r-hilbertcurve + r-knitr + r-ks + r-org.hs.eg.db + r-pheatmap + r-pkgndep + r-rmarkdown + r-sc3 + r-scater + r-shinydashboard + r-simplifyenrichment + r-singlecellexperiment + r-summarizedexperiment + r-testthat + r-tidyheatmap + r-tidyverse +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-interactivecomplexheatmap/lilac.py b/prepare/r-interactivecomplexheatmap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-interactivecomplexheatmap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-interactivecomplexheatmap/lilac.yaml b/prepare/r-interactivecomplexheatmap/lilac.yaml new file mode 100644 index 0000000000..b5155c0588 --- /dev/null +++ b/prepare/r-interactivecomplexheatmap/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clisymbols +- r-complexheatmap +- r-digest +- r-fontawesome +- r-getoptlong +- r-htmltools +- r-iranges +- r-jsonlite +- r-kableextra +- r-rcolorbrewer +- r-s4vectors +- r-shiny +- r-svglite +update_on: +- regex: InteractiveComplexHeatmap_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/InteractiveComplexHeatmap diff --git a/prepare/r-interactivedisplay/PKGBUILD b/prepare/r-interactivedisplay/PKGBUILD new file mode 100644 index 0000000000..1eefb09842 --- /dev/null +++ b/prepare/r-interactivedisplay/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=interactiveDisplay +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Package for enabling powerful shiny web displays of Bioconductor objects' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biocgenerics + r-category + r-ggplot2 + r-gridsvg + r-interactivedisplaybase + r-plyr + r-rcolorbrewer + r-reshape2 + r-shiny + r-xml +) +optdepends=( + r-biobase + r-genomicranges + r-ggbio + r-go.db + r-gostats + r-gplots + r-gviz + r-hgu95av2.db + r-knitr + r-metagenomeseq + r-rstudio + r-rtracklayer + r-runit + r-summarizedexperiment + r-vegan +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-interactivedisplay/lilac.py b/prepare/r-interactivedisplay/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-interactivedisplay/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-interactivedisplay/lilac.yaml b/prepare/r-interactivedisplay/lilac.yaml new file mode 100644 index 0000000000..d83a387ee9 --- /dev/null +++ b/prepare/r-interactivedisplay/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-category +- r-ggplot2 +- r-gridsvg +- r-interactivedisplaybase +- r-plyr +- r-rcolorbrewer +- r-reshape2 +- r-shiny +- r-xml +update_on: +- regex: interactiveDisplay_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/interactiveDisplay diff --git a/prepare/r-interactivedisplaybase/PKGBUILD b/prepare/r-interactivedisplaybase/PKGBUILD new file mode 100644 index 0000000000..02a3afff78 --- /dev/null +++ b/prepare/r-interactivedisplaybase/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=interactiveDisplayBase +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Base package for enabling powerful shiny web displays of Bioconductor objects' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-dt + r-shiny +) +optdepends=( + r-knitr + r-markdown + r-rstudioapi +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-interactivedisplaybase/lilac.py b/prepare/r-interactivedisplaybase/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-interactivedisplaybase/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-interactivedisplaybase/lilac.yaml b/prepare/r-interactivedisplaybase/lilac.yaml new file mode 100644 index 0000000000..bfbbad06a4 --- /dev/null +++ b/prepare/r-interactivedisplaybase/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-dt +- r-shiny +update_on: +- regex: interactiveDisplayBase_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/interactiveDisplayBase diff --git a/prepare/r-intercellar/PKGBUILD b/prepare/r-intercellar/PKGBUILD new file mode 100644 index 0000000000..f084146bb2 --- /dev/null +++ b/prepare/r-intercellar/PKGBUILD @@ -0,0 +1,73 @@ +# Maintainer: Guoyi Zhang + +_pkgname=InterCellar +_pkgver=2.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biomart + r-circlize + r-colorspace + r-colourpicker + r-complexheatmap + r-config + r-data.table + r-dendextend + r-dplyr + r-dt + r-factoextra + r-fmsb + r-fs + r-ggplot2 + r-golem + r-htmltools + r-htmlwidgets + r-igraph + r-plotly + r-plyr + r-readxl + r-rlang + r-scales + r-shiny + r-shinyalert + r-shinycssloaders + r-shinydashboard + r-shinyfeedback + r-shinyfiles + r-signal + r-tibble + r-tidyr + r-umap + r-visnetwork + r-wordcloud2 +) +optdepends=( + r-attempt + r-biocstyle + r-glue + r-graphite + r-httr + r-knitr + r-processx + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-intercellar/lilac.py b/prepare/r-intercellar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-intercellar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-intercellar/lilac.yaml b/prepare/r-intercellar/lilac.yaml new file mode 100644 index 0000000000..18fc36dfc5 --- /dev/null +++ b/prepare/r-intercellar/lilac.yaml @@ -0,0 +1,44 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-circlize +- r-colorspace +- r-colourpicker +- r-complexheatmap +- r-config +- r-data.table +- r-dendextend +- r-dplyr +- r-dt +- r-factoextra +- r-fmsb +- r-fs +- r-ggplot2 +- r-golem +- r-htmltools +- r-htmlwidgets +- r-igraph +- r-plotly +- r-plyr +- r-readxl +- r-rlang +- r-scales +- r-shiny +- r-shinyalert +- r-shinycssloaders +- r-shinydashboard +- r-shinyfeedback +- r-shinyfiles +- r-signal +- r-tibble +- r-tidyr +- r-umap +- r-visnetwork +- r-wordcloud2 +update_on: +- regex: InterCellar_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/InterCellar diff --git a/prepare/r-interest/PKGBUILD b/prepare/r-interest/PKGBUILD new file mode 100644 index 0000000000..cf909da3cc --- /dev/null +++ b/prepare/r-interest/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IntEREst +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Intron-Exon Retention Estimator' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-dbi + r-deseq2 + r-dexseq + r-edger + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-rmysql + r-rsamtools + r-s4vectors + r-seqinr + r-seqlogo + r-summarizedexperiment +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg19 + r-clinfun + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-interest/lilac.py b/prepare/r-interest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-interest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-interest/lilac.yaml b/prepare/r-interest/lilac.yaml new file mode 100644 index 0000000000..57a047b0fa --- /dev/null +++ b/prepare/r-interest/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-dbi +- r-deseq2 +- r-dexseq +- r-edger +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-rmysql +- r-rsamtools +- r-s4vectors +- r-seqinr +- r-seqlogo +- r-summarizedexperiment +update_on: +- regex: IntEREst_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IntEREst diff --git a/prepare/r-intergraph/PKGBUILD b/prepare/r-intergraph/PKGBUILD new file mode 100644 index 0000000000..1797671ad6 --- /dev/null +++ b/prepare/r-intergraph/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=intergraph +_pkgver=2.0-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Coercion Routines for Network Data Objects' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-igraph + r-network +) +optdepends=( + r-knitr + r-roxygen2 + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-intergraph/lilac.py b/prepare/r-intergraph/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-intergraph/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-intergraph/lilac.yaml b/prepare/r-intergraph/lilac.yaml new file mode 100644 index 0000000000..291238a6d7 --- /dev/null +++ b/prepare/r-intergraph/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +- r-network +update_on: +- regex: intergraph_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=intergraph diff --git a/prepare/r-interminer/PKGBUILD b/prepare/r-interminer/PKGBUILD new file mode 100644 index 0000000000..dc114ddf21 --- /dev/null +++ b/prepare/r-interminer/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=InterMineR +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Interface with InterMine-Powered Databases' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biostrings + r-genomicranges + r-httr + r-igraph + r-iranges + r-rcurl + r-rjsonio + r-s4vectors + r-sqldf + r-summarizedexperiment + r-xml + r-xml2 +) +optdepends=( + r-biocstyle + r-geneanswers + r-go.db + r-gviz + r-knitr + r-org.hs.eg.db + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-interminer/lilac.py b/prepare/r-interminer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-interminer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-interminer/lilac.yaml b/prepare/r-interminer/lilac.yaml new file mode 100644 index 0000000000..2204f98ced --- /dev/null +++ b/prepare/r-interminer/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-genomicranges +- r-httr +- r-igraph +- r-iranges +- r-rcurl +- r-rjsonio +- r-s4vectors +- r-sqldf +- r-summarizedexperiment +- r-xml +- r-xml2 +update_on: +- regex: InterMineR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/InterMineR diff --git a/prepare/r-interp/PKGBUILD b/prepare/r-interp/PKGBUILD new file mode 100644 index 0000000000..3df6242b82 --- /dev/null +++ b/prepare/r-interp/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=interp +_pkgver=1.0-33 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interpolation Methods' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-deldir + r-rcpp + r-rcppeigen +) +optdepends=( + r-deriv + r-sp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-interp/lilac.py b/prepare/r-interp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-interp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-interp/lilac.yaml b/prepare/r-interp/lilac.yaml new file mode 100644 index 0000000000..2fc3315072 --- /dev/null +++ b/prepare/r-interp/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-deldir +- r-rcpp +- r-rcppeigen +update_on: +- regex: interp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=interp diff --git a/prepare/r-intervals/PKGBUILD b/prepare/r-intervals/PKGBUILD new file mode 100644 index 0000000000..e84ee3689c --- /dev/null +++ b/prepare/r-intervals/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=intervals +_pkgver=0.15.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Working with Points and Intervals' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-intervals/lilac.py b/prepare/r-intervals/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-intervals/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-intervals/lilac.yaml b/prepare/r-intervals/lilac.yaml new file mode 100644 index 0000000000..8127738da1 --- /dev/null +++ b/prepare/r-intervals/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: intervals_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=intervals diff --git a/prepare/r-intramirexplorer/PKGBUILD b/prepare/r-intramirexplorer/PKGBUILD new file mode 100644 index 0000000000..f17f27633d --- /dev/null +++ b/prepare/r-intramirexplorer/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IntramiRExploreR +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Predicting Targets for Drosophila Intragenic miRNAs' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-fgnet + r-igraph + r-knitr +) +optdepends=( + r-gprofiler + r-org.dm.eg.db + r-rmarkdown + r-testthat + r-topgo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-intramirexplorer/lilac.py b/prepare/r-intramirexplorer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-intramirexplorer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-intramirexplorer/lilac.yaml b/prepare/r-intramirexplorer/lilac.yaml new file mode 100644 index 0000000000..550ac85128 --- /dev/null +++ b/prepare/r-intramirexplorer/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fgnet +- r-igraph +- r-knitr +update_on: +- regex: IntramiRExploreR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IntramiRExploreR diff --git a/prepare/r-intrinsicdimension/PKGBUILD b/prepare/r-intrinsicdimension/PKGBUILD new file mode 100644 index 0000000000..967358d05a --- /dev/null +++ b/prepare/r-intrinsicdimension/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=intrinsicDimension +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Intrinsic Dimension Estimation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-yaimpute +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-intrinsicdimension/lilac.py b/prepare/r-intrinsicdimension/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-intrinsicdimension/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-intrinsicdimension/lilac.yaml b/prepare/r-intrinsicdimension/lilac.yaml new file mode 100644 index 0000000000..7f982ad16b --- /dev/null +++ b/prepare/r-intrinsicdimension/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-yaimpute +update_on: +- regex: intrinsicDimension_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=intrinsicDimension diff --git a/prepare/r-inum/PKGBUILD b/prepare/r-inum/PKGBUILD new file mode 100644 index 0000000000..4f1fae3d6b --- /dev/null +++ b/prepare/r-inum/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=inum +_pkgver=1.0-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interval and Enum-Type Representation of Vectors' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-libcoin +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-inum/lilac.py b/prepare/r-inum/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-inum/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-inum/lilac.yaml b/prepare/r-inum/lilac.yaml new file mode 100644 index 0000000000..a1f4bb52e8 --- /dev/null +++ b/prepare/r-inum/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-libcoin +update_on: +- regex: inum_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=inum diff --git a/prepare/r-invariantcausalprediction/PKGBUILD b/prepare/r-invariantcausalprediction/PKGBUILD new file mode 100644 index 0000000000..3a3ca4a804 --- /dev/null +++ b/prepare/r-invariantcausalprediction/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=InvariantCausalPrediction +_pkgver=0.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Invariant Causal Prediction' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-glmnet + r-mboost +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-invariantcausalprediction/lilac.py b/prepare/r-invariantcausalprediction/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-invariantcausalprediction/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-invariantcausalprediction/lilac.yaml b/prepare/r-invariantcausalprediction/lilac.yaml new file mode 100644 index 0000000000..9ea11033e1 --- /dev/null +++ b/prepare/r-invariantcausalprediction/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-glmnet +- r-mboost +update_on: +- regex: InvariantCausalPrediction_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=InvariantCausalPrediction diff --git a/prepare/r-inversion/PKGBUILD b/prepare/r-inversion/PKGBUILD new file mode 100644 index 0000000000..227af932dd --- /dev/null +++ b/prepare/r-inversion/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=inveRsion +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Inversions in genotype data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-haplo.stats +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-inversion/lilac.py b/prepare/r-inversion/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-inversion/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-inversion/lilac.yaml b/prepare/r-inversion/lilac.yaml new file mode 100644 index 0000000000..320989b81b --- /dev/null +++ b/prepare/r-inversion/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-haplo.stats +update_on: +- regex: inveRsion_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/inveRsion diff --git a/prepare/r-investr/PKGBUILD b/prepare/r-investr/PKGBUILD new file mode 100644 index 0000000000..920112e6fd --- /dev/null +++ b/prepare/r-investr/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=investr +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Inverse Estimation/Calibration Functions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-boot + r-datasets + r-knitr + r-mass + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-investr/lilac.py b/prepare/r-investr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-investr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-investr/lilac.yaml b/prepare/r-investr/lilac.yaml new file mode 100644 index 0000000000..b07d6fea25 --- /dev/null +++ b/prepare/r-investr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: investr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=investr diff --git a/prepare/r-invgamma/PKGBUILD b/prepare/r-invgamma/PKGBUILD new file mode 100644 index 0000000000..7cd277f84f --- /dev/null +++ b/prepare/r-invgamma/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=invgamma +_pkgver=1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The Inverse Gamma Distribution' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-invgamma/lilac.py b/prepare/r-invgamma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-invgamma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-invgamma/lilac.yaml b/prepare/r-invgamma/lilac.yaml new file mode 100644 index 0000000000..918591d9a4 --- /dev/null +++ b/prepare/r-invgamma/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: invgamma_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=invgamma diff --git a/prepare/r-ioniser/PKGBUILD b/prepare/r-ioniser/PKGBUILD new file mode 100644 index 0000000000..454e07be74 --- /dev/null +++ b/prepare/r-ioniser/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IONiseR +_pkgver=2.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quality Assessment Tools for Oxford Nanopore MinION data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-bit64 + r-dplyr + r-ggplot2 + r-magrittr + r-rhdf5 + r-shortread + r-stringr + r-tibble + r-tidyr + r-xvector +) +optdepends=( + r-biocstyle + r-gridextra + r-knitr + r-minionsummarydata + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ioniser/lilac.py b/prepare/r-ioniser/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ioniser/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ioniser/lilac.yaml b/prepare/r-ioniser/lilac.yaml new file mode 100644 index 0000000000..649377b893 --- /dev/null +++ b/prepare/r-ioniser/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bit64 +- r-dplyr +- r-ggplot2 +- r-magrittr +- r-rhdf5 +- r-shortread +- r-stringr +- r-tibble +- r-tidyr +- r-xvector +update_on: +- regex: IONiseR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IONiseR diff --git a/prepare/r-ipac/PKGBUILD b/prepare/r-ipac/PKGBUILD new file mode 100644 index 0000000000..a06bcf4098 --- /dev/null +++ b/prepare/r-ipac/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iPAC +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identification of Protein Amino acid Clustering' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-gdata + r-multtest + r-scatterplot3d +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ipac/lilac.py b/prepare/r-ipac/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ipac/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ipac/lilac.yaml b/prepare/r-ipac/lilac.yaml new file mode 100644 index 0000000000..b9d002bc93 --- /dev/null +++ b/prepare/r-ipac/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-gdata +- r-multtest +- r-scatterplot3d +update_on: +- regex: iPAC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iPAC diff --git a/prepare/r-ipath/PKGBUILD b/prepare/r-ipath/PKGBUILD new file mode 100644 index 0000000000..a224201fc2 --- /dev/null +++ b/prepare/r-ipath/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=iPath +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='iPath pipeline for detecting perturbed pathways at individual level' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-ggplot2 + r-ggpubr + r-matrixstats + r-mclust + r-rcpp + r-rcpparmadillo + r-survminer +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ipath/lilac.py b/prepare/r-ipath/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ipath/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ipath/lilac.yaml b/prepare/r-ipath/lilac.yaml new file mode 100644 index 0000000000..53a801355b --- /dev/null +++ b/prepare/r-ipath/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-ggplot2 +- r-ggpubr +- r-matrixstats +- r-mclust +- r-rcpp +- r-rcpparmadillo +- r-survminer +update_on: +- regex: iPath_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iPath diff --git a/prepare/r-ipddb/PKGBUILD b/prepare/r-ipddb/PKGBUILD new file mode 100644 index 0000000000..947e10d302 --- /dev/null +++ b/prepare/r-ipddb/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ipdDb +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='IPD IMGT/HLA and IPD KIR database for Homo sapiens' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-annotationhub + r-assertthat + r-biostrings + r-dbi + r-genomicranges + r-iranges + r-rsqlite +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ipddb/lilac.py b/prepare/r-ipddb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ipddb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ipddb/lilac.yaml b/prepare/r-ipddb/lilac.yaml new file mode 100644 index 0000000000..ce0a746127 --- /dev/null +++ b/prepare/r-ipddb/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-assertthat +- r-biostrings +- r-dbi +- r-genomicranges +- r-iranges +- r-rsqlite +update_on: +- regex: ipdDb_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ipdDb diff --git a/prepare/r-ipo/PKGBUILD b/prepare/r-ipo/PKGBUILD new file mode 100644 index 0000000000..10de703c82 --- /dev/null +++ b/prepare/r-ipo/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IPO +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automated Optimization of XCMS Data Processing parameters' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-camera + r-rsm + r-xcms +) +optdepends=( + r-biocgenerics + r-faahko + r-knitr + r-msdata + r-mtbls2 + r-parallel + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ipo/lilac.py b/prepare/r-ipo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ipo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ipo/lilac.yaml b/prepare/r-ipo/lilac.yaml new file mode 100644 index 0000000000..be7c231db2 --- /dev/null +++ b/prepare/r-ipo/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-camera +- r-rsm +- r-xcms +update_on: +- regex: IPO_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IPO diff --git a/prepare/r-ipred/PKGBUILD b/prepare/r-ipred/PKGBUILD new file mode 100644 index 0000000000..f6c64d15bc --- /dev/null +++ b/prepare/r-ipred/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ipred +_pkgver=0.9-12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Improved Predictors' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-prodlim +) +optdepends=( + r-mlbench + r-mvtnorm + r-party + r-randomforest + r-th.data +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ipred/lilac.py b/prepare/r-ipred/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ipred/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ipred/lilac.yaml b/prepare/r-ipred/lilac.yaml new file mode 100644 index 0000000000..d75a7e48c3 --- /dev/null +++ b/prepare/r-ipred/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-prodlim +update_on: +- regex: ipred_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ipred diff --git a/prepare/r-iranges/PKGBUILD b/prepare/r-iranges/PKGBUILD new file mode 100644 index 0000000000..c193aa6fc1 --- /dev/null +++ b/prepare/r-iranges/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IRanges +_pkgver=2.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Foundation of integer range manipulation in Bioconductor' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-s4vectors +) +optdepends=( + r-biocstyle + r-bsgenome.celegans.ucsc.ce2 + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-pasillabamsubset + r-rsamtools + r-runit + r-xvector +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-iranges/lilac.py b/prepare/r-iranges/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-iranges/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-iranges/lilac.yaml b/prepare/r-iranges/lilac.yaml new file mode 100644 index 0000000000..cf8ba77188 --- /dev/null +++ b/prepare/r-iranges/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-s4vectors +update_on: +- regex: IRanges_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IRanges diff --git a/prepare/r-irdisplay/PKGBUILD b/prepare/r-irdisplay/PKGBUILD new file mode 100644 index 0000000000..5996e1128b --- /dev/null +++ b/prepare/r-irdisplay/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IRdisplay +_pkgver=1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'Jupyter' Display Machinery" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-repr +) +optdepends=( + r-testthat + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-irdisplay/lilac.py b/prepare/r-irdisplay/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-irdisplay/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-irdisplay/lilac.yaml b/prepare/r-irdisplay/lilac.yaml new file mode 100644 index 0000000000..52a8101705 --- /dev/null +++ b/prepare/r-irdisplay/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-repr +update_on: +- regex: IRdisplay_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=IRdisplay diff --git a/prepare/r-irisfgm/PKGBUILD b/prepare/r-irisfgm/PKGBUILD new file mode 100644 index 0000000000..7d934d2271 --- /dev/null +++ b/prepare/r-irisfgm/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IRISFGM +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-adaptgauss + r-annotationdbi + r-anocva + r-clusterprofiler + r-colorspace + r-desingle + r-drimpute + r-ggplot2 + r-ggpubr + r-ggraph + r-igraph + r-knitr + r-mcl + r-mixtools + r-org.hs.eg.db + r-org.mm.eg.db + r-pheatmap + r-polychrome + r-rcolorbrewer + r-rcpp + r-scater + r-scran + r-seurat + r-singlecellexperiment +) +optdepends=( + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-irisfgm/lilac.py b/prepare/r-irisfgm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-irisfgm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-irisfgm/lilac.yaml b/prepare/r-irisfgm/lilac.yaml new file mode 100644 index 0000000000..9c4fc9432c --- /dev/null +++ b/prepare/r-irisfgm/lilac.yaml @@ -0,0 +1,33 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-adaptgauss +- r-annotationdbi +- r-anocva +- r-clusterprofiler +- r-colorspace +- r-desingle +- r-drimpute +- r-ggplot2 +- r-ggpubr +- r-ggraph +- r-igraph +- r-knitr +- r-mcl +- r-mixtools +- r-org.hs.eg.db +- r-org.mm.eg.db +- r-pheatmap +- r-polychrome +- r-rcolorbrewer +- r-rcpp +- r-scater +- r-scran +- r-seurat +- r-singlecellexperiment +update_on: +- regex: IRISFGM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IRISFGM diff --git a/prepare/r-irkernel/PKGBUILD b/prepare/r-irkernel/PKGBUILD new file mode 100644 index 0000000000..a15b5ab9ea --- /dev/null +++ b/prepare/r-irkernel/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: jupyter, jupyter_kernel_test (Python package fortesting) +# Maintainer: Guoyi Zhang + +_pkgname=IRkernel +_pkgver=1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Native R Kernel for the 'Jupyter Notebook'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-crayon + r-digest + r-evaluate + r-irdisplay + r-jsonlite + r-pbdzmq + r-repr + r-uuid +) +optdepends=( + r-roxygen2 + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-irkernel/lilac.py b/prepare/r-irkernel/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-irkernel/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-irkernel/lilac.yaml b/prepare/r-irkernel/lilac.yaml new file mode 100644 index 0000000000..832af651a8 --- /dev/null +++ b/prepare/r-irkernel/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-crayon +- r-digest +- r-evaluate +- r-irdisplay +- r-jsonlite +- r-pbdzmq +- r-repr +- r-uuid +update_on: +- regex: IRkernel_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=IRkernel diff --git a/prepare/r-irlba/PKGBUILD b/prepare/r-irlba/PKGBUILD new file mode 100644 index 0000000000..75e5d36703 --- /dev/null +++ b/prepare/r-irlba/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=irlba +_pkgver=2.3.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast Truncated Singular Value Decomposition and Principal Components Analysis for Large Dense and Sparse Matrices' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-irlba/lilac.py b/prepare/r-irlba/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-irlba/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-irlba/lilac.yaml b/prepare/r-irlba/lilac.yaml new file mode 100644 index 0000000000..e52cdc5dc7 --- /dev/null +++ b/prepare/r-irlba/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: irlba_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=irlba diff --git a/prepare/r-irr/PKGBUILD b/prepare/r-irr/PKGBUILD new file mode 100644 index 0000000000..9dde144baa --- /dev/null +++ b/prepare/r-irr/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=irr +_pkgver=0.84.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Various Coefficients of Interrater Reliability and Agreement' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-lpsolve +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-irr/lilac.py b/prepare/r-irr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-irr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-irr/lilac.yaml b/prepare/r-irr/lilac.yaml new file mode 100644 index 0000000000..fbcf4e07cf --- /dev/null +++ b/prepare/r-irr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lpsolve +update_on: +- regex: irr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=irr diff --git a/prepare/r-isa2/PKGBUILD b/prepare/r-isa2/PKGBUILD new file mode 100644 index 0000000000..f197b2a864 --- /dev/null +++ b/prepare/r-isa2/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=isa2 +_pkgver=0.3.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The Iterative Signature Algorithm' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('CCPL:by-nc-sa') +depends=( + r +) +optdepends=( + r-biclust + r-igraph +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-isa2/lilac.py b/prepare/r-isa2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-isa2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-isa2/lilac.yaml b/prepare/r-isa2/lilac.yaml new file mode 100644 index 0000000000..c5a2baad08 --- /dev/null +++ b/prepare/r-isa2/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: isa2_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=isa2 diff --git a/prepare/r-isanalytics/PKGBUILD b/prepare/r-isanalytics/PKGBUILD new file mode 100644 index 0000000000..b345217e26 --- /dev/null +++ b/prepare/r-isanalytics/PKGBUILD @@ -0,0 +1,68 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ISAnalytics +_pkgver=1.4.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CCPL:by-nc-sa') +depends=( + r + r-biocparallel + r-data.table + r-dplyr + r-fs + r-ggplot2 + r-ggrepel + r-lifecycle + r-lubridate + r-magrittr + r-psych + r-purrr + r-rcapture + r-readr + r-readxl + r-rlang + r-stringr + r-tibble + r-tidyr + r-zip +) +optdepends=( + r-biocstyle + r-circlize + r-covr + r-dt + r-eulerr + r-extradistr + r-flexdashboard + r-ggalluvial + r-gridextra + r-gtools + r-knitr + r-plotly + r-r.utils + r-refmanager + r-rmarkdown + r-roxygen2 + r-scales + r-sessioninfo + r-testthat + r-vegan + r-withr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-isanalytics/lilac.py b/prepare/r-isanalytics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-isanalytics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-isanalytics/lilac.yaml b/prepare/r-isanalytics/lilac.yaml new file mode 100644 index 0000000000..95ed65ffda --- /dev/null +++ b/prepare/r-isanalytics/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-data.table +- r-dplyr +- r-fs +- r-ggplot2 +- r-ggrepel +- r-lifecycle +- r-lubridate +- r-magrittr +- r-psych +- r-purrr +- r-rcapture +- r-readr +- r-readxl +- r-rlang +- r-stringr +- r-tibble +- r-tidyr +- r-zip +update_on: +- regex: ISAnalytics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ISAnalytics diff --git a/prepare/r-isee/PKGBUILD b/prepare/r-isee/PKGBUILD new file mode 100644 index 0000000000..44b67ae176 --- /dev/null +++ b/prepare/r-isee/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iSEE +_pkgver=2.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive SummarizedExperiment Explorer' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-circlize + r-colourpicker + r-complexheatmap + r-dt + r-ggplot2 + r-ggrepel + r-igraph + r-rintrojs + r-s4vectors + r-shiny + r-shinyace + r-shinydashboard + r-shinyjs + r-shinywidgets + r-singlecellexperiment + r-summarizedexperiment + r-vipor + r-viridislite +) +optdepends=( + r-biocstyle + r-delayedarray + r-hdf5array + r-htmltools + r-knitr + r-rcolorbrewer + r-rmarkdown + r-scater + r-scrnaseq + r-tenxpbmcdata + r-testthat + r-viridis +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-isee/lilac.py b/prepare/r-isee/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-isee/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-isee/lilac.yaml b/prepare/r-isee/lilac.yaml new file mode 100644 index 0000000000..e5e09ab817 --- /dev/null +++ b/prepare/r-isee/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-circlize +- r-colourpicker +- r-complexheatmap +- r-dt +- r-ggplot2 +- r-ggrepel +- r-igraph +- r-rintrojs +- r-s4vectors +- r-shiny +- r-shinyace +- r-shinydashboard +- r-shinyjs +- r-shinywidgets +- r-singlecellexperiment +- r-summarizedexperiment +- r-vipor +- r-viridislite +update_on: +- regex: iSEE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iSEE diff --git a/prepare/r-iseeu/PKGBUILD b/prepare/r-iseeu/PKGBUILD new file mode 100644 index 0000000000..4cecd61245 --- /dev/null +++ b/prepare/r-iseeu/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iSEEu +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='iSEE Universe' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-colourpicker + r-dt + r-ggplot2 + r-iranges + r-isee + r-s4vectors + r-shiny + r-shinyace + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-airway + r-annotationdbi + r-biocstyle + r-covr + r-edger + r-go.db + r-htmltools + r-igraph + r-keggrest + r-knitr + r-org.hs.eg.db + r-rmarkdown + r-rtsne + r-scater + r-scran + r-scrnaseq + r-testthat + r-uwot +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-iseeu/lilac.py b/prepare/r-iseeu/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-iseeu/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-iseeu/lilac.yaml b/prepare/r-iseeu/lilac.yaml new file mode 100644 index 0000000000..205f6703e0 --- /dev/null +++ b/prepare/r-iseeu/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colourpicker +- r-dt +- r-ggplot2 +- r-iranges +- r-isee +- r-s4vectors +- r-shiny +- r-shinyace +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: iSEEu_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iSEEu diff --git a/prepare/r-iseq/PKGBUILD b/prepare/r-iseq/PKGBUILD new file mode 100644 index 0000000000..b3b0c04ed9 --- /dev/null +++ b/prepare/r-iseq/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iSeq +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-iseq/lilac.py b/prepare/r-iseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-iseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-iseq/lilac.yaml b/prepare/r-iseq/lilac.yaml new file mode 100644 index 0000000000..3e3cd4b056 --- /dev/null +++ b/prepare/r-iseq/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: iSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iSeq diff --git a/prepare/r-ismev/PKGBUILD b/prepare/r-ismev/PKGBUILD new file mode 100644 index 0000000000..4275bd7fca --- /dev/null +++ b/prepare/r-ismev/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ismev +_pkgver=1.42 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Introduction to Statistical Modeling of Extreme Values' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ismev/lilac.py b/prepare/r-ismev/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ismev/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ismev/lilac.yaml b/prepare/r-ismev/lilac.yaml new file mode 100644 index 0000000000..c3639843b9 --- /dev/null +++ b/prepare/r-ismev/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ismev_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ismev diff --git a/prepare/r-iso/PKGBUILD b/prepare/r-iso/PKGBUILD new file mode 100644 index 0000000000..af6296f04b --- /dev/null +++ b/prepare/r-iso/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Iso +_pkgver=0.0-18.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions to Perform Isotonic Regression' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-iso/lilac.py b/prepare/r-iso/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-iso/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-iso/lilac.yaml b/prepare/r-iso/lilac.yaml new file mode 100644 index 0000000000..bd55ab592f --- /dev/null +++ b/prepare/r-iso/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Iso_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Iso diff --git a/prepare/r-isoband/PKGBUILD b/prepare/r-isoband/PKGBUILD new file mode 100644 index 0000000000..8006e75689 --- /dev/null +++ b/prepare/r-isoband/PKGBUILD @@ -0,0 +1,39 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=isoband +_pkgver=0.2.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generate Isolines and Isobands from Regularly Spaced Elevation Grids' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-covr + r-ggplot2 + r-knitr + r-magick + r-microbenchmark + r-rmarkdown + r-sf + r-testthat + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-isoband/lilac.py b/prepare/r-isoband/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-isoband/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-isoband/lilac.yaml b/prepare/r-isoband/lilac.yaml new file mode 100644 index 0000000000..c0205f1e61 --- /dev/null +++ b/prepare/r-isoband/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: isoband_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=isoband diff --git a/prepare/r-isobar/PKGBUILD b/prepare/r-isobar/PKGBUILD new file mode 100644 index 0000000000..0699ebedaa --- /dev/null +++ b/prepare/r-isobar/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=isobar +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis and quantitation of isobarically tagged MSMS proteomics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-biomart + r-distr + r-ggplot2 + r-plyr +) +optdepends=( + r-boot + r-dbi + r-gplots + r-gridextra + r-hmisc + r-limma + r-mass + r-msnbase + r-orgmassspecr + r-rcolorbrewer + r-rjsonio + r-xml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-isobar/lilac.py b/prepare/r-isobar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-isobar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-isobar/lilac.yaml b/prepare/r-isobar/lilac.yaml new file mode 100644 index 0000000000..a63d6a9e02 --- /dev/null +++ b/prepare/r-isobar/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biomart +- r-distr +- r-ggplot2 +- r-plyr +update_on: +- regex: isobar_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/isobar diff --git a/prepare/r-isocodes/PKGBUILD b/prepare/r-isocodes/PKGBUILD new file mode 100644 index 0000000000..469a4d992f --- /dev/null +++ b/prepare/r-isocodes/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ISOcodes +_pkgver=2022.01.10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Selected ISO Codes' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-isocodes/lilac.py b/prepare/r-isocodes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-isocodes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-isocodes/lilac.yaml b/prepare/r-isocodes/lilac.yaml new file mode 100644 index 0000000000..6b2a6f75e6 --- /dev/null +++ b/prepare/r-isocodes/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ISOcodes_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ISOcodes diff --git a/prepare/r-isocorrector/PKGBUILD b/prepare/r-isocorrector/PKGBUILD new file mode 100644 index 0000000000..a1283799bd --- /dev/null +++ b/prepare/r-isocorrector/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IsoCorrectoR +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-magrittr + r-pracma + r-quadprog + r-readr + r-readxl + r-stringr + r-tibble + r-writexls +) +optdepends=( + r-isocorrectorgui + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-isocorrector/lilac.py b/prepare/r-isocorrector/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-isocorrector/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-isocorrector/lilac.yaml b/prepare/r-isocorrector/lilac.yaml new file mode 100644 index 0000000000..6c388872d0 --- /dev/null +++ b/prepare/r-isocorrector/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-magrittr +- r-pracma +- r-quadprog +- r-readr +- r-readxl +- r-stringr +- r-tibble +- r-writexls +update_on: +- regex: IsoCorrectoR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IsoCorrectoR diff --git a/prepare/r-isocorrectorgui/PKGBUILD b/prepare/r-isocorrectorgui/PKGBUILD new file mode 100644 index 0000000000..2dab3bb2e1 --- /dev/null +++ b/prepare/r-isocorrectorgui/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IsoCorrectoRGUI +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Graphical User Interface for IsoCorrectoR' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-isocorrector + r-readxl + r-tcltk2 +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-isocorrectorgui/lilac.py b/prepare/r-isocorrectorgui/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-isocorrectorgui/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-isocorrectorgui/lilac.yaml b/prepare/r-isocorrectorgui/lilac.yaml new file mode 100644 index 0000000000..925ae0984a --- /dev/null +++ b/prepare/r-isocorrectorgui/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-isocorrector +- r-readxl +- r-tcltk2 +update_on: +- regex: IsoCorrectoRGUI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IsoCorrectoRGUI diff --git a/prepare/r-isoformswitchanalyzer/PKGBUILD b/prepare/r-isoformswitchanalyzer/PKGBUILD new file mode 100644 index 0000000000..d5d9918ed0 --- /dev/null +++ b/prepare/r-isoformswitchanalyzer/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IsoformSwitchAnalyzeR +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-biostrings + r-bsgenome + r-dbi + r-dexseq + r-dplyr + r-drimseq + r-edger + r-futile.logger + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gridextra + r-iranges + r-limma + r-magrittr + r-plyr + r-rcolorbrewer + r-rcurl + r-readr + r-reshape2 + r-rtracklayer + r-stringr + r-tibble + r-tximeta + r-tximport + r-venndiagram + r-xvector +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg19 + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-isoformswitchanalyzer/lilac.py b/prepare/r-isoformswitchanalyzer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-isoformswitchanalyzer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-isoformswitchanalyzer/lilac.yaml b/prepare/r-isoformswitchanalyzer/lilac.yaml new file mode 100644 index 0000000000..1ca29e856d --- /dev/null +++ b/prepare/r-isoformswitchanalyzer/lilac.yaml @@ -0,0 +1,38 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-dbi +- r-dexseq +- r-dplyr +- r-drimseq +- r-edger +- r-futile.logger +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-gridextra +- r-iranges +- r-limma +- r-magrittr +- r-plyr +- r-rcolorbrewer +- r-rcurl +- r-readr +- r-reshape2 +- r-rtracklayer +- r-stringr +- r-tibble +- r-tximeta +- r-tximport +- r-venndiagram +- r-xvector +update_on: +- regex: IsoformSwitchAnalyzeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IsoformSwitchAnalyzeR diff --git a/prepare/r-isogene/PKGBUILD b/prepare/r-isogene/PKGBUILD new file mode 100644 index 0000000000..5d49bb3e00 --- /dev/null +++ b/prepare/r-isogene/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IsoGene +_pkgver=1.0-24 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Order-Restricted Inference for Microarray Experiments' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-biobase + r-ff + r-iso + r-xtable +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-isogene/lilac.py b/prepare/r-isogene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-isogene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-isogene/lilac.yaml b/prepare/r-isogene/lilac.yaml new file mode 100644 index 0000000000..5c776e9c33 --- /dev/null +++ b/prepare/r-isogene/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +- r-ff +- r-iso +- r-xtable +update_on: +- regex: IsoGene_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=IsoGene diff --git a/prepare/r-isogenegui/PKGBUILD b/prepare/r-isogenegui/PKGBUILD new file mode 100644 index 0000000000..0cc6561451 --- /dev/null +++ b/prepare/r-isogenegui/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IsoGeneGUI +_pkgver=2.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A graphical user interface to conduct a dose-response analysis of microarray data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-ff + r-geneplotter + r-goric + r-iso + r-isogene + r-jpeg + r-multtest + r-orcme + r-oriclust + r-orqa + r-rcolorbrewer + r-rcpp + r-relimp + r-tkrplot + r-xlsx +) +optdepends=( + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-isogenegui/lilac.py b/prepare/r-isogenegui/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-isogenegui/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-isogenegui/lilac.yaml b/prepare/r-isogenegui/lilac.yaml new file mode 100644 index 0000000000..1edd57b021 --- /dev/null +++ b/prepare/r-isogenegui/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-ff +- r-geneplotter +- r-goric +- r-iso +- r-isogene +- r-jpeg +- r-multtest +- r-orcme +- r-oriclust +- r-orqa +- r-rcolorbrewer +- r-rcpp +- r-relimp +- r-tkrplot +- r-xlsx +update_on: +- regex: IsoGeneGUI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IsoGeneGUI diff --git a/prepare/r-isolde/PKGBUILD b/prepare/r-isolde/PKGBUILD new file mode 100644 index 0000000000..c7ce67b6ce --- /dev/null +++ b/prepare/r-isolde/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ISoLDE +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integrative Statistics of alleLe Dependent Expression' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-isolde/lilac.py b/prepare/r-isolde/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-isolde/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-isolde/lilac.yaml b/prepare/r-isolde/lilac.yaml new file mode 100644 index 0000000000..9694a6c1cb --- /dev/null +++ b/prepare/r-isolde/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ISoLDE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ISoLDE diff --git a/prepare/r-isomirs/PKGBUILD b/prepare/r-isomirs/PKGBUILD new file mode 100644 index 0000000000..fe662db99e --- /dev/null +++ b/prepare/r-isomirs/PKGBUILD @@ -0,0 +1,63 @@ +# Maintainer: Guoyi Zhang + +_pkgname=isomiRs +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analyze isomiRs and miRNAs from small RNA-seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-assertive.sets + r-biobase + r-biocgenerics + r-broom + r-cowplot + r-degreport + r-deseq2 + r-discriminer + r-dplyr + r-genomicranges + r-ggally + r-ggplot2 + r-gplots + r-gridextra + r-gtools + r-iranges + r-limma + r-rcolorbrewer + r-readr + r-reshape + r-rlang + r-s4vectors + r-stringr + r-summarizedexperiment + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-org.mm.eg.db + r-pheatmap + r-rmarkdown + r-targetscan.hs.eg.db + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-isomirs/lilac.py b/prepare/r-isomirs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-isomirs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-isomirs/lilac.yaml b/prepare/r-isomirs/lilac.yaml new file mode 100644 index 0000000000..8069e18da9 --- /dev/null +++ b/prepare/r-isomirs/lilac.yaml @@ -0,0 +1,36 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-assertive.sets +- r-biobase +- r-biocgenerics +- r-broom +- r-cowplot +- r-degreport +- r-deseq2 +- r-discriminer +- r-dplyr +- r-genomicranges +- r-ggally +- r-ggplot2 +- r-gplots +- r-gridextra +- r-gtools +- r-iranges +- r-limma +- r-rcolorbrewer +- r-readr +- r-reshape +- r-rlang +- r-s4vectors +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-tidyr +update_on: +- regex: isomiRs_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/isomiRs diff --git a/prepare/r-isva/PKGBUILD b/prepare/r-isva/PKGBUILD new file mode 100644 index 0000000000..4dd7562e72 --- /dev/null +++ b/prepare/r-isva/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=isva +_pkgver=1.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Independent Surrogate Variable Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-fastica + r-jade + r-qvalue +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-isva/lilac.py b/prepare/r-isva/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-isva/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-isva/lilac.yaml b/prepare/r-isva/lilac.yaml new file mode 100644 index 0000000000..1d4d2aa1cd --- /dev/null +++ b/prepare/r-isva/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fastica +- r-jade +- r-qvalue +update_on: +- regex: isva_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=isva diff --git a/prepare/r-italics/PKGBUILD b/prepare/r-italics/PKGBUILD new file mode 100644 index 0000000000..44aa125ec4 --- /dev/null +++ b/prepare/r-italics/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ITALICS +_pkgver=2.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ITALICS' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affxparser + r-dbi + r-glad + r-italicsdata + r-oligo + r-oligoclasses + r-pd.mapping50k.xba240 +) +optdepends=( + r-pd.mapping250k.nsp + r-pd.mapping250k.sty + r-pd.mapping50k.hind240 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-italics/lilac.py b/prepare/r-italics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-italics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-italics/lilac.yaml b/prepare/r-italics/lilac.yaml new file mode 100644 index 0000000000..b5af4f9e2b --- /dev/null +++ b/prepare/r-italics/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affxparser +- r-dbi +- r-glad +- r-italicsdata +- r-oligo +- r-oligoclasses +- r-pd.mapping50k.xba240 +update_on: +- regex: ITALICS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ITALICS diff --git a/prepare/r-italicsdata/PKGBUILD b/prepare/r-italicsdata/PKGBUILD new file mode 100644 index 0000000000..8d8bb387fa --- /dev/null +++ b/prepare/r-italicsdata/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ITALICSData +_pkgver=2.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ITALICSData' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-italicsdata/lilac.py b/prepare/r-italicsdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-italicsdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-italicsdata/lilac.yaml b/prepare/r-italicsdata/lilac.yaml new file mode 100644 index 0000000000..952346ae84 --- /dev/null +++ b/prepare/r-italicsdata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ITALICSData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ITALICSData diff --git a/prepare/r-iterativebma/PKGBUILD b/prepare/r-iterativebma/PKGBUILD new file mode 100644 index 0000000000..267e3ea647 --- /dev/null +++ b/prepare/r-iterativebma/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iterativeBMA +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The Iterative Bayesian Model Averaging (BMA) algorithm' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-bma + r-leaps +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-iterativebma/lilac.py b/prepare/r-iterativebma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-iterativebma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-iterativebma/lilac.yaml b/prepare/r-iterativebma/lilac.yaml new file mode 100644 index 0000000000..a7081793c0 --- /dev/null +++ b/prepare/r-iterativebma/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-bma +- r-leaps +update_on: +- regex: iterativeBMA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iterativeBMA diff --git a/prepare/r-iterativebmasurv/PKGBUILD b/prepare/r-iterativebmasurv/PKGBUILD new file mode 100644 index 0000000000..023ac52ecc --- /dev/null +++ b/prepare/r-iterativebmasurv/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iterativeBMAsurv +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bma + r-leaps +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-iterativebmasurv/lilac.py b/prepare/r-iterativebmasurv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-iterativebmasurv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-iterativebmasurv/lilac.yaml b/prepare/r-iterativebmasurv/lilac.yaml new file mode 100644 index 0000000000..bfa20bbf0d --- /dev/null +++ b/prepare/r-iterativebmasurv/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bma +- r-leaps +update_on: +- regex: iterativeBMAsurv_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iterativeBMAsurv diff --git a/prepare/r-iterators/PKGBUILD b/prepare/r-iterators/PKGBUILD new file mode 100644 index 0000000000..b223a9cc8b --- /dev/null +++ b/prepare/r-iterators/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iterators +_pkgver=1.0.13 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Provides Iterator Construct' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r +) +optdepends=( + r-foreach + r-runit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-iterators/lilac.py b/prepare/r-iterators/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-iterators/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-iterators/lilac.yaml b/prepare/r-iterators/lilac.yaml new file mode 100644 index 0000000000..1244889deb --- /dev/null +++ b/prepare/r-iterators/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: iterators_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=iterators diff --git a/prepare/r-iterclust/PKGBUILD b/prepare/r-iterclust/PKGBUILD new file mode 100644 index 0000000000..1980dd4c09 --- /dev/null +++ b/prepare/r-iterclust/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iterClust +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Iterative Clustering' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-biobase +) +optdepends=( + r-bcellviper + r-tsne +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-iterclust/lilac.py b/prepare/r-iterclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-iterclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-iterclust/lilac.yaml b/prepare/r-iterclust/lilac.yaml new file mode 100644 index 0000000000..94059a2856 --- /dev/null +++ b/prepare/r-iterclust/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: iterClust_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iterClust diff --git a/prepare/r-iteremoval/PKGBUILD b/prepare/r-iteremoval/PKGBUILD new file mode 100644 index 0000000000..de98561e03 --- /dev/null +++ b/prepare/r-iteremoval/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=iteremoval +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Iteration removal method for feature selection' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicranges + r-ggplot2 + r-magrittr + r-summarizedexperiment +) +optdepends=( + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-iteremoval/lilac.py b/prepare/r-iteremoval/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-iteremoval/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-iteremoval/lilac.yaml b/prepare/r-iteremoval/lilac.yaml new file mode 100644 index 0000000000..78d6197046 --- /dev/null +++ b/prepare/r-iteremoval/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-ggplot2 +- r-magrittr +- r-summarizedexperiment +update_on: +- regex: iteremoval_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/iteremoval diff --git a/prepare/r-itertools/PKGBUILD b/prepare/r-itertools/PKGBUILD new file mode 100644 index 0000000000..4290f6d88a --- /dev/null +++ b/prepare/r-itertools/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=itertools +_pkgver=0.1-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Iterator Tools' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-iterators +) +optdepends=( + r-foreach +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-itertools/lilac.py b/prepare/r-itertools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-itertools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-itertools/lilac.yaml b/prepare/r-itertools/lilac.yaml new file mode 100644 index 0000000000..6f82e73be4 --- /dev/null +++ b/prepare/r-itertools/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-iterators +update_on: +- regex: itertools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=itertools diff --git a/prepare/r-ivas/PKGBUILD b/prepare/r-ivas/PKGBUILD new file mode 100644 index 0000000000..f6e98ea9b0 --- /dev/null +++ b/prepare/r-ivas/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IVAS +_pkgver=2.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identification of genetic Variants affecting Alternative Splicing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-doparallel + r-foreach + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggfortify + r-ggplot2 + r-iranges + r-lme4 + r-s4vectors +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ivas/lilac.py b/prepare/r-ivas/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ivas/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ivas/lilac.yaml b/prepare/r-ivas/lilac.yaml new file mode 100644 index 0000000000..e4a8eb6465 --- /dev/null +++ b/prepare/r-ivas/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-doparallel +- r-foreach +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggfortify +- r-ggplot2 +- r-iranges +- r-lme4 +- r-s4vectors +update_on: +- regex: IVAS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IVAS diff --git a/prepare/r-ivygapse/PKGBUILD b/prepare/r-ivygapse/PKGBUILD new file mode 100644 index 0000000000..256f197735 --- /dev/null +++ b/prepare/r-ivygapse/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ivygapSE +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A SummarizedExperiment for Ivy-GAP data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ggplot2 + r-hwriter + r-plotly + r-s4vectors + r-shiny + r-summarizedexperiment + r-survminer + r-upsetr +) +optdepends=( + r-digest + r-dt + r-grid + r-knitr + r-limma + r-png + r-randomforest + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ivygapse/lilac.py b/prepare/r-ivygapse/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ivygapse/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ivygapse/lilac.yaml b/prepare/r-ivygapse/lilac.yaml new file mode 100644 index 0000000000..537eaba2e1 --- /dev/null +++ b/prepare/r-ivygapse/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-hwriter +- r-plotly +- r-s4vectors +- r-shiny +- r-summarizedexperiment +- r-survminer +- r-upsetr +update_on: +- regex: ivygapSE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ivygapSE diff --git a/prepare/r-iwtomics/PKGBUILD b/prepare/r-iwtomics/PKGBUILD new file mode 100644 index 0000000000..71dede4a9c --- /dev/null +++ b/prepare/r-iwtomics/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=IWTomics +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interval-Wise Testing for Omics Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-fda + r-genomicranges + r-gtable + r-iranges + r-s4vectors +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-iwtomics/lilac.py b/prepare/r-iwtomics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-iwtomics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-iwtomics/lilac.yaml b/prepare/r-iwtomics/lilac.yaml new file mode 100644 index 0000000000..a2c2951c0f --- /dev/null +++ b/prepare/r-iwtomics/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fda +- r-genomicranges +- r-gtable +- r-iranges +- r-s4vectors +update_on: +- regex: IWTomics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/IWTomics diff --git a/prepare/r-jackstraw/PKGBUILD b/prepare/r-jackstraw/PKGBUILD new file mode 100644 index 0000000000..88dce28345 --- /dev/null +++ b/prepare/r-jackstraw/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=jackstraw +_pkgver=1.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Inference for Unsupervised Learning' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-clusterr + r-corpcor + r-irlba + r-lfa + r-qvalue + r-rsvd +) +optdepends=( + r-knitr + r-parallel + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-jackstraw/lilac.py b/prepare/r-jackstraw/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-jackstraw/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-jackstraw/lilac.yaml b/prepare/r-jackstraw/lilac.yaml new file mode 100644 index 0000000000..7653073f65 --- /dev/null +++ b/prepare/r-jackstraw/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clusterr +- r-corpcor +- r-irlba +- r-lfa +- r-qvalue +- r-rsvd +update_on: +- regex: jackstraw_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=jackstraw diff --git a/prepare/r-jade/PKGBUILD b/prepare/r-jade/PKGBUILD new file mode 100644 index 0000000000..06320ccf47 --- /dev/null +++ b/prepare/r-jade/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=JADE +_pkgver=2.0-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Blind Source Separation Methods Based on Joint Diagonalization and Some BSS Performance Criteria' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-clue +) +optdepends=( + r-ics + r-icsnp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-jade/lilac.py b/prepare/r-jade/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-jade/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-jade/lilac.yaml b/prepare/r-jade/lilac.yaml new file mode 100644 index 0000000000..4baaeda24e --- /dev/null +++ b/prepare/r-jade/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clue +update_on: +- regex: JADE_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=JADE diff --git a/prepare/r-janeaustenr/PKGBUILD b/prepare/r-janeaustenr/PKGBUILD new file mode 100644 index 0000000000..5c34858a6d --- /dev/null +++ b/prepare/r-janeaustenr/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=janeaustenr +_pkgver=0.1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Jane Austen's Complete Novels" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-dplyr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-janeaustenr/lilac.py b/prepare/r-janeaustenr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-janeaustenr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-janeaustenr/lilac.yaml b/prepare/r-janeaustenr/lilac.yaml new file mode 100644 index 0000000000..8ab49c8a88 --- /dev/null +++ b/prepare/r-janeaustenr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: janeaustenr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=janeaustenr diff --git a/prepare/r-jaspar2018/PKGBUILD b/prepare/r-jaspar2018/PKGBUILD new file mode 100644 index 0000000000..6c4c5f354e --- /dev/null +++ b/prepare/r-jaspar2018/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=JASPAR2018 +_pkgver=1.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data package for JASPAR 2018' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-tfbstools +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-jaspar2018/lilac.py b/prepare/r-jaspar2018/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-jaspar2018/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-jaspar2018/lilac.yaml b/prepare/r-jaspar2018/lilac.yaml new file mode 100644 index 0000000000..da538d2b6e --- /dev/null +++ b/prepare/r-jaspar2018/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: JASPAR2018_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/JASPAR2018 diff --git a/prepare/r-jpeg/PKGBUILD b/prepare/r-jpeg/PKGBUILD new file mode 100644 index 0000000000..9284e82974 --- /dev/null +++ b/prepare/r-jpeg/PKGBUILD @@ -0,0 +1,27 @@ +# system requirements: libjpeg +# Maintainer: Guoyi Zhang + +_pkgname=jpeg +_pkgver=0.1-9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Read and write JPEG images' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-jpeg/lilac.py b/prepare/r-jpeg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-jpeg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-jpeg/lilac.yaml b/prepare/r-jpeg/lilac.yaml new file mode 100644 index 0000000000..6375fae52b --- /dev/null +++ b/prepare/r-jpeg/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: jpeg_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=jpeg diff --git a/prepare/r-jquerylib/PKGBUILD b/prepare/r-jquerylib/PKGBUILD new file mode 100644 index 0000000000..4b6818b090 --- /dev/null +++ b/prepare/r-jquerylib/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=jquerylib +_pkgver=0.1.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Obtain 'jQuery' as an HTML Dependency Object" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmltools +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-jquerylib/lilac.py b/prepare/r-jquerylib/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-jquerylib/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-jquerylib/lilac.yaml b/prepare/r-jquerylib/lilac.yaml new file mode 100644 index 0000000000..abd865a66f --- /dev/null +++ b/prepare/r-jquerylib/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +update_on: +- regex: jquerylib_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=jquerylib diff --git a/prepare/r-jsonlite/PKGBUILD b/prepare/r-jsonlite/PKGBUILD new file mode 100644 index 0000000000..75945385f8 --- /dev/null +++ b/prepare/r-jsonlite/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=jsonlite +_pkgver=1.7.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Simple and Robust JSON Parser and Generator for R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-curl + r-httr + r-knitr + r-plyr + r-r.rsp + r-rmarkdown + r-sf + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-jsonlite/lilac.py b/prepare/r-jsonlite/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-jsonlite/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-jsonlite/lilac.yaml b/prepare/r-jsonlite/lilac.yaml new file mode 100644 index 0000000000..939bd8f891 --- /dev/null +++ b/prepare/r-jsonlite/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: jsonlite_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=jsonlite diff --git a/prepare/r-kableextra/PKGBUILD b/prepare/r-kableextra/PKGBUILD new file mode 100644 index 0000000000..826399397d --- /dev/null +++ b/prepare/r-kableextra/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=kableExtra +_pkgver=1.3.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Construct Complex Table with 'kable' and Pipe Syntax" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-digest + r-glue + r-htmltools + r-knitr + r-magrittr + r-rmarkdown + r-rstudioapi + r-rvest + r-scales + r-stringr + r-svglite + r-viridislite + r-webshot + r-xml2 +) +optdepends=( + r-formattable + r-magick + r-sparkline + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kableextra/lilac.py b/prepare/r-kableextra/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kableextra/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kableextra/lilac.yaml b/prepare/r-kableextra/lilac.yaml new file mode 100644 index 0000000000..7c28fb8874 --- /dev/null +++ b/prepare/r-kableextra/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-glue +- r-htmltools +- r-knitr +- r-magrittr +- r-rmarkdown +- r-rstudioapi +- r-rvest +- r-scales +- r-stringr +- r-svglite +- r-viridislite +- r-webshot +- r-xml2 +update_on: +- regex: kableExtra_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=kableExtra diff --git a/prepare/r-karyoploter/PKGBUILD b/prepare/r-karyoploter/PKGBUILD new file mode 100644 index 0000000000..c4a03e15f8 --- /dev/null +++ b/prepare/r-karyoploter/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=karyoploteR +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Plot customizable linear genomes displaying arbitrary data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-bamsignals + r-bezier + r-biovizbase + r-digest + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-memoise + r-regioner + r-rsamtools + r-rtracklayer + r-s4vectors + r-variantannotation +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.hsapiens.ucsc.hg19.masked + r-knitr + r-magrittr + r-markdown + r-org.hs.eg.db + r-org.mm.eg.db + r-pasillabamsubset + r-rmarkdown + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.mmusculus.ucsc.mm10.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-karyoploter/lilac.py b/prepare/r-karyoploter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-karyoploter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-karyoploter/lilac.yaml b/prepare/r-karyoploter/lilac.yaml new file mode 100644 index 0000000000..c5aa701bf1 --- /dev/null +++ b/prepare/r-karyoploter/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-bamsignals +- r-bezier +- r-biovizbase +- r-digest +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-memoise +- r-regioner +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-variantannotation +update_on: +- regex: karyoploteR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/karyoploteR diff --git a/prepare/r-kboost/PKGBUILD b/prepare/r-kboost/PKGBUILD new file mode 100644 index 0000000000..7eb92b5597 --- /dev/null +++ b/prepare/r-kboost/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=KBoost +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Inference of gene regulatory networks from gene expression data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kboost/lilac.py b/prepare/r-kboost/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kboost/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kboost/lilac.yaml b/prepare/r-kboost/lilac.yaml new file mode 100644 index 0000000000..1a3a6855c7 --- /dev/null +++ b/prepare/r-kboost/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: KBoost_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/KBoost diff --git a/prepare/r-kcsmart/PKGBUILD b/prepare/r-kcsmart/PKGBUILD new file mode 100644 index 0000000000..ba1115aeb1 --- /dev/null +++ b/prepare/r-kcsmart/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=KCsmart +_pkgver=2.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multi sample aCGH analysis package using kernel convolution' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-multtest + r-siggenes +) +optdepends=( + r-biobase + r-cghbase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kcsmart/lilac.py b/prepare/r-kcsmart/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kcsmart/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kcsmart/lilac.yaml b/prepare/r-kcsmart/lilac.yaml new file mode 100644 index 0000000000..f2496d0cd4 --- /dev/null +++ b/prepare/r-kcsmart/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-multtest +- r-siggenes +update_on: +- regex: KCsmart_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/KCsmart diff --git a/prepare/r-kebabs/PKGBUILD b/prepare/r-kebabs/PKGBUILD new file mode 100644 index 0000000000..89998832ab --- /dev/null +++ b/prepare/r-kebabs/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=kebabs +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Kernel-Based Analysis Of Biological Sequences' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-apcluster + r-biostrings + r-e1071 + r-iranges + r-kernlab + r-liblinear + r-rcpp + r-s4vectors + r-xvector +) +optdepends=( + r-biobase + r-biocgenerics + r-knitr + r-sparsem +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kebabs/lilac.py b/prepare/r-kebabs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kebabs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kebabs/lilac.yaml b/prepare/r-kebabs/lilac.yaml new file mode 100644 index 0000000000..a258130c1f --- /dev/null +++ b/prepare/r-kebabs/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-apcluster +- r-biostrings +- r-e1071 +- r-iranges +- r-kernlab +- r-liblinear +- r-rcpp +- r-s4vectors +- r-xvector +update_on: +- regex: kebabs_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/kebabs diff --git a/prepare/r-keggandmetacoredzpathwaysgeo/PKGBUILD b/prepare/r-keggandmetacoredzpathwaysgeo/PKGBUILD new file mode 100644 index 0000000000..d40d7d1041 --- /dev/null +++ b/prepare/r-keggandmetacoredzpathwaysgeo/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=KEGGandMetacoreDzPathwaysGEO +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Disease Datasets from GEO' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-keggandmetacoredzpathwaysgeo/lilac.py b/prepare/r-keggandmetacoredzpathwaysgeo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-keggandmetacoredzpathwaysgeo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-keggandmetacoredzpathwaysgeo/lilac.yaml b/prepare/r-keggandmetacoredzpathwaysgeo/lilac.yaml new file mode 100644 index 0000000000..72cb4d77b3 --- /dev/null +++ b/prepare/r-keggandmetacoredzpathwaysgeo/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +update_on: +- regex: KEGGandMetacoreDzPathwaysGEO_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/KEGGandMetacoreDzPathwaysGEO diff --git a/prepare/r-keggdzpathwaysgeo/PKGBUILD b/prepare/r-keggdzpathwaysgeo/PKGBUILD new file mode 100644 index 0000000000..27207da01d --- /dev/null +++ b/prepare/r-keggdzpathwaysgeo/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=KEGGdzPathwaysGEO +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='KEGG Disease Datasets from GEO' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-keggdzpathwaysgeo/lilac.py b/prepare/r-keggdzpathwaysgeo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-keggdzpathwaysgeo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-keggdzpathwaysgeo/lilac.yaml b/prepare/r-keggdzpathwaysgeo/lilac.yaml new file mode 100644 index 0000000000..84c8902fbf --- /dev/null +++ b/prepare/r-keggdzpathwaysgeo/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +update_on: +- regex: KEGGdzPathwaysGEO_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/KEGGdzPathwaysGEO diff --git a/prepare/r-kegggraph/PKGBUILD b/prepare/r-kegggraph/PKGBUILD new file mode 100644 index 0000000000..c0c43b2a72 --- /dev/null +++ b/prepare/r-kegggraph/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=KEGGgraph +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-graph + r-rcurl + r-rgraphviz + r-xml +) +optdepends=( + r-hgu133plus2.db + r-org.hs.eg.db + r-rbgl + r-rcolorbrewer + r-spia + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kegggraph/lilac.py b/prepare/r-kegggraph/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kegggraph/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kegggraph/lilac.yaml b/prepare/r-kegggraph/lilac.yaml new file mode 100644 index 0000000000..8067660506 --- /dev/null +++ b/prepare/r-kegggraph/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +- r-rcurl +- r-rgraphviz +- r-xml +update_on: +- regex: KEGGgraph_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/KEGGgraph diff --git a/prepare/r-kegglincs/PKGBUILD b/prepare/r-kegglincs/PKGBUILD new file mode 100644 index 0000000000..6ae1b066a9 --- /dev/null +++ b/prepare/r-kegglincs/PKGBUILD @@ -0,0 +1,44 @@ +# system requirements: Cytoscape (>= 3.3.0), Java (>= 8) +# Maintainer: Guoyi Zhang + +_pkgname=KEGGlincs +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualize all edges within a KEGG pathway and overlay LINCS data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-gtools + r-hgu133a.db + r-httr + r-igraph + r-kegggraph + r-keggrest + r-kodata + r-org.hs.eg.db + r-plyr + r-rjsonio + r-xml +) +optdepends=( + r-biocmanager + r-graph + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kegglincs/lilac.py b/prepare/r-kegglincs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kegglincs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kegglincs/lilac.yaml b/prepare/r-kegglincs/lilac.yaml new file mode 100644 index 0000000000..c0fdb09b37 --- /dev/null +++ b/prepare/r-kegglincs/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-gtools +- r-hgu133a.db +- r-httr +- r-igraph +- r-kegggraph +- r-keggrest +- r-kodata +- r-org.hs.eg.db +- r-plyr +- r-rjsonio +- r-xml +update_on: +- regex: KEGGlincs_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/KEGGlincs diff --git a/prepare/r-keggorthology/PKGBUILD b/prepare/r-keggorthology/PKGBUILD new file mode 100644 index 0000000000..e08db1c9e9 --- /dev/null +++ b/prepare/r-keggorthology/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=keggorthology +_pkgver=2.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='graph support for KO, KEGG Orthology' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-dbi + r-graph + r-hgu95av2.db +) +optdepends=( + r-all + r-rbgl +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-keggorthology/lilac.py b/prepare/r-keggorthology/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-keggorthology/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-keggorthology/lilac.yaml b/prepare/r-keggorthology/lilac.yaml new file mode 100644 index 0000000000..af1f276eaa --- /dev/null +++ b/prepare/r-keggorthology/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-dbi +- r-graph +- r-hgu95av2.db +update_on: +- regex: keggorthology_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/keggorthology diff --git a/prepare/r-keggprofile/PKGBUILD b/prepare/r-keggprofile/PKGBUILD new file mode 100644 index 0000000000..4a70a6195c --- /dev/null +++ b/prepare/r-keggprofile/PKGBUILD @@ -0,0 +1,39 @@ + +_pkgname=KEGGprofile +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-png + r-teachingdemos + r-xml + r-keggrest + r-biomart + r-rcurl + r-ggplot2 + r-reshape2 +) +makedepends=( + git + tar +) +source=("git+https://git.bioconductor.org/packages/${_pkgname}.git") +sha256sums=('SKIP') + +build() { + tar -zcvf ${_pkgname}.tar.gz ${_pkgname} + R CMD INSTALL ${_pkgname}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-keggprofile/lilac.py b/prepare/r-keggprofile/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-keggprofile/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-keggprofile/lilac.yaml b/prepare/r-keggprofile/lilac.yaml new file mode 100644 index 0000000000..07bd1b9270 --- /dev/null +++ b/prepare/r-keggprofile/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-png +- r-teachingdemos +- r-xml +- r-keggrest +- r-biomart +- r-rcurl +- r-ggplot2 +- r-reshape2 +update_on: +- regex: Version(\d+.\d+.\d+) + source: regex + url: https://bioconductor.org/packages/KEGGprofile diff --git a/prepare/r-keggrest/PKGBUILD b/prepare/r-keggrest/PKGBUILD new file mode 100644 index 0000000000..808a3f0783 --- /dev/null +++ b/prepare/r-keggrest/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=KEGGREST +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-httr + r-png +) +optdepends=( + r-biocgenerics + r-knitr + r-markdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-keggrest/lilac.py b/prepare/r-keggrest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-keggrest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-keggrest/lilac.yaml b/prepare/r-keggrest/lilac.yaml new file mode 100644 index 0000000000..466a95565f --- /dev/null +++ b/prepare/r-keggrest/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-httr +- r-png +update_on: +- regex: KEGGREST_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/KEGGREST diff --git a/prepare/r-keras/PKGBUILD b/prepare/r-keras/PKGBUILD new file mode 100644 index 0000000000..5bcf74897d --- /dev/null +++ b/prepare/r-keras/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=keras +_pkgver=2.7.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="R Interface to 'Keras'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-ellipsis + r-generics + r-glue + r-magrittr + r-r6 + r-reticulate + r-rlang + r-tensorflow + r-tfruns + r-zeallot +) +optdepends=( + r-callr + r-ggplot2 + r-jpeg + r-knitr + r-rmarkdown + r-testthat + r-tfdatasets +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-keras/lilac.py b/prepare/r-keras/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-keras/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-keras/lilac.yaml b/prepare/r-keras/lilac.yaml new file mode 100644 index 0000000000..0a263b039a --- /dev/null +++ b/prepare/r-keras/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ellipsis +- r-generics +- r-glue +- r-magrittr +- r-r6 +- r-reticulate +- r-rlang +- r-tensorflow +- r-tfruns +- r-zeallot +update_on: +- regex: keras_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=keras diff --git a/prepare/r-kernlab/PKGBUILD b/prepare/r-kernlab/PKGBUILD new file mode 100644 index 0000000000..3f0f7a55f1 --- /dev/null +++ b/prepare/r-kernlab/PKGBUILD @@ -0,0 +1,27 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=kernlab +_pkgver=0.9-29 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Kernel-Based Machine Learning Lab' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kernlab/lilac.py b/prepare/r-kernlab/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kernlab/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kernlab/lilac.yaml b/prepare/r-kernlab/lilac.yaml new file mode 100644 index 0000000000..a620ebf4f6 --- /dev/null +++ b/prepare/r-kernlab/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: kernlab_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=kernlab diff --git a/prepare/r-kinship2/PKGBUILD b/prepare/r-kinship2/PKGBUILD new file mode 100644 index 0000000000..2275b8f27b --- /dev/null +++ b/prepare/r-kinship2/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=kinship2 +_pkgver=1.8.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pedigree Functions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-quadprog +) +optdepends=( + r-knitr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kinship2/lilac.py b/prepare/r-kinship2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kinship2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kinship2/lilac.yaml b/prepare/r-kinship2/lilac.yaml new file mode 100644 index 0000000000..732a230bd0 --- /dev/null +++ b/prepare/r-kinship2/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-quadprog +update_on: +- regex: kinship2_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=kinship2 diff --git a/prepare/r-kinswingr/PKGBUILD b/prepare/r-kinswingr/PKGBUILD new file mode 100644 index 0000000000..400d7b170a --- /dev/null +++ b/prepare/r-kinswingr/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=KinSwingR +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='KinSwingR: network-based kinase activity prediction' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-data.table + r-sqldf +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kinswingr/lilac.py b/prepare/r-kinswingr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kinswingr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kinswingr/lilac.yaml b/prepare/r-kinswingr/lilac.yaml new file mode 100644 index 0000000000..c5cdb7253b --- /dev/null +++ b/prepare/r-kinswingr/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-data.table +- r-sqldf +update_on: +- regex: KinSwingR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/KinSwingR diff --git a/prepare/r-kissde/PKGBUILD b/prepare/r-kissde/PKGBUILD new file mode 100644 index 0000000000..6ad1e5e460 --- /dev/null +++ b/prepare/r-kissde/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=kissDE +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Retrieves Condition-Specific Variants in RNA-Seq Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-aod + r-biobase + r-deseq2 + r-doparallel + r-dss + r-foreach + r-ggplot2 + r-gplots + r-matrixstats +) +optdepends=( + r-biocstyle + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kissde/lilac.py b/prepare/r-kissde/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kissde/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kissde/lilac.yaml b/prepare/r-kissde/lilac.yaml new file mode 100644 index 0000000000..408a36097f --- /dev/null +++ b/prepare/r-kissde/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aod +- r-biobase +- r-deseq2 +- r-doparallel +- r-dss +- r-foreach +- r-ggplot2 +- r-gplots +- r-matrixstats +update_on: +- regex: kissDE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/kissDE diff --git a/prepare/r-kknn/PKGBUILD b/prepare/r-kknn/PKGBUILD new file mode 100644 index 0000000000..40ec3142c2 --- /dev/null +++ b/prepare/r-kknn/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=kknn +_pkgver=1.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Weighted k-Nearest Neighbors' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-igraph +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kknn/lilac.py b/prepare/r-kknn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kknn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kknn/lilac.yaml b/prepare/r-kknn/lilac.yaml new file mode 100644 index 0000000000..194b1f771b --- /dev/null +++ b/prepare/r-kknn/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +update_on: +- regex: kknn_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=kknn diff --git a/prepare/r-klar/PKGBUILD b/prepare/r-klar/PKGBUILD new file mode 100644 index 0000000000..90a98bc7c1 --- /dev/null +++ b/prepare/r-klar/PKGBUILD @@ -0,0 +1,36 @@ +# system requirements: SVMlight +# Maintainer: Guoyi Zhang + +_pkgname=klaR +_pkgver=0.6-15 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Classification and Visualization' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-combinat + r-questionr +) +optdepends=( + r-e1071 + r-mlbench + r-rpart + r-scatterplot3d + r-som +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-klar/lilac.py b/prepare/r-klar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-klar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-klar/lilac.yaml b/prepare/r-klar/lilac.yaml new file mode 100644 index 0000000000..5f59bd53cc --- /dev/null +++ b/prepare/r-klar/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-combinat +- r-questionr +update_on: +- regex: klaR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=klaR diff --git a/prepare/r-km.ci/PKGBUILD b/prepare/r-km.ci/PKGBUILD new file mode 100644 index 0000000000..3ac0dc6c23 --- /dev/null +++ b/prepare/r-km.ci/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=km.ci +_pkgver=0.5-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Confidence intervals for the Kaplan-Meier estimator' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-km.ci/lilac.py b/prepare/r-km.ci/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-km.ci/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-km.ci/lilac.yaml b/prepare/r-km.ci/lilac.yaml new file mode 100644 index 0000000000..325dc1c150 --- /dev/null +++ b/prepare/r-km.ci/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: km.ci_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=km.ci diff --git a/prepare/r-kmer/PKGBUILD b/prepare/r-kmer/PKGBUILD new file mode 100644 index 0000000000..f0a71fce14 --- /dev/null +++ b/prepare/r-kmer/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=kmer +_pkgver=1.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast K-Mer Counting and Clustering for Biological Sequence Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-openssl + r-phylogram + r-rcpp +) +optdepends=( + r-ape + r-dendextend + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kmer/lilac.py b/prepare/r-kmer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kmer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kmer/lilac.yaml b/prepare/r-kmer/lilac.yaml new file mode 100644 index 0000000000..e1bc6a5fed --- /dev/null +++ b/prepare/r-kmer/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-openssl +- r-phylogram +- r-rcpp +update_on: +- regex: kmer_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=kmer diff --git a/prepare/r-kml/PKGBUILD b/prepare/r-kml/PKGBUILD new file mode 100644 index 0000000000..290fa1bef1 --- /dev/null +++ b/prepare/r-kml/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=kml +_pkgver=2.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='K-Means for Longitudinal Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-clv + r-longitudinaldata +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kml/lilac.py b/prepare/r-kml/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kml/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kml/lilac.yaml b/prepare/r-kml/lilac.yaml new file mode 100644 index 0000000000..2f4fff8ac1 --- /dev/null +++ b/prepare/r-kml/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clv +- r-longitudinaldata +update_on: +- regex: kml_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=kml diff --git a/prepare/r-kmlshape/PKGBUILD b/prepare/r-kmlshape/PKGBUILD new file mode 100644 index 0000000000..a5336a66a1 --- /dev/null +++ b/prepare/r-kmlshape/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=kmlShape +_pkgver=0.9.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='K-Means for Longitudinal Data using Shape-Respecting Distance' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-kml + r-longitudinaldata +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kmlshape/lilac.py b/prepare/r-kmlshape/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kmlshape/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kmlshape/lilac.yaml b/prepare/r-kmlshape/lilac.yaml new file mode 100644 index 0000000000..7b867fc8de --- /dev/null +++ b/prepare/r-kmlshape/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-kml +- r-longitudinaldata +update_on: +- regex: kmlShape_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=kmlShape diff --git a/prepare/r-kmsurv/PKGBUILD b/prepare/r-kmsurv/PKGBUILD new file mode 100644 index 0000000000..cf4f92ad16 --- /dev/null +++ b/prepare/r-kmsurv/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=KMsurv +_pkgver=0.1-5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data sets from Klein and Moeschberger (1997), Survival Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kmsurv/lilac.py b/prepare/r-kmsurv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kmsurv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kmsurv/lilac.yaml b/prepare/r-kmsurv/lilac.yaml new file mode 100644 index 0000000000..fc8255cc7e --- /dev/null +++ b/prepare/r-kmsurv/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: KMsurv_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=KMsurv diff --git a/prepare/r-knitr/PKGBUILD b/prepare/r-knitr/PKGBUILD new file mode 100644 index 0000000000..a26dc1674e --- /dev/null +++ b/prepare/r-knitr/PKGBUILD @@ -0,0 +1,61 @@ +# system requirements: Package vignettes based on R Markdown v2 orreStructuredText require Pandoc (http://pandoc.org). Thefunction rst2pdf() require rst2pdf(https://github.com/rst2pdf/rst2pdf). +# Maintainer: Guoyi Zhang + +_pkgname=knitr +_pkgver=1.37 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A General-Purpose Package for Dynamic Report Generation in R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-evaluate + r-highr + r-stringr + r-xfun + r-yaml +) +optdepends=( + r-bslib + r-codetools + r-dbi + r-digest + r-formatr + r-gifski + r-htmlwidgets + r-httr + r-jpeg + r-juliacall + r-magick + r-markdown + r-png + r-ragg + r-reticulate + r-rgl + r-rmarkdown + r-sass + r-showtext + r-styler + r-targets + r-testit + r-tibble + r-tikzdevice + r-tinytex + r-webshot + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-knitr/lilac.py b/prepare/r-knitr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-knitr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-knitr/lilac.yaml b/prepare/r-knitr/lilac.yaml new file mode 100644 index 0000000000..629dab6c30 --- /dev/null +++ b/prepare/r-knitr/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-evaluate +- r-highr +- r-stringr +- r-xfun +- r-yaml +update_on: +- regex: knitr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=knitr diff --git a/prepare/r-knitrbootstrap/PKGBUILD b/prepare/r-knitrbootstrap/PKGBUILD new file mode 100644 index 0000000000..687213d9a9 --- /dev/null +++ b/prepare/r-knitrbootstrap/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=knitrBootstrap +_pkgver=1.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'knitr' Bootstrap Framework" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-knitr + r-markdown + r-rmarkdown +) +optdepends=( + r-corrplot + r-ggplot2 + r-igraph + r-mapproj + r-maps + r-maptools + r-plyr + r-reshape2 + r-roxygen2 + r-testthat + r-xtable +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-knitrbootstrap/lilac.py b/prepare/r-knitrbootstrap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-knitrbootstrap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-knitrbootstrap/lilac.yaml b/prepare/r-knitrbootstrap/lilac.yaml new file mode 100644 index 0000000000..d76a36d3e9 --- /dev/null +++ b/prepare/r-knitrbootstrap/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-knitr +- r-markdown +- r-rmarkdown +update_on: +- regex: knitrBootstrap_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=knitrBootstrap diff --git a/prepare/r-knn.covertree/PKGBUILD b/prepare/r-knn.covertree/PKGBUILD new file mode 100644 index 0000000000..ec3d6ee054 --- /dev/null +++ b/prepare/r-knn.covertree/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=knn.covertree +_pkgver=1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Accurate kNN Implementation with Multiple Distance Measures' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('AGPL') +depends=( + r + r-rcpp + r-rcppeigen +) +optdepends=( + r-fnn + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-knn.covertree/lilac.py b/prepare/r-knn.covertree/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-knn.covertree/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-knn.covertree/lilac.yaml b/prepare/r-knn.covertree/lilac.yaml new file mode 100644 index 0000000000..7f07cf9777 --- /dev/null +++ b/prepare/r-knn.covertree/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcppeigen +update_on: +- regex: knn.covertree_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=knn.covertree diff --git a/prepare/r-knowseq/PKGBUILD b/prepare/r-knowseq/PKGBUILD new file mode 100644 index 0000000000..80f430feb5 --- /dev/null +++ b/prepare/r-knowseq/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=KnowSeq +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-caret + r-cqn + r-e1071 + r-edger + r-ggplot2 + r-gridextra + r-hmisc + r-httr + r-jsonlite + r-kernlab + r-limma + r-praznik + r-r.utils + r-randomforest + r-reshape2 + r-rlist + r-rmarkdown + r-stringr + r-sva + r-xml +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-knowseq/lilac.py b/prepare/r-knowseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-knowseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-knowseq/lilac.yaml b/prepare/r-knowseq/lilac.yaml new file mode 100644 index 0000000000..d2c94f0704 --- /dev/null +++ b/prepare/r-knowseq/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-caret +- r-cqn +- r-e1071 +- r-edger +- r-ggplot2 +- r-gridextra +- r-hmisc +- r-httr +- r-jsonlite +- r-kernlab +- r-limma +- r-praznik +- r-r.utils +- r-randomforest +- r-reshape2 +- r-rlist +- r-rmarkdown +- r-stringr +- r-sva +- r-xml +update_on: +- regex: KnowSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/KnowSeq diff --git a/prepare/r-kodata/PKGBUILD b/prepare/r-kodata/PKGBUILD new file mode 100644 index 0000000000..b461192f74 --- /dev/null +++ b/prepare/r-kodata/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=KOdata +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='LINCS Knock-Out Data Package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kodata/lilac.py b/prepare/r-kodata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kodata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kodata/lilac.yaml b/prepare/r-kodata/lilac.yaml new file mode 100644 index 0000000000..91cceb6fc4 --- /dev/null +++ b/prepare/r-kodata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: KOdata_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/KOdata diff --git a/prepare/r-kohonen/PKGBUILD b/prepare/r-kohonen/PKGBUILD new file mode 100644 index 0000000000..e729f2cbe8 --- /dev/null +++ b/prepare/r-kohonen/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=kohonen +_pkgver=3.0.10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Supervised and Unsupervised Self-Organising Maps' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kohonen/lilac.py b/prepare/r-kohonen/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kohonen/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kohonen/lilac.yaml b/prepare/r-kohonen/lilac.yaml new file mode 100644 index 0000000000..453bf07b55 --- /dev/null +++ b/prepare/r-kohonen/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: kohonen_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=kohonen diff --git a/prepare/r-korpus.lang.en/PKGBUILD b/prepare/r-korpus.lang.en/PKGBUILD new file mode 100644 index 0000000000..854f2c91f9 --- /dev/null +++ b/prepare/r-korpus.lang.en/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=koRpus.lang.en +_pkgver=0.1-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Language Support for 'koRpus' Package: English" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-korpus + r-sylly.en +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-korpus.lang.en/lilac.py b/prepare/r-korpus.lang.en/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-korpus.lang.en/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-korpus.lang.en/lilac.yaml b/prepare/r-korpus.lang.en/lilac.yaml new file mode 100644 index 0000000000..8c1521ee1e --- /dev/null +++ b/prepare/r-korpus.lang.en/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-korpus +- r-sylly.en +update_on: +- regex: koRpus.lang.en_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=koRpus.lang.en diff --git a/prepare/r-korpus/PKGBUILD b/prepare/r-korpus/PKGBUILD new file mode 100644 index 0000000000..f312935ab0 --- /dev/null +++ b/prepare/r-korpus/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=koRpus +_pkgver=0.13-8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Text Analysis with Emphasis on POS Tagging, Readability, and Lexical Diversity' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-sylly +) +optdepends=( + r-knitr + r-korpus.lang.de + r-korpus.lang.en + r-korpus.lang.es + r-korpus.lang.fr + r-korpus.lang.it + r-korpus.lang.nl + r-korpus.lang.pt + r-korpus.lang.ru + r-rkward + r-rmarkdown + r-shiny + r-snowballc + r-testthat + r-tm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-korpus/lilac.py b/prepare/r-korpus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-korpus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-korpus/lilac.yaml b/prepare/r-korpus/lilac.yaml new file mode 100644 index 0000000000..c69a6ee95d --- /dev/null +++ b/prepare/r-korpus/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-sylly +update_on: +- regex: koRpus_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=koRpus diff --git a/prepare/r-kpeaks/PKGBUILD b/prepare/r-kpeaks/PKGBUILD new file mode 100644 index 0000000000..560b84975f --- /dev/null +++ b/prepare/r-kpeaks/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=kpeaks +_pkgver=1.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Determination of K Using Peak Counts of Features for Clustering' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kpeaks/lilac.py b/prepare/r-kpeaks/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kpeaks/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kpeaks/lilac.yaml b/prepare/r-kpeaks/lilac.yaml new file mode 100644 index 0000000000..34cfdfb703 --- /dev/null +++ b/prepare/r-kpeaks/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: kpeaks_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=kpeaks diff --git a/prepare/r-kpmt/PKGBUILD b/prepare/r-kpmt/PKGBUILD new file mode 100644 index 0000000000..fa3817a17f --- /dev/null +++ b/prepare/r-kpmt/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=kpmt +_pkgver=0.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Known Population Median Test' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-matrixstats +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kpmt/lilac.py b/prepare/r-kpmt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kpmt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kpmt/lilac.yaml b/prepare/r-kpmt/lilac.yaml new file mode 100644 index 0000000000..c5b62c9681 --- /dev/null +++ b/prepare/r-kpmt/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-matrixstats +update_on: +- regex: kpmt_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=kpmt diff --git a/prepare/r-kriging/PKGBUILD b/prepare/r-kriging/PKGBUILD new file mode 100644 index 0000000000..6fb3340f01 --- /dev/null +++ b/prepare/r-kriging/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=kriging +_pkgver=1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Ordinary Kriging' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-maps +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-kriging/lilac.py b/prepare/r-kriging/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-kriging/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-kriging/lilac.yaml b/prepare/r-kriging/lilac.yaml new file mode 100644 index 0000000000..cfd1c0ff51 --- /dev/null +++ b/prepare/r-kriging/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: kriging_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=kriging diff --git a/prepare/r-ks/PKGBUILD b/prepare/r-ks/PKGBUILD new file mode 100644 index 0000000000..da064e405d --- /dev/null +++ b/prepare/r-ks/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ks +_pkgver=1.13.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Kernel Smoothing' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-fnn + r-kernlab + r-mclust + r-multicool + r-mvtnorm + r-plot3d + r-pracma +) +optdepends=( + r-geometry + r-mass + r-misc3d + r-oz + r-rgl +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ks/lilac.py b/prepare/r-ks/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ks/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ks/lilac.yaml b/prepare/r-ks/lilac.yaml new file mode 100644 index 0000000000..6dc3378371 --- /dev/null +++ b/prepare/r-ks/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fnn +- r-kernlab +- r-mclust +- r-multicool +- r-mvtnorm +- r-plot3d +- r-pracma +update_on: +- regex: ks_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ks diff --git a/prepare/r-ksamples/PKGBUILD b/prepare/r-ksamples/PKGBUILD new file mode 100644 index 0000000000..4d16a384a5 --- /dev/null +++ b/prepare/r-ksamples/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=kSamples +_pkgver=1.2-9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='K-Sample Rank Tests and their Combinations' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-suppdists +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ksamples/lilac.py b/prepare/r-ksamples/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ksamples/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ksamples/lilac.yaml b/prepare/r-ksamples/lilac.yaml new file mode 100644 index 0000000000..4bb3afdf76 --- /dev/null +++ b/prepare/r-ksamples/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-suppdists +update_on: +- regex: kSamples_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=kSamples diff --git a/prepare/r-labeling/PKGBUILD b/prepare/r-labeling/PKGBUILD new file mode 100644 index 0000000000..686a2feaf8 --- /dev/null +++ b/prepare/r-labeling/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=labeling +_pkgver=0.4.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Axis Labeling' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-labeling/lilac.py b/prepare/r-labeling/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-labeling/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-labeling/lilac.yaml b/prepare/r-labeling/lilac.yaml new file mode 100644 index 0000000000..040d2558ac --- /dev/null +++ b/prepare/r-labeling/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: labeling_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=labeling diff --git a/prepare/r-labelled/PKGBUILD b/prepare/r-labelled/PKGBUILD new file mode 100644 index 0000000000..9417f424b8 --- /dev/null +++ b/prepare/r-labelled/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=labelled +_pkgver=2.9.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Manipulating Labelled Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-haven + r-lifecycle + r-rlang + r-stringr + r-tidyr + r-vctrs +) +optdepends=( + r-covr + r-knitr + r-memisc + r-questionr + r-rmarkdown + r-snakecase + r-spelling + r-testthat + r-utf8 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-labelled/lilac.py b/prepare/r-labelled/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-labelled/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-labelled/lilac.yaml b/prepare/r-labelled/lilac.yaml new file mode 100644 index 0000000000..7da279b656 --- /dev/null +++ b/prepare/r-labelled/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-haven +- r-lifecycle +- r-rlang +- r-stringr +- r-tidyr +- r-vctrs +update_on: +- regex: labelled_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=labelled diff --git a/prepare/r-lace/PKGBUILD b/prepare/r-lace/PKGBUILD new file mode 100644 index 0000000000..e75ac76656 --- /dev/null +++ b/prepare/r-lace/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LACE +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Longitudinal Analysis of Cancer Evolution (LACE)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-data.tree + r-igraph + r-rcolorbrewer + r-rfast + r-summarizedexperiment +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lace/lilac.py b/prepare/r-lace/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lace/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lace/lilac.yaml b/prepare/r-lace/lilac.yaml new file mode 100644 index 0000000000..9402033625 --- /dev/null +++ b/prepare/r-lace/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.tree +- r-igraph +- r-rcolorbrewer +- r-rfast +- r-summarizedexperiment +update_on: +- regex: LACE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LACE diff --git a/prepare/r-laeken/PKGBUILD b/prepare/r-laeken/PKGBUILD new file mode 100644 index 0000000000..71ab8fd1ab --- /dev/null +++ b/prepare/r-laeken/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=laeken +_pkgver=0.5.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimation of Indicators on Social Exclusion and Poverty' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-laeken/lilac.py b/prepare/r-laeken/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-laeken/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-laeken/lilac.yaml b/prepare/r-laeken/lilac.yaml new file mode 100644 index 0000000000..fee6c270a0 --- /dev/null +++ b/prepare/r-laeken/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: laeken_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=laeken diff --git a/prepare/r-laplacesdemon/PKGBUILD b/prepare/r-laplacesdemon/PKGBUILD new file mode 100644 index 0000000000..8322b5e376 --- /dev/null +++ b/prepare/r-laplacesdemon/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LaplacesDemon +_pkgver=16.1.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Complete Environment for Bayesian Inference' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-kernsmooth +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-laplacesdemon/lilac.py b/prepare/r-laplacesdemon/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-laplacesdemon/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-laplacesdemon/lilac.yaml b/prepare/r-laplacesdemon/lilac.yaml new file mode 100644 index 0000000000..2aec8e5bc5 --- /dev/null +++ b/prepare/r-laplacesdemon/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: LaplacesDemon_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=LaplacesDemon diff --git a/prepare/r-lapmix/PKGBUILD b/prepare/r-lapmix/PKGBUILD new file mode 100644 index 0000000000..14154f4dc5 --- /dev/null +++ b/prepare/r-lapmix/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lapmix +_pkgver=1.60.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Laplace Mixture Model in Microarray Experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lapmix/lilac.py b/prepare/r-lapmix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lapmix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lapmix/lilac.yaml b/prepare/r-lapmix/lilac.yaml new file mode 100644 index 0000000000..08e5769134 --- /dev/null +++ b/prepare/r-lapmix/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: lapmix_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/lapmix diff --git a/prepare/r-lars/PKGBUILD b/prepare/r-lars/PKGBUILD new file mode 100644 index 0000000000..c5e2670cbe --- /dev/null +++ b/prepare/r-lars/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lars +_pkgver=1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Least Angle Regression, Lasso and Forward Stagewise' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lars/lilac.py b/prepare/r-lars/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lars/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lars/lilac.yaml b/prepare/r-lars/lilac.yaml new file mode 100644 index 0000000000..05de8208b3 --- /dev/null +++ b/prepare/r-lars/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: lars_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lars diff --git a/prepare/r-lasso2/PKGBUILD b/prepare/r-lasso2/PKGBUILD new file mode 100644 index 0000000000..c35679c19a --- /dev/null +++ b/prepare/r-lasso2/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lasso2 +_pkgver=1.2-22 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="L1 Constrained Estimation aka `lasso'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lasso2/lilac.py b/prepare/r-lasso2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lasso2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lasso2/lilac.yaml b/prepare/r-lasso2/lilac.yaml new file mode 100644 index 0000000000..c9bc545345 --- /dev/null +++ b/prepare/r-lasso2/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: lasso2_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lasso2 diff --git a/prepare/r-lassopv/PKGBUILD b/prepare/r-lassopv/PKGBUILD new file mode 100644 index 0000000000..6c4d1b63f1 --- /dev/null +++ b/prepare/r-lassopv/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lassopv +_pkgver=0.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Nonparametric P-Value Estimation for Predictors in Lasso' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-lars +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lassopv/lilac.py b/prepare/r-lassopv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lassopv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lassopv/lilac.yaml b/prepare/r-lassopv/lilac.yaml new file mode 100644 index 0000000000..7241976ad9 --- /dev/null +++ b/prepare/r-lassopv/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lars +update_on: +- regex: lassopv_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lassopv diff --git a/prepare/r-later/PKGBUILD b/prepare/r-later/PKGBUILD new file mode 100644 index 0000000000..377d607b12 --- /dev/null +++ b/prepare/r-later/PKGBUILD @@ -0,0 +1,35 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=later +_pkgver=1.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities for Scheduling Functions to Execute Later with Event Loops' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-rcpp + r-rlang +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-later/lilac.py b/prepare/r-later/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-later/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-later/lilac.yaml b/prepare/r-later/lilac.yaml new file mode 100644 index 0000000000..e290fa4ee9 --- /dev/null +++ b/prepare/r-later/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rlang +update_on: +- regex: later_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=later diff --git a/prepare/r-latex2exp/PKGBUILD b/prepare/r-latex2exp/PKGBUILD new file mode 100644 index 0000000000..583daa2740 --- /dev/null +++ b/prepare/r-latex2exp/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=latex2exp +_pkgver=0.5.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Use LaTeX Expressions in Plots' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-magrittr + r-stringr +) +optdepends=( + r-ggplot2 + r-knitr + r-plyr + r-purrr + r-rmarkdown + r-testthat + r-tibble +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-latex2exp/lilac.py b/prepare/r-latex2exp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-latex2exp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-latex2exp/lilac.yaml b/prepare/r-latex2exp/lilac.yaml new file mode 100644 index 0000000000..66e46eda6f --- /dev/null +++ b/prepare/r-latex2exp/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-magrittr +- r-stringr +update_on: +- regex: latex2exp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=latex2exp diff --git a/prepare/r-lattice/PKGBUILD b/prepare/r-lattice/PKGBUILD new file mode 100644 index 0000000000..c8b16fc8c6 --- /dev/null +++ b/prepare/r-lattice/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lattice +_pkgver=0.20-45 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Trellis Graphics for R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-chron + r-kernsmooth + r-latticeextra + r-mass +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lattice/lilac.py b/prepare/r-lattice/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lattice/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lattice/lilac.yaml b/prepare/r-lattice/lilac.yaml new file mode 100644 index 0000000000..93f00eeccd --- /dev/null +++ b/prepare/r-lattice/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: lattice_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lattice diff --git a/prepare/r-latticeextra/PKGBUILD b/prepare/r-latticeextra/PKGBUILD new file mode 100644 index 0000000000..8f3a097d10 --- /dev/null +++ b/prepare/r-latticeextra/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=latticeExtra +_pkgver=0.6-29 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Extra Graphical Utilities Based on Lattice' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-jpeg + r-png + r-rcolorbrewer +) +optdepends=( + r-deldir + r-mapproj + r-maps + r-mass + r-mgcv + r-quantreg + r-tripack + r-zoo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-latticeextra/lilac.py b/prepare/r-latticeextra/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-latticeextra/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-latticeextra/lilac.yaml b/prepare/r-latticeextra/lilac.yaml new file mode 100644 index 0000000000..bd85876cdc --- /dev/null +++ b/prepare/r-latticeextra/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-jpeg +- r-png +- r-rcolorbrewer +update_on: +- regex: latticeExtra_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=latticeExtra diff --git a/prepare/r-lava/PKGBUILD b/prepare/r-lava/PKGBUILD new file mode 100644 index 0000000000..596e3816a4 --- /dev/null +++ b/prepare/r-lava/PKGBUILD @@ -0,0 +1,59 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lava +_pkgver=1.6.10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Latent Variable Models' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-future.apply + r-numderiv + r-progressr + r-squarem +) +optdepends=( + r-bookdown + r-data.table + r-ellipse + r-fields + r-geepack + r-gof + r-graph + r-igraph + r-kernsmooth + r-knitr + r-lava.tobit + r-lavasearch2 + r-lme4 + r-magrittr + r-matrix + r-mets + r-nlme + r-optimx + r-polycor + r-quantreg + r-r.rsp + r-rgl + r-rgraphviz + r-rmarkdown + r-testthat + r-visnetwork + r-zoo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lava/lilac.py b/prepare/r-lava/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lava/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lava/lilac.yaml b/prepare/r-lava/lilac.yaml new file mode 100644 index 0000000000..b358afdf98 --- /dev/null +++ b/prepare/r-lava/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-future.apply +- r-numderiv +- r-progressr +- r-squarem +update_on: +- regex: lava_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lava diff --git a/prepare/r-lazyeval/PKGBUILD b/prepare/r-lazyeval/PKGBUILD new file mode 100644 index 0000000000..5ce44664d5 --- /dev/null +++ b/prepare/r-lazyeval/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lazyeval +_pkgver=0.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Lazy (Non-Standard) Evaluation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lazyeval/lilac.py b/prepare/r-lazyeval/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lazyeval/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lazyeval/lilac.yaml b/prepare/r-lazyeval/lilac.yaml new file mode 100644 index 0000000000..38acea460e --- /dev/null +++ b/prepare/r-lazyeval/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: lazyeval_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lazyeval diff --git a/prepare/r-lbe/PKGBUILD b/prepare/r-lbe/PKGBUILD new file mode 100644 index 0000000000..3dc2592474 --- /dev/null +++ b/prepare/r-lbe/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LBE +_pkgver=1.62.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimation of the false discovery rate.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-qvalue +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lbe/lilac.py b/prepare/r-lbe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lbe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lbe/lilac.yaml b/prepare/r-lbe/lilac.yaml new file mode 100644 index 0000000000..e7ea591c1d --- /dev/null +++ b/prepare/r-lbe/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: LBE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LBE diff --git a/prepare/r-ldblock/PKGBUILD b/prepare/r-ldblock/PKGBUILD new file mode 100644 index 0000000000..1ff3bbec7e --- /dev/null +++ b/prepare/r-ldblock/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ldblock +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='data structures for linkage disequilibrium measures in populations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-ensdb.hsapiens.v75 + r-ensembldb + r-genomeinfodb + r-genomicfiles + r-httr + r-rsamtools + r-snpstats + r-variantannotation +) +optdepends=( + r-biocstyle + r-gwascat + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ldblock/lilac.py b/prepare/r-ldblock/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ldblock/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ldblock/lilac.yaml b/prepare/r-ldblock/lilac.yaml new file mode 100644 index 0000000000..6449c88b8d --- /dev/null +++ b/prepare/r-ldblock/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-ensdb.hsapiens.v75 +- r-ensembldb +- r-genomeinfodb +- r-genomicfiles +- r-httr +- r-rsamtools +- r-snpstats +- r-variantannotation +update_on: +- regex: ldblock_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ldblock diff --git a/prepare/r-lea/PKGBUILD b/prepare/r-lea/PKGBUILD new file mode 100644 index 0000000000..2f332d2bfb --- /dev/null +++ b/prepare/r-lea/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LEA +_pkgver=3.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='LEA: an R package for Landscape and Ecological Association Studies' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lea/lilac.py b/prepare/r-lea/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lea/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lea/lilac.yaml b/prepare/r-lea/lilac.yaml new file mode 100644 index 0000000000..630fad1377 --- /dev/null +++ b/prepare/r-lea/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: LEA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LEA diff --git a/prepare/r-leaps/PKGBUILD b/prepare/r-leaps/PKGBUILD new file mode 100644 index 0000000000..26f8491840 --- /dev/null +++ b/prepare/r-leaps/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=leaps +_pkgver=3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Regression Subset Selection' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biglm +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-leaps/lilac.py b/prepare/r-leaps/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-leaps/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-leaps/lilac.yaml b/prepare/r-leaps/lilac.yaml new file mode 100644 index 0000000000..3750c81f7b --- /dev/null +++ b/prepare/r-leaps/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: leaps_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=leaps diff --git a/prepare/r-learnr/PKGBUILD b/prepare/r-learnr/PKGBUILD new file mode 100644 index 0000000000..8e64f5d160 --- /dev/null +++ b/prepare/r-learnr/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=learnr +_pkgver=0.10.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive Tutorials for R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-checkmate + r-ellipsis + r-evaluate + r-htmltools + r-htmlwidgets + r-jsonlite + r-knitr + r-markdown + r-rappdirs + r-renv + r-rmarkdown + r-rprojroot + r-shiny + r-withr +) +optdepends=( + r-callr + r-rlang + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-learnr/lilac.py b/prepare/r-learnr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-learnr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-learnr/lilac.yaml b/prepare/r-learnr/lilac.yaml new file mode 100644 index 0000000000..058287737a --- /dev/null +++ b/prepare/r-learnr/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-checkmate +- r-ellipsis +- r-evaluate +- r-htmltools +- r-htmlwidgets +- r-jsonlite +- r-knitr +- r-markdown +- r-rappdirs +- r-renv +- r-rmarkdown +- r-rprojroot +- r-shiny +- r-withr +update_on: +- regex: learnr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=learnr diff --git a/prepare/r-ledpred/PKGBUILD b/prepare/r-ledpred/PKGBUILD new file mode 100644 index 0000000000..c8d750cd8a --- /dev/null +++ b/prepare/r-ledpred/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LedPred +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Learning from DNA to Predict Enhancers' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-akima + r-e1071 + r-ggplot2 + r-irr + r-jsonlite + r-plot3d + r-plyr + r-rcurl + r-rocr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ledpred/lilac.py b/prepare/r-ledpred/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ledpred/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ledpred/lilac.yaml b/prepare/r-ledpred/lilac.yaml new file mode 100644 index 0000000000..6f9f868f18 --- /dev/null +++ b/prepare/r-ledpred/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-akima +- r-e1071 +- r-ggplot2 +- r-irr +- r-jsonlite +- r-plot3d +- r-plyr +- r-rcurl +- r-rocr +- r-testthat +update_on: +- regex: LedPred_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LedPred diff --git a/prepare/r-lefser/PKGBUILD b/prepare/r-lefser/PKGBUILD new file mode 100644 index 0000000000..00380a6a28 --- /dev/null +++ b/prepare/r-lefser/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lefser +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R implementation of the LEfSE method for microbiome biomarker discovery' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-coin + r-ggplot2 + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-covr + r-curatedmetagenomicdata + r-knitr + r-pkgdown + r-rmarkdown + r-testthat + r-withr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lefser/lilac.py b/prepare/r-lefser/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lefser/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lefser/lilac.yaml b/prepare/r-lefser/lilac.yaml new file mode 100644 index 0000000000..99131baac2 --- /dev/null +++ b/prepare/r-lefser/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-coin +- r-ggplot2 +- r-summarizedexperiment +update_on: +- regex: lefser_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/lefser diff --git a/prepare/r-leiden/PKGBUILD b/prepare/r-leiden/PKGBUILD new file mode 100644 index 0000000000..9dd4a581e9 --- /dev/null +++ b/prepare/r-leiden/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=leiden +_pkgver=0.3.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Implementation of Leiden Clustering Algorithm' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-igraph + r-reticulate +) +optdepends=( + r-bipartite + r-covr + r-data.table + r-devtools + r-graphsim + r-knitr + r-markdown + r-multinet + r-multiplex + r-network + r-rcolorbrewer + r-rmarkdown + r-spelling + r-testthat + r-tibble +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-leiden/lilac.py b/prepare/r-leiden/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-leiden/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-leiden/lilac.yaml b/prepare/r-leiden/lilac.yaml new file mode 100644 index 0000000000..4e0e0898bc --- /dev/null +++ b/prepare/r-leiden/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +- r-reticulate +update_on: +- regex: leiden_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=leiden diff --git a/prepare/r-les/PKGBUILD b/prepare/r-les/PKGBUILD new file mode 100644 index 0000000000..68808a916a --- /dev/null +++ b/prepare/r-les/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=les +_pkgver=1.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identifying Differential Effects in Tiling Microarray Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-fdrtool + r-gplots + r-rcolorbrewer +) +optdepends=( + r-biobase + r-limma + r-parallel +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-les/lilac.py b/prepare/r-les/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-les/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-les/lilac.yaml b/prepare/r-les/lilac.yaml new file mode 100644 index 0000000000..03b5bc0185 --- /dev/null +++ b/prepare/r-les/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fdrtool +- r-gplots +- r-rcolorbrewer +update_on: +- regex: les_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/les diff --git a/prepare/r-levi/PKGBUILD b/prepare/r-levi/PKGBUILD new file mode 100644 index 0000000000..f5b1344ae6 --- /dev/null +++ b/prepare/r-levi/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=levi +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Landscape Expression Visualization Interface' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-colorspace + r-dplyr + r-dt + r-ggplot2 + r-httr + r-igraph + r-knitr + r-rcolorbrewer + r-rcpp + r-reshape2 + r-rmarkdown + r-shiny + r-shinydashboard + r-shinyjs + r-testthat + r-xml2 +) +optdepends=( + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-levi/lilac.py b/prepare/r-levi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-levi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-levi/lilac.yaml b/prepare/r-levi/lilac.yaml new file mode 100644 index 0000000000..dce6e057f4 --- /dev/null +++ b/prepare/r-levi/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colorspace +- r-dplyr +- r-dt +- r-ggplot2 +- r-httr +- r-igraph +- r-knitr +- r-rcolorbrewer +- r-rcpp +- r-reshape2 +- r-rmarkdown +- r-shiny +- r-shinydashboard +- r-shinyjs +- r-testthat +- r-xml2 +update_on: +- regex: levi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/levi diff --git a/prepare/r-lexicon/PKGBUILD b/prepare/r-lexicon/PKGBUILD new file mode 100644 index 0000000000..6b7ebef455 --- /dev/null +++ b/prepare/r-lexicon/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lexicon +_pkgver=1.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Lexicons for Text Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-syuzhet +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lexicon/lilac.py b/prepare/r-lexicon/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lexicon/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lexicon/lilac.yaml b/prepare/r-lexicon/lilac.yaml new file mode 100644 index 0000000000..74e6142994 --- /dev/null +++ b/prepare/r-lexicon/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-syuzhet +update_on: +- regex: lexicon_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lexicon diff --git a/prepare/r-lfa/PKGBUILD b/prepare/r-lfa/PKGBUILD new file mode 100644 index 0000000000..dbb89ba3e2 --- /dev/null +++ b/prepare/r-lfa/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lfa +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Logistic Factor Analysis for Categorical Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-corpcor +) +optdepends=( + r-ggplot2 + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lfa/lilac.py b/prepare/r-lfa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lfa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lfa/lilac.yaml b/prepare/r-lfa/lilac.yaml new file mode 100644 index 0000000000..3fbbb55e03 --- /dev/null +++ b/prepare/r-lfa/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-corpcor +update_on: +- regex: lfa_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/lfa diff --git a/prepare/r-lfda/PKGBUILD b/prepare/r-lfda/PKGBUILD new file mode 100644 index 0000000000..b8cfd06ca6 --- /dev/null +++ b/prepare/r-lfda/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lfda +_pkgver=1.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Local Fisher Discriminant Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-plyr + r-rarpack +) +optdepends=( + r-rgl + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lfda/lilac.py b/prepare/r-lfda/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lfda/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lfda/lilac.yaml b/prepare/r-lfda/lilac.yaml new file mode 100644 index 0000000000..e9312e272e --- /dev/null +++ b/prepare/r-lfda/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-plyr +- r-rarpack +update_on: +- regex: lfda_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lfda diff --git a/prepare/r-lgr/PKGBUILD b/prepare/r-lgr/PKGBUILD new file mode 100644 index 0000000000..bc448bc3da --- /dev/null +++ b/prepare/r-lgr/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lgr +_pkgver=0.4.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Fully Featured Logging Framework' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-r6 +) +optdepends=( + r-cli + r-covr + r-crayon + r-data.table + r-desc + r-future + r-future.apply + r-glue + r-jsonlite + r-knitr + r-rmarkdown + r-rotor + r-rprojroot + r-testthat + r-tibble + r-tools + r-utils + r-whoami + r-yaml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lgr/lilac.py b/prepare/r-lgr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lgr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lgr/lilac.yaml b/prepare/r-lgr/lilac.yaml new file mode 100644 index 0000000000..df563442df --- /dev/null +++ b/prepare/r-lgr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-r6 +update_on: +- regex: lgr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lgr diff --git a/prepare/r-lhs/PKGBUILD b/prepare/r-lhs/PKGBUILD new file mode 100644 index 0000000000..3254d1bc44 --- /dev/null +++ b/prepare/r-lhs/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lhs +_pkgver=1.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Latin Hypercube Samples' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-assertthat + r-covr + r-doe.base + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lhs/lilac.py b/prepare/r-lhs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lhs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lhs/lilac.yaml b/prepare/r-lhs/lilac.yaml new file mode 100644 index 0000000000..e01841f09e --- /dev/null +++ b/prepare/r-lhs/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: lhs_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lhs diff --git a/prepare/r-libcoin/PKGBUILD b/prepare/r-libcoin/PKGBUILD new file mode 100644 index 0000000000..73e571b627 --- /dev/null +++ b/prepare/r-libcoin/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=libcoin +_pkgver=1.0-9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Linear Test Statistics for Permutation Inference' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mvtnorm +) +optdepends=( + r-coin +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-libcoin/lilac.py b/prepare/r-libcoin/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-libcoin/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-libcoin/lilac.yaml b/prepare/r-libcoin/lilac.yaml new file mode 100644 index 0000000000..1ed36f3ac4 --- /dev/null +++ b/prepare/r-libcoin/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mvtnorm +update_on: +- regex: libcoin_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=libcoin diff --git a/prepare/r-liblinear/PKGBUILD b/prepare/r-liblinear/PKGBUILD new file mode 100644 index 0000000000..9eb1e698d8 --- /dev/null +++ b/prepare/r-liblinear/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LiblineaR +_pkgver=2.10-12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Linear Predictive Models Based on the LIBLINEAR C/C++ Library' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-matrix + r-sparsem +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-liblinear/lilac.py b/prepare/r-liblinear/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-liblinear/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-liblinear/lilac.yaml b/prepare/r-liblinear/lilac.yaml new file mode 100644 index 0000000000..5efe19d8a4 --- /dev/null +++ b/prepare/r-liblinear/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: LiblineaR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=LiblineaR diff --git a/prepare/r-lim/PKGBUILD b/prepare/r-lim/PKGBUILD new file mode 100644 index 0000000000..676ebccd22 --- /dev/null +++ b/prepare/r-lim/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LIM +_pkgver=1.4.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Linear Inverse Model examples and solution methods.' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-diagram + r-limsolve +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lim/lilac.py b/prepare/r-lim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lim/lilac.yaml b/prepare/r-lim/lilac.yaml new file mode 100644 index 0000000000..0819a08474 --- /dev/null +++ b/prepare/r-lim/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-diagram +- r-limsolve +update_on: +- regex: LIM_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=LIM diff --git a/prepare/r-limma/PKGBUILD b/prepare/r-limma/PKGBUILD new file mode 100644 index 0000000000..96dd0fd8c7 --- /dev/null +++ b/prepare/r-limma/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=limma +_pkgver=3.50.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Linear Models for Microarray Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-affy + r-annotationdbi + r-biasedurn + r-biobase + r-ellipse + r-go.db + r-gplots + r-illuminaio + r-locfit + r-mass + r-org.hs.eg.db + r-splines + r-statmod + r-vsn +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-limma/lilac.py b/prepare/r-limma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-limma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-limma/lilac.yaml b/prepare/r-limma/lilac.yaml new file mode 100644 index 0000000000..831f177be3 --- /dev/null +++ b/prepare/r-limma/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: limma_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/limma diff --git a/prepare/r-limmagui/PKGBUILD b/prepare/r-limmagui/PKGBUILD new file mode 100644 index 0000000000..704d3016c5 --- /dev/null +++ b/prepare/r-limmagui/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=limmaGUI +_pkgver=1.70.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GUI for limma Package With Two Color Microarrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-limma + r-r2html + r-tkrplot + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-limmagui/lilac.py b/prepare/r-limmagui/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-limmagui/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-limmagui/lilac.yaml b/prepare/r-limmagui/lilac.yaml new file mode 100644 index 0000000000..9ecdab3477 --- /dev/null +++ b/prepare/r-limmagui/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-limma +- r-r2html +- r-tkrplot +- r-xtable +update_on: +- regex: limmaGUI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/limmaGUI diff --git a/prepare/r-limsolve/PKGBUILD b/prepare/r-limsolve/PKGBUILD new file mode 100644 index 0000000000..3020a5ea85 --- /dev/null +++ b/prepare/r-limsolve/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=limSolve +_pkgver=1.5.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Solving Linear Inverse Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-lpsolve + r-quadprog +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-limsolve/lilac.py b/prepare/r-limsolve/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-limsolve/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-limsolve/lilac.yaml b/prepare/r-limsolve/lilac.yaml new file mode 100644 index 0000000000..f92fcff775 --- /dev/null +++ b/prepare/r-limsolve/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lpsolve +- r-quadprog +update_on: +- regex: limSolve_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=limSolve diff --git a/prepare/r-lineagepulse/PKGBUILD b/prepare/r-lineagepulse/PKGBUILD new file mode 100644 index 0000000000..643f26200a --- /dev/null +++ b/prepare/r-lineagepulse/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LineagePulse +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential expression analysis and model fitting for single-cell RNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-circlize + r-complexheatmap + r-ggplot2 + r-gplots + r-knitr + r-rcolorbrewer + r-singlecellexperiment + r-summarizedexperiment +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lineagepulse/lilac.py b/prepare/r-lineagepulse/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lineagepulse/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lineagepulse/lilac.yaml b/prepare/r-lineagepulse/lilac.yaml new file mode 100644 index 0000000000..c7e87430a2 --- /dev/null +++ b/prepare/r-lineagepulse/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-circlize +- r-complexheatmap +- r-ggplot2 +- r-gplots +- r-knitr +- r-rcolorbrewer +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: LineagePulse_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LineagePulse diff --git a/prepare/r-linkcomm/PKGBUILD b/prepare/r-linkcomm/PKGBUILD new file mode 100644 index 0000000000..3575fb917a --- /dev/null +++ b/prepare/r-linkcomm/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=linkcomm +_pkgver=1.0-14 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Generating, Visualizing, and Analysing Link Communities in Networks' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dynamictreecut + r-igraph + r-rcolorbrewer +) +optdepends=( + r-fastcluster + r-r.rsp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-linkcomm/lilac.py b/prepare/r-linkcomm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-linkcomm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-linkcomm/lilac.yaml b/prepare/r-linkcomm/lilac.yaml new file mode 100644 index 0000000000..231c116c67 --- /dev/null +++ b/prepare/r-linkcomm/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dynamictreecut +- r-igraph +- r-rcolorbrewer +update_on: +- regex: linkcomm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=linkcomm diff --git a/prepare/r-linkhd/PKGBUILD b/prepare/r-linkhd/PKGBUILD new file mode 100644 index 0000000000..7e5a8c6bf6 --- /dev/null +++ b/prepare/r-linkhd/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LinkHD +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='LinkHD: a versatile framework to explore and integrate heterogeneous data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-emmeans + r-ggplot2 + r-ggpubr + r-gridextra + r-multiassayexperiment + r-reshape2 + r-rio + r-scales + r-vegan +) +optdepends=( + r-biocstyle + r-knitr + r-mass + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-linkhd/lilac.py b/prepare/r-linkhd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-linkhd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-linkhd/lilac.yaml b/prepare/r-linkhd/lilac.yaml new file mode 100644 index 0000000000..794c38b4ce --- /dev/null +++ b/prepare/r-linkhd/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-emmeans +- r-ggplot2 +- r-ggpubr +- r-gridextra +- r-multiassayexperiment +- r-reshape2 +- r-rio +- r-scales +- r-vegan +update_on: +- regex: LinkHD_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LinkHD diff --git a/prepare/r-linnorm/PKGBUILD b/prepare/r-linnorm/PKGBUILD new file mode 100644 index 0000000000..3b5a1e0af2 --- /dev/null +++ b/prepare/r-linnorm/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Linnorm +_pkgver=2.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Linear model and normality based normalization and transformation method (Linnorm)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-amap + r-apcluster + r-ellipse + r-fastcluster + r-fpc + r-ggdendro + r-ggplot2 + r-gmodels + r-igraph + r-limma + r-mclust + r-rcpp + r-rcpparmadillo + r-rtsne + r-statmod + r-vegan + r-zoo +) +optdepends=( + r-biocstyle + r-gplots + r-knitr + r-markdown + r-moments + r-rcolorbrewer + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-linnorm/lilac.py b/prepare/r-linnorm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-linnorm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-linnorm/lilac.yaml b/prepare/r-linnorm/lilac.yaml new file mode 100644 index 0000000000..7aa55d41c6 --- /dev/null +++ b/prepare/r-linnorm/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-amap +- r-apcluster +- r-ellipse +- r-fastcluster +- r-fpc +- r-ggdendro +- r-ggplot2 +- r-gmodels +- r-igraph +- r-limma +- r-mclust +- r-rcpp +- r-rcpparmadillo +- r-rtsne +- r-statmod +- r-vegan +- r-zoo +update_on: +- regex: Linnorm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Linnorm diff --git a/prepare/r-linprog/PKGBUILD b/prepare/r-linprog/PKGBUILD new file mode 100644 index 0000000000..426cc38fee --- /dev/null +++ b/prepare/r-linprog/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=linprog +_pkgver=0.9-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Linear Programming / Optimization' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-lpsolve +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-linprog/lilac.py b/prepare/r-linprog/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-linprog/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-linprog/lilac.yaml b/prepare/r-linprog/lilac.yaml new file mode 100644 index 0000000000..63a17a4635 --- /dev/null +++ b/prepare/r-linprog/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lpsolve +update_on: +- regex: linprog_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=linprog diff --git a/prepare/r-lionessr/PKGBUILD b/prepare/r-lionessr/PKGBUILD new file mode 100644 index 0000000000..a101581f1b --- /dev/null +++ b/prepare/r-lionessr/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lionessR +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Modeling networks for individual samples using LIONESS' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-igraph + r-knitr + r-limma + r-reshape2 + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lionessr/lilac.py b/prepare/r-lionessr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lionessr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lionessr/lilac.yaml b/prepare/r-lionessr/lilac.yaml new file mode 100644 index 0000000000..a6c346fda4 --- /dev/null +++ b/prepare/r-lionessr/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: lionessR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/lionessR diff --git a/prepare/r-lipidr/PKGBUILD b/prepare/r-lipidr/PKGBUILD new file mode 100644 index 0000000000..148ccc55b1 --- /dev/null +++ b/prepare/r-lipidr/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lipidr +_pkgver=2.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data Mining and Analysis of Lipidomics Datasets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-data.table + r-dplyr + r-fgsea + r-forcats + r-ggplot2 + r-imputelcmd + r-limma + r-magrittr + r-rlang + r-ropls + r-s4vectors + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-biocstyle + r-ggrepel + r-iheatmapr + r-knitr + r-plotly + r-rmarkdown + r-spelling + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lipidr/lilac.py b/prepare/r-lipidr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lipidr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lipidr/lilac.yaml b/prepare/r-lipidr/lilac.yaml new file mode 100644 index 0000000000..235fa17887 --- /dev/null +++ b/prepare/r-lipidr/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-dplyr +- r-fgsea +- r-forcats +- r-ggplot2 +- r-imputelcmd +- r-limma +- r-magrittr +- r-rlang +- r-ropls +- r-s4vectors +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: lipidr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/lipidr diff --git a/prepare/r-liquidassociation/PKGBUILD b/prepare/r-liquidassociation/PKGBUILD new file mode 100644 index 0000000000..8d5f6864f9 --- /dev/null +++ b/prepare/r-liquidassociation/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LiquidAssociation +_pkgver=1.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='LiquidAssociation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-geepack + r-org.sc.sgd.db + r-yeastcc +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-liquidassociation/lilac.py b/prepare/r-liquidassociation/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-liquidassociation/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-liquidassociation/lilac.yaml b/prepare/r-liquidassociation/lilac.yaml new file mode 100644 index 0000000000..c2aec07566 --- /dev/null +++ b/prepare/r-liquidassociation/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-geepack +- r-org.sc.sgd.db +- r-yeastcc +update_on: +- regex: LiquidAssociation_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LiquidAssociation diff --git a/prepare/r-lisaclust/PKGBUILD b/prepare/r-lisaclust/PKGBUILD new file mode 100644 index 0000000000..45e85772dd --- /dev/null +++ b/prepare/r-lisaclust/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lisaClust +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='lisaClust: Clustering of Local Indicators of Spatial Association' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-concaveman + r-data.table + r-dplyr + r-ggplot2 + r-purrr + r-s4vectors + r-spatstat.core + r-spatstat.geom + r-spicyr + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lisaclust/lilac.py b/prepare/r-lisaclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lisaclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lisaclust/lilac.yaml b/prepare/r-lisaclust/lilac.yaml new file mode 100644 index 0000000000..89a6f14d6f --- /dev/null +++ b/prepare/r-lisaclust/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-concaveman +- r-data.table +- r-dplyr +- r-ggplot2 +- r-purrr +- r-s4vectors +- r-spatstat.core +- r-spatstat.geom +- r-spicyr +- r-tidyr +update_on: +- regex: lisaClust_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/lisaClust diff --git a/prepare/r-listenv/PKGBUILD b/prepare/r-listenv/PKGBUILD new file mode 100644 index 0000000000..9d4c6c5e3d --- /dev/null +++ b/prepare/r-listenv/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=listenv +_pkgver=0.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Environments Behaving (Almost) as Lists' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +optdepends=( + r-markdown + r-r.rsp + r-r.utils +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-listenv/lilac.py b/prepare/r-listenv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-listenv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-listenv/lilac.yaml b/prepare/r-listenv/lilac.yaml new file mode 100644 index 0000000000..580b17d2b8 --- /dev/null +++ b/prepare/r-listenv/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: listenv_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=listenv diff --git a/prepare/r-lmdme/PKGBUILD b/prepare/r-lmdme/PKGBUILD new file mode 100644 index 0000000000..c7c9d1c63b --- /dev/null +++ b/prepare/r-lmdme/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lmdme +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Linear Model decomposition for Designed Multivariate Experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-limma + r-pls + r-stemhypoxia +) +optdepends=( + r-parallel +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lmdme/lilac.py b/prepare/r-lmdme/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lmdme/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lmdme/lilac.yaml b/prepare/r-lmdme/lilac.yaml new file mode 100644 index 0000000000..222e0dbb00 --- /dev/null +++ b/prepare/r-lmdme/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-limma +- r-pls +- r-stemhypoxia +update_on: +- regex: lmdme_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/lmdme diff --git a/prepare/r-lme4/PKGBUILD b/prepare/r-lme4/PKGBUILD new file mode 100644 index 0000000000..80238a1ea1 --- /dev/null +++ b/prepare/r-lme4/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lme4 +_pkgver=1.1-27.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Linear Mixed-Effects Models using 'Eigen' and S4" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-minqa + r-nloptr + r-rcpp + r-rcppeigen +) +optdepends=( + r-car + r-dfoptim + r-gamm4 + r-ggplot2 + r-hsaur3 + r-knitr + r-memss + r-mgcv + r-mlmrev + r-numderiv + r-optimx + r-pbkrtest + r-pkpdmodels + r-rmarkdown + r-rr2 + r-semeff + r-statmod + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lme4/lilac.py b/prepare/r-lme4/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lme4/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lme4/lilac.yaml b/prepare/r-lme4/lilac.yaml new file mode 100644 index 0000000000..4b0f7103b4 --- /dev/null +++ b/prepare/r-lme4/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-minqa +- r-nloptr +- r-rcpp +- r-rcppeigen +update_on: +- regex: lme4_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lme4 diff --git a/prepare/r-lmertest/PKGBUILD b/prepare/r-lmertest/PKGBUILD new file mode 100644 index 0000000000..0579c31fe1 --- /dev/null +++ b/prepare/r-lmertest/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lmerTest +_pkgver=3.1-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tests in Linear Mixed Effects Models' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-lme4 + r-numderiv +) +optdepends=( + r-pbkrtest + r-tools +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lmertest/lilac.py b/prepare/r-lmertest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lmertest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lmertest/lilac.yaml b/prepare/r-lmertest/lilac.yaml new file mode 100644 index 0000000000..c5e99f19eb --- /dev/null +++ b/prepare/r-lmertest/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-lme4 +- r-numderiv +update_on: +- regex: lmerTest_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lmerTest diff --git a/prepare/r-lmodel2/PKGBUILD b/prepare/r-lmodel2/PKGBUILD new file mode 100644 index 0000000000..9efacec1d3 --- /dev/null +++ b/prepare/r-lmodel2/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lmodel2 +_pkgver=1.7-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Model II Regression' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lmodel2/lilac.py b/prepare/r-lmodel2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lmodel2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lmodel2/lilac.yaml b/prepare/r-lmodel2/lilac.yaml new file mode 100644 index 0000000000..bd62ebfeee --- /dev/null +++ b/prepare/r-lmodel2/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: lmodel2_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lmodel2 diff --git a/prepare/r-lmom/PKGBUILD b/prepare/r-lmom/PKGBUILD new file mode 100644 index 0000000000..d394dd1407 --- /dev/null +++ b/prepare/r-lmom/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lmom +_pkgver=2.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='L-Moments' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('CPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lmom/lilac.py b/prepare/r-lmom/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lmom/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lmom/lilac.yaml b/prepare/r-lmom/lilac.yaml new file mode 100644 index 0000000000..0ed0ff3cdc --- /dev/null +++ b/prepare/r-lmom/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: lmom_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lmom diff --git a/prepare/r-lmoments/PKGBUILD b/prepare/r-lmoments/PKGBUILD new file mode 100644 index 0000000000..1b6319bc56 --- /dev/null +++ b/prepare/r-lmoments/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Lmoments +_pkgver=1.3-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='L-Moments and Quantile Mixtures' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcpparmadillo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lmoments/lilac.py b/prepare/r-lmoments/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lmoments/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lmoments/lilac.yaml b/prepare/r-lmoments/lilac.yaml new file mode 100644 index 0000000000..a49137cb19 --- /dev/null +++ b/prepare/r-lmoments/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: Lmoments_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Lmoments diff --git a/prepare/r-lmtest/PKGBUILD b/prepare/r-lmtest/PKGBUILD new file mode 100644 index 0000000000..8e0acca927 --- /dev/null +++ b/prepare/r-lmtest/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lmtest +_pkgver=0.9-39 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Testing Linear Regression Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-zoo +) +optdepends=( + r-aer + r-car + r-dynlm + r-sandwich + r-stats4 + r-strucchange + r-survival +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lmtest/lilac.py b/prepare/r-lmtest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lmtest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lmtest/lilac.yaml b/prepare/r-lmtest/lilac.yaml new file mode 100644 index 0000000000..d6ad1b081d --- /dev/null +++ b/prepare/r-lmtest/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-zoo +update_on: +- regex: lmtest_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lmtest diff --git a/prepare/r-lobstahs/PKGBUILD b/prepare/r-lobstahs/PKGBUILD new file mode 100644 index 0000000000..2c94a68812 --- /dev/null +++ b/prepare/r-lobstahs/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LOBSTAHS +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-camera + r-xcms +) +optdepends=( + r-knitr + r-pth2o2lipids + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lobstahs/lilac.py b/prepare/r-lobstahs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lobstahs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lobstahs/lilac.yaml b/prepare/r-lobstahs/lilac.yaml new file mode 100644 index 0000000000..b4720ad0cb --- /dev/null +++ b/prepare/r-lobstahs/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-camera +- r-xcms +update_on: +- regex: LOBSTAHS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LOBSTAHS diff --git a/prepare/r-lobstr/PKGBUILD b/prepare/r-lobstr/PKGBUILD new file mode 100644 index 0000000000..c62f99c084 --- /dev/null +++ b/prepare/r-lobstr/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lobstr +_pkgver=1.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualize R Data Structures with Trees' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-crayon + r-rcpp + r-rlang +) +optdepends=( + r-covr + r-pillar + r-pkgdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lobstr/lilac.py b/prepare/r-lobstr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lobstr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lobstr/lilac.yaml b/prepare/r-lobstr/lilac.yaml new file mode 100644 index 0000000000..b19e7bf8c1 --- /dev/null +++ b/prepare/r-lobstr/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-crayon +- r-rcpp +- r-rlang +update_on: +- regex: lobstr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lobstr diff --git a/prepare/r-locfdr/PKGBUILD b/prepare/r-locfdr/PKGBUILD new file mode 100644 index 0000000000..092ecf754c --- /dev/null +++ b/prepare/r-locfdr/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=locfdr +_pkgver=1.1-8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Computes Local False Discovery Rates' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-locfdr/lilac.py b/prepare/r-locfdr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-locfdr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-locfdr/lilac.yaml b/prepare/r-locfdr/lilac.yaml new file mode 100644 index 0000000000..57b19bf049 --- /dev/null +++ b/prepare/r-locfdr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: locfdr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=locfdr diff --git a/prepare/r-locfit/PKGBUILD b/prepare/r-locfit/PKGBUILD new file mode 100644 index 0000000000..7679ef1bac --- /dev/null +++ b/prepare/r-locfit/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=locfit +_pkgver=1.5-9.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Local Regression, Likelihood and Density Estimation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-gam + r-interp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-locfit/lilac.py b/prepare/r-locfit/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-locfit/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-locfit/lilac.yaml b/prepare/r-locfit/lilac.yaml new file mode 100644 index 0000000000..c2743d819c --- /dev/null +++ b/prepare/r-locfit/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: locfit_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=locfit diff --git a/prepare/r-loci2path/PKGBUILD b/prepare/r-loci2path/PKGBUILD new file mode 100644 index 0000000000..c1f6cc4b4a --- /dev/null +++ b/prepare/r-loci2path/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=loci2path +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-data.table + r-genomicranges + r-pheatmap + r-rcolorbrewer + r-s4vectors + r-wordcloud +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-loci2path/lilac.py b/prepare/r-loci2path/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-loci2path/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-loci2path/lilac.yaml b/prepare/r-loci2path/lilac.yaml new file mode 100644 index 0000000000..617c60a2f2 --- /dev/null +++ b/prepare/r-loci2path/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-data.table +- r-genomicranges +- r-pheatmap +- r-rcolorbrewer +- r-s4vectors +- r-wordcloud +update_on: +- regex: loci2path_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/loci2path diff --git a/prepare/r-log4r/PKGBUILD b/prepare/r-log4r/PKGBUILD new file mode 100644 index 0000000000..5527d4c885 --- /dev/null +++ b/prepare/r-log4r/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=log4r +_pkgver=0.4.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="A Fast and Lightweight Logging System for R, Based on 'log4j'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-futile.logger + r-httr + r-jsonlite + r-knitr + r-lgr + r-logger + r-logging + r-loggit + r-microbenchmark + r-rlog + r-rmarkdown + r-rsyslog + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-log4r/lilac.py b/prepare/r-log4r/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-log4r/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-log4r/lilac.yaml b/prepare/r-log4r/lilac.yaml new file mode 100644 index 0000000000..050ad94fbc --- /dev/null +++ b/prepare/r-log4r/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: log4r_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=log4r diff --git a/prepare/r-logger/PKGBUILD b/prepare/r-logger/PKGBUILD new file mode 100644 index 0000000000..733dfd15ec --- /dev/null +++ b/prepare/r-logger/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=logger +_pkgver=0.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Lightweight, Modern and Flexible Logging Utility' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('AGPL') +depends=( + r +) +optdepends=( + r-botor + r-callr + r-covr + r-crayon + r-devtools + r-futile.logger + r-glue + r-jsonlite + r-knitr + r-log4r + r-logging + r-pander + r-parallel + r-r.utils + r-rmarkdown + r-roxygen2 + r-rpushbullet + r-rsyslog + r-shiny + r-slackr + r-syslognet + r-telegram + r-testthat + r-txtq +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-logger/lilac.py b/prepare/r-logger/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-logger/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-logger/lilac.yaml b/prepare/r-logger/lilac.yaml new file mode 100644 index 0000000000..b52ba86d0b --- /dev/null +++ b/prepare/r-logger/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: logger_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=logger diff --git a/prepare/r-logging/PKGBUILD b/prepare/r-logging/PKGBUILD new file mode 100644 index 0000000000..7c54d4faf2 --- /dev/null +++ b/prepare/r-logging/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=logging +_pkgver=0.10-108 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Logging Package' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-crayon + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-logging/lilac.py b/prepare/r-logging/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-logging/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-logging/lilac.yaml b/prepare/r-logging/lilac.yaml new file mode 100644 index 0000000000..65059ae298 --- /dev/null +++ b/prepare/r-logging/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: logging_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=logging diff --git a/prepare/r-logicfs/PKGBUILD b/prepare/r-logicfs/PKGBUILD new file mode 100644 index 0000000000..8bc3a1799d --- /dev/null +++ b/prepare/r-logicfs/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=logicFS +_pkgver=2.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identification of SNP Interactions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-logicreg + r-mcbiopi +) +optdepends=( + r-genefilter + r-siggenes +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-logicfs/lilac.py b/prepare/r-logicfs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-logicfs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-logicfs/lilac.yaml b/prepare/r-logicfs/lilac.yaml new file mode 100644 index 0000000000..e9b5492a13 --- /dev/null +++ b/prepare/r-logicfs/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-logicreg +- r-mcbiopi +update_on: +- regex: logicFS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/logicFS diff --git a/prepare/r-logicreg/PKGBUILD b/prepare/r-logicreg/PKGBUILD new file mode 100644 index 0000000000..1b57eb3073 --- /dev/null +++ b/prepare/r-logicreg/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LogicReg +_pkgver=1.6.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Logic Regression' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-logicreg/lilac.py b/prepare/r-logicreg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-logicreg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-logicreg/lilac.yaml b/prepare/r-logicreg/lilac.yaml new file mode 100644 index 0000000000..9409b8a9c3 --- /dev/null +++ b/prepare/r-logicreg/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: LogicReg_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=LogicReg diff --git a/prepare/r-logistf/PKGBUILD b/prepare/r-logistf/PKGBUILD new file mode 100644 index 0000000000..4ea0b1fec6 --- /dev/null +++ b/prepare/r-logistf/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=logistf +_pkgver=1.24 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Firth's Bias-Reduced Logistic Regression" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-formula.tools + r-mice +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-logistf/lilac.py b/prepare/r-logistf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-logistf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-logistf/lilac.yaml b/prepare/r-logistf/lilac.yaml new file mode 100644 index 0000000000..daf2cb8059 --- /dev/null +++ b/prepare/r-logistf/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-formula.tools +- r-mice +update_on: +- regex: logistf_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=logistf diff --git a/prepare/r-logitt/PKGBUILD b/prepare/r-logitt/PKGBUILD new file mode 100644 index 0000000000..40295a475c --- /dev/null +++ b/prepare/r-logitt/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=logitT +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='logit-t Package' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy +) +optdepends=( + r-spikeinsubset +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-logitt/lilac.py b/prepare/r-logitt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-logitt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-logitt/lilac.yaml b/prepare/r-logitt/lilac.yaml new file mode 100644 index 0000000000..ed41fbc6ff --- /dev/null +++ b/prepare/r-logitt/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +update_on: +- regex: logitT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/logitT diff --git a/prepare/r-logspline/PKGBUILD b/prepare/r-logspline/PKGBUILD new file mode 100644 index 0000000000..65b183478c --- /dev/null +++ b/prepare/r-logspline/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=logspline +_pkgver=2.1.16 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Routines for Logspline Density Estimation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-logspline/lilac.py b/prepare/r-logspline/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-logspline/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-logspline/lilac.yaml b/prepare/r-logspline/lilac.yaml new file mode 100644 index 0000000000..57280a8266 --- /dev/null +++ b/prepare/r-logspline/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: logspline_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=logspline diff --git a/prepare/r-lokern/PKGBUILD b/prepare/r-lokern/PKGBUILD new file mode 100644 index 0000000000..5aa555fa7f --- /dev/null +++ b/prepare/r-lokern/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lokern +_pkgver=1.1-9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Kernel Regression Smoothing with Local or Global Plug-in Bandwidth' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-sfsmisc +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lokern/lilac.py b/prepare/r-lokern/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lokern/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lokern/lilac.yaml b/prepare/r-lokern/lilac.yaml new file mode 100644 index 0000000000..bc1e440ac6 --- /dev/null +++ b/prepare/r-lokern/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-sfsmisc +update_on: +- regex: lokern_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lokern diff --git a/prepare/r-lola/PKGBUILD b/prepare/r-lola/PKGBUILD new file mode 100644 index 0000000000..33c67fc3e2 --- /dev/null +++ b/prepare/r-lola/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LOLA +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Locus overlap analysis for enrichment of genomic ranges' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-data.table + r-genomicranges + r-iranges + r-reshape2 + r-s4vectors +) +optdepends=( + r-biocstyle + r-ggplot2 + r-knitr + r-parallel + r-qvalue + r-rmarkdown + r-simplecache + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lola/lilac.py b/prepare/r-lola/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lola/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lola/lilac.yaml b/prepare/r-lola/lilac.yaml new file mode 100644 index 0000000000..9d976b5658 --- /dev/null +++ b/prepare/r-lola/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-data.table +- r-genomicranges +- r-iranges +- r-reshape2 +- r-s4vectors +update_on: +- regex: LOLA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LOLA diff --git a/prepare/r-longitudinal/PKGBUILD b/prepare/r-longitudinal/PKGBUILD new file mode 100644 index 0000000000..d1ceb1beb9 --- /dev/null +++ b/prepare/r-longitudinal/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=longitudinal +_pkgver=1.1.13 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Multiple Time Course Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-corpcor +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-longitudinal/lilac.py b/prepare/r-longitudinal/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-longitudinal/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-longitudinal/lilac.yaml b/prepare/r-longitudinal/lilac.yaml new file mode 100644 index 0000000000..a779c4ba4a --- /dev/null +++ b/prepare/r-longitudinal/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-corpcor +update_on: +- regex: longitudinal_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=longitudinal diff --git a/prepare/r-longitudinaldata/PKGBUILD b/prepare/r-longitudinaldata/PKGBUILD new file mode 100644 index 0000000000..7eda825ad1 --- /dev/null +++ b/prepare/r-longitudinaldata/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=longitudinalData +_pkgver=2.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Longitudinal Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-clv + r-misc3d + r-rgl +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-longitudinaldata/lilac.py b/prepare/r-longitudinaldata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-longitudinaldata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-longitudinaldata/lilac.yaml b/prepare/r-longitudinaldata/lilac.yaml new file mode 100644 index 0000000000..a888f0b770 --- /dev/null +++ b/prepare/r-longitudinaldata/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clv +- r-misc3d +- r-rgl +update_on: +- regex: longitudinalData_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=longitudinalData diff --git a/prepare/r-loo/PKGBUILD b/prepare/r-loo/PKGBUILD new file mode 100644 index 0000000000..021eb9bfb1 --- /dev/null +++ b/prepare/r-loo/PKGBUILD @@ -0,0 +1,42 @@ +# system requirements: pandoc (>= 1.12.3), pandoc-citeproc +# Maintainer: Guoyi Zhang + +_pkgname=loo +_pkgver=2.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-checkmate + r-matrixstats +) +optdepends=( + r-bayesplot + r-brms + r-ggplot2 + r-graphics + r-knitr + r-rmarkdown + r-rstan + r-rstanarm + r-rstantools + r-spdep + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-loo/lilac.py b/prepare/r-loo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-loo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-loo/lilac.yaml b/prepare/r-loo/lilac.yaml new file mode 100644 index 0000000000..5468204cc7 --- /dev/null +++ b/prepare/r-loo/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-checkmate +- r-matrixstats +update_on: +- regex: loo_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=loo diff --git a/prepare/r-loomexperiment/PKGBUILD b/prepare/r-loomexperiment/PKGBUILD new file mode 100644 index 0000000000..c71d70c00d --- /dev/null +++ b/prepare/r-loomexperiment/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LoomExperiment +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='LoomExperiment container' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocio + r-delayedarray + r-genomicranges + r-hdf5array + r-rhdf5 + r-s4vectors + r-singlecellexperiment + r-stringr + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-reticulate + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-loomexperiment/lilac.py b/prepare/r-loomexperiment/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-loomexperiment/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-loomexperiment/lilac.yaml b/prepare/r-loomexperiment/lilac.yaml new file mode 100644 index 0000000000..2aac993daf --- /dev/null +++ b/prepare/r-loomexperiment/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocio +- r-delayedarray +- r-genomicranges +- r-hdf5array +- r-rhdf5 +- r-s4vectors +- r-singlecellexperiment +- r-stringr +- r-summarizedexperiment +update_on: +- regex: LoomExperiment_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LoomExperiment diff --git a/prepare/r-loose.rock/PKGBUILD b/prepare/r-loose.rock/PKGBUILD new file mode 100644 index 0000000000..319ebce9c6 --- /dev/null +++ b/prepare/r-loose.rock/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=loose.rock +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Survival Analysis and Data Science' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-digest + r-dplyr + r-futile.options + r-ggplot2 + r-httr + r-reshape2 +) +optdepends=( + r-biomart + r-knitr + r-rmarkdown + r-roxygen2 + r-survival + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-loose.rock/lilac.py b/prepare/r-loose.rock/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-loose.rock/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-loose.rock/lilac.yaml b/prepare/r-loose.rock/lilac.yaml new file mode 100644 index 0000000000..2338cf1a9c --- /dev/null +++ b/prepare/r-loose.rock/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-dplyr +- r-futile.options +- r-ggplot2 +- r-httr +- r-reshape2 +update_on: +- regex: loose.rock_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=loose.rock diff --git a/prepare/r-lowmaca/PKGBUILD b/prepare/r-lowmaca/PKGBUILD new file mode 100644 index 0000000000..5075dc8254 --- /dev/null +++ b/prepare/r-lowmaca/PKGBUILD @@ -0,0 +1,43 @@ +# system requirements: clustalo, gs, perl +# Maintainer: Guoyi Zhang + +_pkgname=LowMACA +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='LowMACA - Low frequency Mutation Analysis via Consensus Alignment' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-biostrings + r-cgdsr + r-data.table + r-gridbase + r-httr + r-lowmacaannotation + r-motifstack + r-rcolorbrewer + r-reshape2 + r-stringr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lowmaca/lilac.py b/prepare/r-lowmaca/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lowmaca/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lowmaca/lilac.yaml b/prepare/r-lowmaca/lilac.yaml new file mode 100644 index 0000000000..2aacc5dd8c --- /dev/null +++ b/prepare/r-lowmaca/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-biostrings +- r-cgdsr +- r-data.table +- r-gridbase +- r-httr +- r-lowmacaannotation +- r-motifstack +- r-rcolorbrewer +- r-reshape2 +- r-stringr +update_on: +- regex: LowMACA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LowMACA diff --git a/prepare/r-lowmacaannotation/PKGBUILD b/prepare/r-lowmacaannotation/PKGBUILD new file mode 100644 index 0000000000..ff5c703114 --- /dev/null +++ b/prepare/r-lowmacaannotation/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LowMACAAnnotation +_pkgver=0.99.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='LowMACAAnnotation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lowmacaannotation/lilac.py b/prepare/r-lowmacaannotation/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lowmacaannotation/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lowmacaannotation/lilac.yaml b/prepare/r-lowmacaannotation/lilac.yaml new file mode 100644 index 0000000000..bb7390e502 --- /dev/null +++ b/prepare/r-lowmacaannotation/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: LowMACAAnnotation_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LowMACAAnnotation diff --git a/prepare/r-lpe/PKGBUILD b/prepare/r-lpe/PKGBUILD new file mode 100644 index 0000000000..faca0003b9 --- /dev/null +++ b/prepare/r-lpe/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LPE +_pkgver=1.68.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methods for analyzing microarray data using Local Pooled Error (LPE) method' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lpe/lilac.py b/prepare/r-lpe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lpe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lpe/lilac.yaml b/prepare/r-lpe/lilac.yaml new file mode 100644 index 0000000000..2d50f373c5 --- /dev/null +++ b/prepare/r-lpe/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: LPE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LPE diff --git a/prepare/r-lpeadj/PKGBUILD b/prepare/r-lpeadj/PKGBUILD new file mode 100644 index 0000000000..74060fced3 --- /dev/null +++ b/prepare/r-lpeadj/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LPEadj +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-lpe +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lpeadj/lilac.py b/prepare/r-lpeadj/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lpeadj/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lpeadj/lilac.yaml b/prepare/r-lpeadj/lilac.yaml new file mode 100644 index 0000000000..cdd9703003 --- /dev/null +++ b/prepare/r-lpeadj/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lpe +update_on: +- regex: LPEadj_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LPEadj diff --git a/prepare/r-lpnet/PKGBUILD b/prepare/r-lpnet/PKGBUILD new file mode 100644 index 0000000000..64997ba741 --- /dev/null +++ b/prepare/r-lpnet/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lpNet +_pkgver=2.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Linear Programming Model for Network Inference' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-lpsolve +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lpnet/lilac.py b/prepare/r-lpnet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lpnet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lpnet/lilac.yaml b/prepare/r-lpnet/lilac.yaml new file mode 100644 index 0000000000..47704f9ecd --- /dev/null +++ b/prepare/r-lpnet/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lpsolve +update_on: +- regex: lpNet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/lpNet diff --git a/prepare/r-lpsolve/PKGBUILD b/prepare/r-lpsolve/PKGBUILD new file mode 100644 index 0000000000..80e6a8f837 --- /dev/null +++ b/prepare/r-lpsolve/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lpSolve +_pkgver=5.6.15 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lpsolve/lilac.py b/prepare/r-lpsolve/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lpsolve/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lpsolve/lilac.yaml b/prepare/r-lpsolve/lilac.yaml new file mode 100644 index 0000000000..7314f30bb8 --- /dev/null +++ b/prepare/r-lpsolve/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: lpSolve_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lpSolve diff --git a/prepare/r-lpsolveapi/PKGBUILD b/prepare/r-lpsolveapi/PKGBUILD new file mode 100644 index 0000000000..b8b9137064 --- /dev/null +++ b/prepare/r-lpsolveapi/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lpSolveAPI +_pkgver=5.5.2.0-17.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="R Interface to 'lp_solve' Version 5.5.2.0" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lpsolveapi/lilac.py b/prepare/r-lpsolveapi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lpsolveapi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lpsolveapi/lilac.yaml b/prepare/r-lpsolveapi/lilac.yaml new file mode 100644 index 0000000000..082b8a43ca --- /dev/null +++ b/prepare/r-lpsolveapi/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: lpSolveAPI_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lpSolveAPI diff --git a/prepare/r-lpsymphony/PKGBUILD b/prepare/r-lpsymphony/PKGBUILD new file mode 100644 index 0000000000..54c2d09a3c --- /dev/null +++ b/prepare/r-lpsymphony/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=lpsymphony +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Symphony integer linear programming solver in R' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('EPL') +depends=( + r +) +optdepends=( + r-biocstyle + r-knitr + r-slam + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lpsymphony/lilac.py b/prepare/r-lpsymphony/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lpsymphony/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lpsymphony/lilac.yaml b/prepare/r-lpsymphony/lilac.yaml new file mode 100644 index 0000000000..d934937722 --- /dev/null +++ b/prepare/r-lpsymphony/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: lpsymphony_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/lpsymphony diff --git a/prepare/r-lrbasedbi/PKGBUILD b/prepare/r-lrbasedbi/PKGBUILD new file mode 100644 index 0000000000..52a803ae81 --- /dev/null +++ b/prepare/r-lrbasedbi/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LRBaseDbi +_pkgver=2.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='DBI to construct LRBase-related package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biobase + r-dbi + r-rsqlite +) +optdepends=( + r-biocstyle + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lrbasedbi/lilac.py b/prepare/r-lrbasedbi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lrbasedbi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lrbasedbi/lilac.yaml b/prepare/r-lrbasedbi/lilac.yaml new file mode 100644 index 0000000000..9847990950 --- /dev/null +++ b/prepare/r-lrbasedbi/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-dbi +- r-rsqlite +update_on: +- regex: LRBaseDbi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LRBaseDbi diff --git a/prepare/r-lrcell/PKGBUILD b/prepare/r-lrcell/PKGBUILD new file mode 100644 index 0000000000..5337a78c1a --- /dev/null +++ b/prepare/r-lrcell/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LRcell +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential cell type change analysis using Logistic/linear Regression' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationhub + r-biocparallel + r-dplyr + r-experimenthub + r-ggplot2 + r-ggrepel + r-magrittr +) +optdepends=( + r-biocstyle + r-knitr + r-lrcelltypemarkers + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lrcell/lilac.py b/prepare/r-lrcell/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lrcell/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lrcell/lilac.yaml b/prepare/r-lrcell/lilac.yaml new file mode 100644 index 0000000000..a15a486e35 --- /dev/null +++ b/prepare/r-lrcell/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-biocparallel +- r-dplyr +- r-experimenthub +- r-ggplot2 +- r-ggrepel +- r-magrittr +update_on: +- regex: LRcell_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LRcell diff --git a/prepare/r-lsa/PKGBUILD b/prepare/r-lsa/PKGBUILD new file mode 100644 index 0000000000..688a7e2619 --- /dev/null +++ b/prepare/r-lsa/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lsa +_pkgver=0.73.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Latent Semantic Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-snowballc +) +optdepends=( + r-tm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lsa/lilac.py b/prepare/r-lsa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lsa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lsa/lilac.yaml b/prepare/r-lsa/lilac.yaml new file mode 100644 index 0000000000..1ab5e72f46 --- /dev/null +++ b/prepare/r-lsa/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-snowballc +update_on: +- regex: lsa_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lsa diff --git a/prepare/r-lsd/PKGBUILD b/prepare/r-lsd/PKGBUILD new file mode 100644 index 0000000000..bf3a6529a1 --- /dev/null +++ b/prepare/r-lsd/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LSD +_pkgver=4.1-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Lots of Superior Depictions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lsd/lilac.py b/prepare/r-lsd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lsd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lsd/lilac.yaml b/prepare/r-lsd/lilac.yaml new file mode 100644 index 0000000000..32b864bd47 --- /dev/null +++ b/prepare/r-lsd/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: LSD_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=LSD diff --git a/prepare/r-lsr/PKGBUILD b/prepare/r-lsr/PKGBUILD new file mode 100644 index 0000000000..704456664e --- /dev/null +++ b/prepare/r-lsr/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lsr +_pkgver=0.5.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Companion to "Learning Statistics with R"' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lsr/lilac.py b/prepare/r-lsr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lsr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lsr/lilac.yaml b/prepare/r-lsr/lilac.yaml new file mode 100644 index 0000000000..551665fe05 --- /dev/null +++ b/prepare/r-lsr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: lsr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lsr diff --git a/prepare/r-lubridate/PKGBUILD b/prepare/r-lubridate/PKGBUILD new file mode 100644 index 0000000000..54fc99f5a9 --- /dev/null +++ b/prepare/r-lubridate/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: C++11, A system with zoneinfo data (e.g./usr/share/zoneinfo). On Windows the zoneinfo included with Ris used. +# Maintainer: Guoyi Zhang + +_pkgname=lubridate +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Make Dealing with Dates a Little Easier' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-cpp11 + r-generics +) +optdepends=( + r-chron + r-covr + r-knitr + r-rmarkdown + r-testthat + r-timedate + r-tis + r-vctrs + r-zoo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lubridate/lilac.py b/prepare/r-lubridate/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lubridate/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lubridate/lilac.yaml b/prepare/r-lubridate/lilac.yaml new file mode 100644 index 0000000000..1ab54ea14d --- /dev/null +++ b/prepare/r-lubridate/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cpp11 +- r-generics +update_on: +- regex: lubridate_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=lubridate diff --git a/prepare/r-lumi/PKGBUILD b/prepare/r-lumi/PKGBUILD new file mode 100644 index 0000000000..5717771655 --- /dev/null +++ b/prepare/r-lumi/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lumi +_pkgver=2.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='BeadArray Specific Methods for Illumina Methylation and Expression Microarrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-affy + r-annotate + r-annotationdbi + r-biobase + r-dbi + r-genomicfeatures + r-genomicranges + r-methylumi + r-nleqslv + r-preprocesscore + r-rsqlite +) +optdepends=( + r-beadarray + r-genefilter + r-limma + r-lumibarnes + r-lumihumanall.db + r-lumihumanidmapping + r-rcolorbrewer + r-vsn +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lumi/lilac.py b/prepare/r-lumi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lumi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lumi/lilac.yaml b/prepare/r-lumi/lilac.yaml new file mode 100644 index 0000000000..d201e57453 --- /dev/null +++ b/prepare/r-lumi/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-annotate +- r-annotationdbi +- r-biobase +- r-dbi +- r-genomicfeatures +- r-genomicranges +- r-methylumi +- r-nleqslv +- r-preprocesscore +- r-rsqlite +update_on: +- regex: lumi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/lumi diff --git a/prepare/r-lumihumanall.db/PKGBUILD b/prepare/r-lumihumanall.db/PKGBUILD new file mode 100644 index 0000000000..72c86c6372 --- /dev/null +++ b/prepare/r-lumihumanall.db/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=lumiHumanAll.db +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Illumina Human Illumina expression annotation data (chip lumiHumanAll)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-org.hs.eg.db +) +optdepends=( + r-annotate + r-runit +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lumihumanall.db/lilac.py b/prepare/r-lumihumanall.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lumihumanall.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lumihumanall.db/lilac.yaml b/prepare/r-lumihumanall.db/lilac.yaml new file mode 100644 index 0000000000..c3571d4fc6 --- /dev/null +++ b/prepare/r-lumihumanall.db/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-org.hs.eg.db +update_on: +- regex: lumiHumanAll.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/lumiHumanAll.db diff --git a/prepare/r-lungcanceracvssccgeo/PKGBUILD b/prepare/r-lungcanceracvssccgeo/PKGBUILD new file mode 100644 index 0000000000..2a2a9effb3 --- /dev/null +++ b/prepare/r-lungcanceracvssccgeo/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LungCancerACvsSCCGEO +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A lung cancer dataset that can be used with maPredictDSC package for developing outcome prediction models from Affymetrix CEL files.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lungcanceracvssccgeo/lilac.py b/prepare/r-lungcanceracvssccgeo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lungcanceracvssccgeo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lungcanceracvssccgeo/lilac.yaml b/prepare/r-lungcanceracvssccgeo/lilac.yaml new file mode 100644 index 0000000000..52e1e24924 --- /dev/null +++ b/prepare/r-lungcanceracvssccgeo/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: LungCancerACvsSCCGEO_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LungCancerACvsSCCGEO diff --git a/prepare/r-lymphoseq/PKGBUILD b/prepare/r-lymphoseq/PKGBUILD new file mode 100644 index 0000000000..8fb5eb1563 --- /dev/null +++ b/prepare/r-lymphoseq/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LymphoSeq +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analyze high-throughput sequencing of T and B cell receptors' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-circlize + r-data.table + r-dplyr + r-ggplot2 + r-ggtree + r-ineq + r-lymphoseqdb + r-msa + r-phangorn + r-plyr + r-rcolorbrewer + r-reshape + r-stringdist + r-upsetr + r-venndiagram +) +optdepends=( + r-knitr + r-pheatmap + r-rmarkdown + r-wordcloud +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lymphoseq/lilac.py b/prepare/r-lymphoseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lymphoseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lymphoseq/lilac.yaml b/prepare/r-lymphoseq/lilac.yaml new file mode 100644 index 0000000000..290db47d7a --- /dev/null +++ b/prepare/r-lymphoseq/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-circlize +- r-data.table +- r-dplyr +- r-ggplot2 +- r-ggtree +- r-ineq +- r-lymphoseqdb +- r-msa +- r-phangorn +- r-plyr +- r-rcolorbrewer +- r-reshape +- r-stringdist +- r-upsetr +- r-venndiagram +update_on: +- regex: LymphoSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LymphoSeq diff --git a/prepare/r-lymphoseqdb/PKGBUILD b/prepare/r-lymphoseqdb/PKGBUILD new file mode 100644 index 0000000000..8348889231 --- /dev/null +++ b/prepare/r-lymphoseqdb/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=LymphoSeqDB +_pkgver=0.99.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='LymphoSeq annotation databases' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-lymphoseqdb/lilac.py b/prepare/r-lymphoseqdb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-lymphoseqdb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-lymphoseqdb/lilac.yaml b/prepare/r-lymphoseqdb/lilac.yaml new file mode 100644 index 0000000000..3b93060f10 --- /dev/null +++ b/prepare/r-lymphoseqdb/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: LymphoSeqDB_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/LymphoSeqDB diff --git a/prepare/r-m3c/PKGBUILD b/prepare/r-m3c/PKGBUILD new file mode 100644 index 0000000000..1897e2c132 --- /dev/null +++ b/prepare/r-m3c/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=M3C +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Monte Carlo Reference-based Consensus Clustering' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-corpcor + r-doparallel + r-dosnow + r-foreach + r-ggplot2 + r-matrixcalc + r-rtsne + r-umap +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-m3c/lilac.py b/prepare/r-m3c/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-m3c/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-m3c/lilac.yaml b/prepare/r-m3c/lilac.yaml new file mode 100644 index 0000000000..7bfd1d305b --- /dev/null +++ b/prepare/r-m3c/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-corpcor +- r-doparallel +- r-dosnow +- r-foreach +- r-ggplot2 +- r-matrixcalc +- r-rtsne +- r-umap +update_on: +- regex: M3C_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/M3C diff --git a/prepare/r-m3drop/PKGBUILD b/prepare/r-m3drop/PKGBUILD new file mode 100644 index 0000000000..baa5266d80 --- /dev/null +++ b/prepare/r-m3drop/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=M3Drop +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Michaelis-Menten Modelling of Dropouts in single-cell RNASeq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bbmle + r-gplots + r-hmisc + r-irlba + r-matrixstats + r-numderiv + r-rcolorbrewer + r-reldist + r-statmod +) +optdepends=( + r-biobase + r-knitr + r-m3dexampledata + r-monocle + r-rocr + r-scater + r-seurat + r-singlecellexperiment +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-m3drop/lilac.py b/prepare/r-m3drop/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-m3drop/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-m3drop/lilac.yaml b/prepare/r-m3drop/lilac.yaml new file mode 100644 index 0000000000..1c06b07abb --- /dev/null +++ b/prepare/r-m3drop/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bbmle +- r-gplots +- r-hmisc +- r-irlba +- r-matrixstats +- r-numderiv +- r-rcolorbrewer +- r-reldist +- r-statmod +update_on: +- regex: M3Drop_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/M3Drop diff --git a/prepare/r-m6aboost/PKGBUILD b/prepare/r-m6aboost/PKGBUILD new file mode 100644 index 0000000000..7a43fb1a72 --- /dev/null +++ b/prepare/r-m6aboost/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=m6Aboost +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='m6Aboost' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-adabag + r-biostrings + r-bsgenome + r-dplyr + r-experimenthub + r-genomicranges + r-iranges + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocstyle + r-bookdown + r-bsgenome.mmusculus.ucsc.mm10 + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-m6aboost/lilac.py b/prepare/r-m6aboost/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-m6aboost/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-m6aboost/lilac.yaml b/prepare/r-m6aboost/lilac.yaml new file mode 100644 index 0000000000..6a63cc5654 --- /dev/null +++ b/prepare/r-m6aboost/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-adabag +- r-biostrings +- r-bsgenome +- r-dplyr +- r-experimenthub +- r-genomicranges +- r-iranges +- r-rtracklayer +- r-s4vectors +update_on: +- regex: m6Aboost_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/m6Aboost diff --git a/prepare/r-maanova/PKGBUILD b/prepare/r-maanova/PKGBUILD new file mode 100644 index 0000000000..6f334c7090 --- /dev/null +++ b/prepare/r-maanova/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=maanova +_pkgver=1.64.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for analyzing Micro Array experiments' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +optdepends=( + r-qvalue + r-rmpi + r-snow +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-maanova/lilac.py b/prepare/r-maanova/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-maanova/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-maanova/lilac.yaml b/prepare/r-maanova/lilac.yaml new file mode 100644 index 0000000000..59f4f42218 --- /dev/null +++ b/prepare/r-maanova/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: maanova_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/maanova diff --git a/prepare/r-maaslin2/PKGBUILD b/prepare/r-maaslin2/PKGBUILD new file mode 100644 index 0000000000..ff3f31ed77 --- /dev/null +++ b/prepare/r-maaslin2/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Maaslin2 +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='"Multivariable Association Discovery in Population-scale Meta-omics Studies"' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biglm + r-car + r-chemometrics + r-cplm + r-data.table + r-dplyr + r-edger + r-ggplot2 + r-glmmtmb + r-hash + r-lme4 + r-lmertest + r-logging + r-lpsymphony + r-metagenomeseq + r-optparse + r-pbapply + r-pcapp + r-pheatmap + r-pscl + r-robustbase + r-vegan +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-maaslin2/lilac.py b/prepare/r-maaslin2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-maaslin2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-maaslin2/lilac.yaml b/prepare/r-maaslin2/lilac.yaml new file mode 100644 index 0000000000..9dea9a2f11 --- /dev/null +++ b/prepare/r-maaslin2/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biglm +- r-car +- r-chemometrics +- r-cplm +- r-data.table +- r-dplyr +- r-edger +- r-ggplot2 +- r-glmmtmb +- r-hash +- r-lme4 +- r-lmertest +- r-logging +- r-lpsymphony +- r-metagenomeseq +- r-optparse +- r-pbapply +- r-pcapp +- r-pheatmap +- r-pscl +- r-robustbase +- r-vegan +update_on: +- regex: Maaslin2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Maaslin2 diff --git a/prepare/r-macat/PKGBUILD b/prepare/r-macat/PKGBUILD new file mode 100644 index 0000000000..19c4c3594d --- /dev/null +++ b/prepare/r-macat/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=macat +_pkgver=1.68.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MicroArray Chromosome Analysis Tool' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotate + r-biobase +) +optdepends=( + r-hgu95av2.db + r-stjudem +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-macat/lilac.py b/prepare/r-macat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-macat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-macat/lilac.yaml b/prepare/r-macat/lilac.yaml new file mode 100644 index 0000000000..acebb6abfa --- /dev/null +++ b/prepare/r-macat/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-biobase +update_on: +- regex: macat_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/macat diff --git a/prepare/r-macorrplot/PKGBUILD b/prepare/r-macorrplot/PKGBUILD new file mode 100644 index 0000000000..d045a21e41 --- /dev/null +++ b/prepare/r-macorrplot/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=maCorrPlot +_pkgver=1.64.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualize artificial correlation in microarray data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-macorrplot/lilac.py b/prepare/r-macorrplot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-macorrplot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-macorrplot/lilac.yaml b/prepare/r-macorrplot/lilac.yaml new file mode 100644 index 0000000000..1f372ebaae --- /dev/null +++ b/prepare/r-macorrplot/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: maCorrPlot_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/maCorrPlot diff --git a/prepare/r-macpet/PKGBUILD b/prepare/r-macpet/PKGBUILD new file mode 100644 index 0000000000..5797d4f1e0 --- /dev/null +++ b/prepare/r-macpet/PKGBUILD @@ -0,0 +1,55 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=MACPET +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Model based analysis for paired-end data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bh + r-bigmemory + r-biocparallel + r-biostrings + r-futile.logger + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-geoquery + r-gtools + r-interactionset + r-intervals + r-iranges + r-knitr + r-plyr + r-rbowtie + r-rcpp + r-rsamtools + r-rtracklayer + r-s4vectors + r-shortread +) +optdepends=( + r-biocstyle + r-ggplot2 + r-igraph + r-reshape2 + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-macpet/lilac.py b/prepare/r-macpet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-macpet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-macpet/lilac.yaml b/prepare/r-macpet/lilac.yaml new file mode 100644 index 0000000000..3c9732f642 --- /dev/null +++ b/prepare/r-macpet/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-bigmemory +- r-biocparallel +- r-biostrings +- r-futile.logger +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-geoquery +- r-gtools +- r-interactionset +- r-intervals +- r-iranges +- r-knitr +- r-plyr +- r-rbowtie +- r-rcpp +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-shortread +update_on: +- regex: MACPET_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MACPET diff --git a/prepare/r-macsquantifyr/PKGBUILD b/prepare/r-macsquantifyr/PKGBUILD new file mode 100644 index 0000000000..9f4c9f9b39 --- /dev/null +++ b/prepare/r-macsquantifyr/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MACSQuantifyR +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast treatment of MACSQuantify FACS data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ggplot2 + r-ggrepel + r-gridextra + r-latticeextra + r-png + r-prettydoc + r-readxl + r-rmarkdown + r-rvest + r-xml2 +) +optdepends=( + r-knitr + r-r.utils + r-spelling + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-macsquantifyr/lilac.py b/prepare/r-macsquantifyr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-macsquantifyr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-macsquantifyr/lilac.yaml b/prepare/r-macsquantifyr/lilac.yaml new file mode 100644 index 0000000000..6c0f33fe42 --- /dev/null +++ b/prepare/r-macsquantifyr/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-ggrepel +- r-gridextra +- r-latticeextra +- r-png +- r-prettydoc +- r-readxl +- r-rmarkdown +- r-rvest +- r-xml2 +update_on: +- regex: MACSQuantifyR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MACSQuantifyR diff --git a/prepare/r-macsr/PKGBUILD b/prepare/r-macsr/PKGBUILD new file mode 100644 index 0000000000..d53ed7c147 --- /dev/null +++ b/prepare/r-macsr/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MACSr +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MACS: Model-based Analysis for ChIP-Seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-annotationhub + r-basilisk + r-experimenthub + r-reticulate + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-macsdata + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-macsr/lilac.py b/prepare/r-macsr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-macsr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-macsr/lilac.yaml b/prepare/r-macsr/lilac.yaml new file mode 100644 index 0000000000..3eb2dc9038 --- /dev/null +++ b/prepare/r-macsr/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-basilisk +- r-experimenthub +- r-reticulate +- r-s4vectors +update_on: +- regex: MACSr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MACSr diff --git a/prepare/r-made4/PKGBUILD b/prepare/r-made4/PKGBUILD new file mode 100644 index 0000000000..fa93039cbd --- /dev/null +++ b/prepare/r-made4/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=made4 +_pkgver=1.68.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multivariate analysis of microarray data using ADE4' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ade4 + r-biobase + r-gplots + r-rcolorbrewer + r-scatterplot3d + r-summarizedexperiment +) +optdepends=( + r-affy + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-made4/lilac.py b/prepare/r-made4/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-made4/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-made4/lilac.yaml b/prepare/r-made4/lilac.yaml new file mode 100644 index 0000000000..b485e552fd --- /dev/null +++ b/prepare/r-made4/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ade4 +- r-biobase +- r-gplots +- r-rcolorbrewer +- r-scatterplot3d +- r-summarizedexperiment +update_on: +- regex: made4_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/made4 diff --git a/prepare/r-madseq/PKGBUILD b/prepare/r-madseq/PKGBUILD new file mode 100644 index 0000000000..2267050861 --- /dev/null +++ b/prepare/r-madseq/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MADSEQ +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-bsgenome + r-bsgenome.hsapiens.ucsc.hg19 + r-coda + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-preprocesscore + r-rjags + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-variantannotation + r-vcfr + r-vgam + r-zlibbioc +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-madseq/lilac.py b/prepare/r-madseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-madseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-madseq/lilac.yaml b/prepare/r-madseq/lilac.yaml new file mode 100644 index 0000000000..7a07ab2ee4 --- /dev/null +++ b/prepare/r-madseq/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome +- r-bsgenome.hsapiens.ucsc.hg19 +- r-coda +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-preprocesscore +- r-rjags +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +- r-variantannotation +- r-vcfr +- r-vgam +- r-zlibbioc +update_on: +- regex: MADSEQ_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MADSEQ diff --git a/prepare/r-mafdb.1kgenomes.phase3.hs37d5/PKGBUILD b/prepare/r-mafdb.1kgenomes.phase3.hs37d5/PKGBUILD new file mode 100644 index 0000000000..7aca5b2354 --- /dev/null +++ b/prepare/r-mafdb.1kgenomes.phase3.hs37d5/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MafDb.1Kgenomes.phase3.hs37d5 +_pkgver=3.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Minor allele frequency data from 1000 Genomes Phase 3 for hs37d5' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bsgenome + r-genomeinfodb + r-genomicranges + r-genomicscores + r-iranges + r-s4vectors +) +optdepends=( + r-snplocs.hsapiens.dbsnp144.grch37 +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mafdb.1kgenomes.phase3.hs37d5/lilac.py b/prepare/r-mafdb.1kgenomes.phase3.hs37d5/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mafdb.1kgenomes.phase3.hs37d5/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mafdb.1kgenomes.phase3.hs37d5/lilac.yaml b/prepare/r-mafdb.1kgenomes.phase3.hs37d5/lilac.yaml new file mode 100644 index 0000000000..5735644af4 --- /dev/null +++ b/prepare/r-mafdb.1kgenomes.phase3.hs37d5/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +- r-genomeinfodb +- r-genomicranges +- r-genomicscores +- r-iranges +- r-s4vectors +update_on: +- regex: MafDb.1Kgenomes.phase3.hs37d5_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MafDb.1Kgenomes.phase3.hs37d5 diff --git a/prepare/r-mafdb.exac.r1.0.nontcga.hs37d5/PKGBUILD b/prepare/r-mafdb.exac.r1.0.nontcga.hs37d5/PKGBUILD new file mode 100644 index 0000000000..7f270f5a93 --- /dev/null +++ b/prepare/r-mafdb.exac.r1.0.nontcga.hs37d5/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MafDb.ExAC.r1.0.nonTCGA.hs37d5 +_pkgver=3.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Minor allele frequency data from ExAC release 1.0 subset of nonTCGA exomes for hs37d5' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bsgenome + r-genomeinfodb + r-genomicranges + r-genomicscores + r-iranges + r-s4vectors +) +optdepends=( + r-snplocs.hsapiens.dbsnp144.grch37 +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mafdb.exac.r1.0.nontcga.hs37d5/lilac.py b/prepare/r-mafdb.exac.r1.0.nontcga.hs37d5/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mafdb.exac.r1.0.nontcga.hs37d5/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mafdb.exac.r1.0.nontcga.hs37d5/lilac.yaml b/prepare/r-mafdb.exac.r1.0.nontcga.hs37d5/lilac.yaml new file mode 100644 index 0000000000..2cf854c486 --- /dev/null +++ b/prepare/r-mafdb.exac.r1.0.nontcga.hs37d5/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +- r-genomeinfodb +- r-genomicranges +- r-genomicscores +- r-iranges +- r-s4vectors +update_on: +- regex: MafDb.ExAC.r1.0.nonTCGA.hs37d5_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MafDb.ExAC.r1.0.nonTCGA.hs37d5 diff --git a/prepare/r-mafdb.gnomadex.r2.1.hs37d5/PKGBUILD b/prepare/r-mafdb.gnomadex.r2.1.hs37d5/PKGBUILD new file mode 100644 index 0000000000..309267c450 --- /dev/null +++ b/prepare/r-mafdb.gnomadex.r2.1.hs37d5/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MafDb.gnomADex.r2.1.hs37d5 +_pkgver=3.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Minor allele frequency data from gnomAD exomes release 2.1 for hs37d5' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bsgenome + r-genomeinfodb + r-genomicranges + r-genomicscores + r-iranges + r-s4vectors +) +optdepends=( + r-snplocs.hsapiens.dbsnp144.grch37 +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mafdb.gnomadex.r2.1.hs37d5/lilac.py b/prepare/r-mafdb.gnomadex.r2.1.hs37d5/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mafdb.gnomadex.r2.1.hs37d5/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mafdb.gnomadex.r2.1.hs37d5/lilac.yaml b/prepare/r-mafdb.gnomadex.r2.1.hs37d5/lilac.yaml new file mode 100644 index 0000000000..5aefb7139e --- /dev/null +++ b/prepare/r-mafdb.gnomadex.r2.1.hs37d5/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +- r-genomeinfodb +- r-genomicranges +- r-genomicscores +- r-iranges +- r-s4vectors +update_on: +- regex: MafDb.gnomADex.r2.1.hs37d5_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MafDb.gnomADex.r2.1.hs37d5 diff --git a/prepare/r-maftools/PKGBUILD b/prepare/r-maftools/PKGBUILD new file mode 100644 index 0000000000..510ae3d342 --- /dev/null +++ b/prepare/r-maftools/PKGBUILD @@ -0,0 +1,50 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=maftools +_pkgver=2.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Summarize, Analyze and Visualize MAF Files' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-data.table + r-rcolorbrewer + r-rhtslib + r-zlibbioc +) +optdepends=( + r-berryfunctions + r-biostrings + r-bsgenome + r-bsgenome.hsapiens.ucsc.hg19 + r-curl + r-genomicranges + r-iranges + r-knitr + r-mclust + r-multiassayexperiment + r-nmf + r-pheatmap + r-r.utils + r-raggedexperiment + r-rmarkdown + r-s4vectors +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-maftools/lilac.py b/prepare/r-maftools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-maftools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-maftools/lilac.yaml b/prepare/r-maftools/lilac.yaml new file mode 100644 index 0000000000..b08ada56ea --- /dev/null +++ b/prepare/r-maftools/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-rcolorbrewer +- r-rhtslib +- r-zlibbioc +update_on: +- regex: maftools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/maftools diff --git a/prepare/r-magar/PKGBUILD b/prepare/r-magar/PKGBUILD new file mode 100644 index 0000000000..a9d9d8561f --- /dev/null +++ b/prepare/r-magar/PKGBUILD @@ -0,0 +1,59 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MAGAR +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-argparse + r-bigstatsr + r-crlmm + r-data.table + r-doparallel + r-ff + r-hdf5array + r-igraph + r-impute + r-jsonlite + r-plyr + r-reshape2 + r-rjson + r-rnbeads + r-rnbeads.hg19 + r-snpstats + r-upsetr +) +optdepends=( + r-biocgenerics + r-biocmanager + r-devtools + r-gridextra + r-jaspar2018 + r-knitr + r-lola + r-qqman + r-rmarkdown + r-rmutil + r-runit + r-seqlogo + r-tfbstools + r-venndiagram +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-magar/lilac.py b/prepare/r-magar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-magar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-magar/lilac.yaml b/prepare/r-magar/lilac.yaml new file mode 100644 index 0000000000..291247481d --- /dev/null +++ b/prepare/r-magar/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-argparse +- r-bigstatsr +- r-crlmm +- r-data.table +- r-doparallel +- r-ff +- r-hdf5array +- r-igraph +- r-impute +- r-jsonlite +- r-plyr +- r-reshape2 +- r-rjson +- r-rnbeads +- r-rnbeads.hg19 +- r-snpstats +- r-upsetr +update_on: +- regex: MAGAR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MAGAR diff --git a/prepare/r-mageckflute/PKGBUILD b/prepare/r-mageckflute/PKGBUILD new file mode 100644 index 0000000000..f8d0a8fb7b --- /dev/null +++ b/prepare/r-mageckflute/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MAGeCKFlute +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-clusterprofiler + r-enrichplot + r-ggplot2 + r-ggrepel + r-gridextra + r-reshape2 +) +optdepends=( + r-biocstyle + r-biomart + r-dendextend + r-dose + r-graphics + r-knitr + r-msigdbr + r-pathview + r-pheatmap + r-png + r-scales + r-sva + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mageckflute/lilac.py b/prepare/r-mageckflute/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mageckflute/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mageckflute/lilac.yaml b/prepare/r-mageckflute/lilac.yaml new file mode 100644 index 0000000000..0c0dbb0284 --- /dev/null +++ b/prepare/r-mageckflute/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-clusterprofiler +- r-enrichplot +- r-ggplot2 +- r-ggrepel +- r-gridextra +- r-reshape2 +update_on: +- regex: MAGeCKFlute_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MAGeCKFlute diff --git a/prepare/r-magic/PKGBUILD b/prepare/r-magic/PKGBUILD new file mode 100644 index 0000000000..313adee715 --- /dev/null +++ b/prepare/r-magic/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=magic +_pkgver=1.5-9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Create and Investigate Magic Squares' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-abind +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-magic/lilac.py b/prepare/r-magic/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-magic/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-magic/lilac.yaml b/prepare/r-magic/lilac.yaml new file mode 100644 index 0000000000..04cdfa83bd --- /dev/null +++ b/prepare/r-magic/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +update_on: +- regex: magic_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=magic diff --git a/prepare/r-magicaxis/PKGBUILD b/prepare/r-magicaxis/PKGBUILD new file mode 100644 index 0000000000..d827298eed --- /dev/null +++ b/prepare/r-magicaxis/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=magicaxis +_pkgver=2.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pretty Scientific Plotting with Minor-Tick and Log Minor-Tick Support' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-celestial + r-mapproj + r-plotrix + r-rann + r-rcolorbrewer + r-sm +) +optdepends=( + r-fst + r-imager +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-magicaxis/lilac.py b/prepare/r-magicaxis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-magicaxis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-magicaxis/lilac.yaml b/prepare/r-magicaxis/lilac.yaml new file mode 100644 index 0000000000..40d35b89d1 --- /dev/null +++ b/prepare/r-magicaxis/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-celestial +- r-mapproj +- r-plotrix +- r-rann +- r-rcolorbrewer +- r-sm +update_on: +- regex: magicaxis_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=magicaxis diff --git a/prepare/r-magick/PKGBUILD b/prepare/r-magick/PKGBUILD new file mode 100644 index 0000000000..b9a9ee22ab --- /dev/null +++ b/prepare/r-magick/PKGBUILD @@ -0,0 +1,47 @@ +# system requirements: ImageMagick++: ImageMagick-c++-devel (rpm) orlibmagick++-dev (deb) +# Maintainer: Guoyi Zhang + +_pkgname=magick +_pkgver=2.7.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Advanced Graphics and Image-Processing in R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-curl + r-magrittr + r-rcpp +) +optdepends=( + r-av + r-gapminder + r-ggplot2 + r-gifski + r-irdisplay + r-jsonlite + r-knitr + r-methods + r-pdftools + r-rmarkdown + r-rsvg + r-spelling + r-tesseract + r-webp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-magick/lilac.py b/prepare/r-magick/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-magick/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-magick/lilac.yaml b/prepare/r-magick/lilac.yaml new file mode 100644 index 0000000000..10811003b0 --- /dev/null +++ b/prepare/r-magick/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-magrittr +- r-rcpp +update_on: +- regex: magick_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=magick diff --git a/prepare/r-mai/PKGBUILD b/prepare/r-mai/PKGBUILD new file mode 100644 index 0000000000..548bf4d426 --- /dev/null +++ b/prepare/r-mai/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MAI +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mechanism-Aware Imputation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-caret + r-doparallel + r-e1071 + r-foreach + r-future + r-future.apply + r-missforest + r-pcamethods + r-s4vectors + r-summarizedexperiment + r-tidyverse +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mai/lilac.py b/prepare/r-mai/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mai/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mai/lilac.yaml b/prepare/r-mai/lilac.yaml new file mode 100644 index 0000000000..0781a2a1c1 --- /dev/null +++ b/prepare/r-mai/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-caret +- r-doparallel +- r-e1071 +- r-foreach +- r-future +- r-future.apply +- r-missforest +- r-pcamethods +- r-s4vectors +- r-summarizedexperiment +- r-tidyverse +update_on: +- regex: MAI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MAI diff --git a/prepare/r-maigespack/PKGBUILD b/prepare/r-maigespack/PKGBUILD new file mode 100644 index 0000000000..5dc331e6c4 --- /dev/null +++ b/prepare/r-maigespack/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=maigesPack +_pkgver=1.58.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions to handle cDNA microarray data, including several methods of data analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-convert + r-graph + r-limma + r-marray +) +optdepends=( + r-amap + r-annotate + r-class + r-e1071 + r-mass + r-multtest + r-olin + r-r2html + r-rgl + r-som +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-maigespack/lilac.py b/prepare/r-maigespack/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-maigespack/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-maigespack/lilac.yaml b/prepare/r-maigespack/lilac.yaml new file mode 100644 index 0000000000..e8371e90a5 --- /dev/null +++ b/prepare/r-maigespack/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-convert +- r-graph +- r-limma +- r-marray +update_on: +- regex: maigesPack_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/maigesPack diff --git a/prepare/r-mait/PKGBUILD b/prepare/r-mait/PKGBUILD new file mode 100644 index 0000000000..06e6d01c97 --- /dev/null +++ b/prepare/r-mait/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MAIT +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Analysis of Metabolomic Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-agricolae + r-camera + r-caret + r-e1071 + r-gplots + r-pls + r-plsgenomics + r-rcpp + r-xcms +) +optdepends=( + r-faahko + r-rgl +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mait/lilac.py b/prepare/r-mait/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mait/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mait/lilac.yaml b/prepare/r-mait/lilac.yaml new file mode 100644 index 0000000000..4a5448346d --- /dev/null +++ b/prepare/r-mait/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-agricolae +- r-camera +- r-caret +- r-e1071 +- r-gplots +- r-pls +- r-plsgenomics +- r-rcpp +- r-xcms +update_on: +- regex: MAIT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MAIT diff --git a/prepare/r-makecdfenv/PKGBUILD b/prepare/r-makecdfenv/PKGBUILD new file mode 100644 index 0000000000..e958c16875 --- /dev/null +++ b/prepare/r-makecdfenv/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=makecdfenv +_pkgver=1.70.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CDF Environment Maker' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-affyio + r-biobase + r-zlibbioc +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-makecdfenv/lilac.py b/prepare/r-makecdfenv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-makecdfenv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-makecdfenv/lilac.yaml b/prepare/r-makecdfenv/lilac.yaml new file mode 100644 index 0000000000..0818fcdd74 --- /dev/null +++ b/prepare/r-makecdfenv/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-affyio +- r-biobase +- r-zlibbioc +update_on: +- regex: makecdfenv_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/makecdfenv diff --git a/prepare/r-maldiquant/PKGBUILD b/prepare/r-maldiquant/PKGBUILD new file mode 100644 index 0000000000..52f7814d20 --- /dev/null +++ b/prepare/r-maldiquant/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MALDIquant +_pkgver=1.21 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quantitative Analysis of Mass Spectrometry Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-maldiquant/lilac.py b/prepare/r-maldiquant/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-maldiquant/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-maldiquant/lilac.yaml b/prepare/r-maldiquant/lilac.yaml new file mode 100644 index 0000000000..d181d5dd0a --- /dev/null +++ b/prepare/r-maldiquant/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: MALDIquant_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MALDIquant diff --git a/prepare/r-manor/PKGBUILD b/prepare/r-manor/PKGBUILD new file mode 100644 index 0000000000..240125a7b2 --- /dev/null +++ b/prepare/r-manor/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MANOR +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CGH Micro-Array NORmalization' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-glad +) +optdepends=( + r-bookdown + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-manor/lilac.py b/prepare/r-manor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-manor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-manor/lilac.yaml b/prepare/r-manor/lilac.yaml new file mode 100644 index 0000000000..293b6c0f92 --- /dev/null +++ b/prepare/r-manor/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-glad +update_on: +- regex: MANOR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MANOR diff --git a/prepare/r-mantelcorr/PKGBUILD b/prepare/r-mantelcorr/PKGBUILD new file mode 100644 index 0000000000..e82ba3f8fc --- /dev/null +++ b/prepare/r-mantelcorr/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MantelCorr +_pkgver=1.64.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Compute Mantel Cluster Correlations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mantelcorr/lilac.py b/prepare/r-mantelcorr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mantelcorr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mantelcorr/lilac.yaml b/prepare/r-mantelcorr/lilac.yaml new file mode 100644 index 0000000000..e226559c54 --- /dev/null +++ b/prepare/r-mantelcorr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: MantelCorr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MantelCorr diff --git a/prepare/r-mapkl/PKGBUILD b/prepare/r-mapkl/PKGBUILD new file mode 100644 index 0000000000..dacbce3352 --- /dev/null +++ b/prepare/r-mapkl/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mAPKL +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Hybrid Feature Selection method for gene expression data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-apcluster + r-biobase + r-clustersim + r-e1071 + r-igraph + r-limma + r-multtest + r-parmigene + r-reactome.db +) +optdepends=( + r-biocgenerics + r-biocstyle + r-hgu133plus2.db + r-knitr + r-mapkldata + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mapkl/lilac.py b/prepare/r-mapkl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mapkl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mapkl/lilac.yaml b/prepare/r-mapkl/lilac.yaml new file mode 100644 index 0000000000..6c71164e10 --- /dev/null +++ b/prepare/r-mapkl/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-apcluster +- r-biobase +- r-clustersim +- r-e1071 +- r-igraph +- r-limma +- r-multtest +- r-parmigene +- r-reactome.db +update_on: +- regex: mAPKL_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mAPKL diff --git a/prepare/r-mapplots/PKGBUILD b/prepare/r-mapplots/PKGBUILD new file mode 100644 index 0000000000..89d8e3529a --- /dev/null +++ b/prepare/r-mapplots/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mapplots +_pkgver=1.5.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data Visualisation on Maps' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-shapefiles +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mapplots/lilac.py b/prepare/r-mapplots/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mapplots/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mapplots/lilac.yaml b/prepare/r-mapplots/lilac.yaml new file mode 100644 index 0000000000..a7fd55af01 --- /dev/null +++ b/prepare/r-mapplots/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: mapplots_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mapplots diff --git a/prepare/r-mapproj/PKGBUILD b/prepare/r-mapproj/PKGBUILD new file mode 100644 index 0000000000..472102b2ae --- /dev/null +++ b/prepare/r-mapproj/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mapproj +_pkgver=1.2.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Map Projections' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Lucent Public License') +depends=( + r + r-maps +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mapproj/lilac.py b/prepare/r-mapproj/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mapproj/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mapproj/lilac.yaml b/prepare/r-mapproj/lilac.yaml new file mode 100644 index 0000000000..1e78ce9217 --- /dev/null +++ b/prepare/r-mapproj/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-maps +update_on: +- regex: mapproj_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mapproj diff --git a/prepare/r-mapredictdsc/PKGBUILD b/prepare/r-mapredictdsc/PKGBUILD new file mode 100644 index 0000000000..dfadc6ed3e --- /dev/null +++ b/prepare/r-mapredictdsc/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=maPredictDSC +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Diagnostic Signature Challenge' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-annotationdbi + r-caret + r-e1071 + r-gcrma + r-hgu133plus2.db + r-limma + r-lungcanceracvssccgeo + r-roc + r-rocr +) +optdepends=( + r-parallel +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mapredictdsc/lilac.py b/prepare/r-mapredictdsc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mapredictdsc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mapredictdsc/lilac.yaml b/prepare/r-mapredictdsc/lilac.yaml new file mode 100644 index 0000000000..60632aa6e5 --- /dev/null +++ b/prepare/r-mapredictdsc/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-annotationdbi +- r-caret +- r-e1071 +- r-gcrma +- r-hgu133plus2.db +- r-limma +- r-lungcanceracvssccgeo +- r-roc +- r-rocr +update_on: +- regex: maPredictDSC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/maPredictDSC diff --git a/prepare/r-maps/PKGBUILD b/prepare/r-maps/PKGBUILD new file mode 100644 index 0000000000..807a33a10f --- /dev/null +++ b/prepare/r-maps/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=maps +_pkgver=3.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Draw Geographical Maps' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-mapdata + r-mapproj + r-rnaturalearth + r-sp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-maps/lilac.py b/prepare/r-maps/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-maps/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-maps/lilac.yaml b/prepare/r-maps/lilac.yaml new file mode 100644 index 0000000000..800c5ad7b2 --- /dev/null +++ b/prepare/r-maps/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: maps_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=maps diff --git a/prepare/r-mapscape/PKGBUILD b/prepare/r-mapscape/PKGBUILD new file mode 100644 index 0000000000..885dabd0c0 --- /dev/null +++ b/prepare/r-mapscape/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mapscape +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='mapscape' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-base64enc + r-htmlwidgets + r-jsonlite + r-stringr +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mapscape/lilac.py b/prepare/r-mapscape/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mapscape/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mapscape/lilac.yaml b/prepare/r-mapscape/lilac.yaml new file mode 100644 index 0000000000..05a08fb352 --- /dev/null +++ b/prepare/r-mapscape/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-htmlwidgets +- r-jsonlite +- r-stringr +update_on: +- regex: mapscape_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mapscape diff --git a/prepare/r-maptools/PKGBUILD b/prepare/r-maptools/PKGBUILD new file mode 100644 index 0000000000..1f54e848ca --- /dev/null +++ b/prepare/r-maptools/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=maptools +_pkgver=1.1-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Handling Spatial Objects' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-sp +) +optdepends=( + r-gpclib + r-maps + r-pbsmapping + r-plotrix + r-polyclip + r-raster + r-rcolorbrewer + r-rgeos + r-spatstat + r-spatstat.geom + r-spatstat.linnet + r-spatstat.utils +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-maptools/lilac.py b/prepare/r-maptools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-maptools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-maptools/lilac.yaml b/prepare/r-maptools/lilac.yaml new file mode 100644 index 0000000000..4544e98794 --- /dev/null +++ b/prepare/r-maptools/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-sp +update_on: +- regex: maptools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=maptools diff --git a/prepare/r-maptpx/PKGBUILD b/prepare/r-maptpx/PKGBUILD new file mode 100644 index 0000000000..e2ac99da81 --- /dev/null +++ b/prepare/r-maptpx/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=maptpx +_pkgver=1.9-7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MAP Estimation of Topic Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-slam +) +optdepends=( + r-mass +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-maptpx/lilac.py b/prepare/r-maptpx/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-maptpx/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-maptpx/lilac.yaml b/prepare/r-maptpx/lilac.yaml new file mode 100644 index 0000000000..c40b295cd7 --- /dev/null +++ b/prepare/r-maptpx/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-slam +update_on: +- regex: maptpx_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=maptpx diff --git a/prepare/r-maptree/PKGBUILD b/prepare/r-maptree/PKGBUILD new file mode 100644 index 0000000000..f5f788b361 --- /dev/null +++ b/prepare/r-maptree/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=maptree +_pkgver=1.4-7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mapping, pruning, and graphing tree models' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Unlimited') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-maptree/lilac.py b/prepare/r-maptree/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-maptree/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-maptree/lilac.yaml b/prepare/r-maptree/lilac.yaml new file mode 100644 index 0000000000..94d5c8f214 --- /dev/null +++ b/prepare/r-maptree/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: maptree_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=maptree diff --git a/prepare/r-markdown/PKGBUILD b/prepare/r-markdown/PKGBUILD new file mode 100644 index 0000000000..c8911576be --- /dev/null +++ b/prepare/r-markdown/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=markdown +_pkgver=1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Render Markdown with the C Library 'Sundown'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mime + r-xfun +) +optdepends=( + r-knitr + r-rcurl +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-markdown/lilac.py b/prepare/r-markdown/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-markdown/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-markdown/lilac.yaml b/prepare/r-markdown/lilac.yaml new file mode 100644 index 0000000000..14c2a51d54 --- /dev/null +++ b/prepare/r-markdown/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mime +- r-xfun +update_on: +- regex: markdown_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=markdown diff --git a/prepare/r-marr/PKGBUILD b/prepare/r-marr/PKGBUILD new file mode 100644 index 0000000000..319537a786 --- /dev/null +++ b/prepare/r-marr/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=marr +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Maximum rank reproducibility' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-ggplot2 + r-magrittr + r-rcpp + r-rlang + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-marr/lilac.py b/prepare/r-marr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-marr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-marr/lilac.yaml b/prepare/r-marr/lilac.yaml new file mode 100644 index 0000000000..c1d887c9be --- /dev/null +++ b/prepare/r-marr/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-magrittr +- r-rcpp +- r-rlang +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: marr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/marr diff --git a/prepare/r-marray/PKGBUILD b/prepare/r-marray/PKGBUILD new file mode 100644 index 0000000000..858df712c3 --- /dev/null +++ b/prepare/r-marray/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=marray +_pkgver=1.72.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Exploratory analysis for two-color spotted microarray data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-limma +) +optdepends=( + r-tkwidgets +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-marray/lilac.py b/prepare/r-marray/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-marray/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-marray/lilac.yaml b/prepare/r-marray/lilac.yaml new file mode 100644 index 0000000000..b46f57b837 --- /dev/null +++ b/prepare/r-marray/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-limma +update_on: +- regex: marray_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/marray diff --git a/prepare/r-martini/PKGBUILD b/prepare/r-martini/PKGBUILD new file mode 100644 index 0000000000..5109b47d03 --- /dev/null +++ b/prepare/r-martini/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=martini +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GWAS Incorporating Networks' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-igraph + r-rcpp + r-rcppeigen + r-snpstats +) +optdepends=( + r-biomart + r-circlize + r-httr + r-iranges + r-knitr + r-memoise + r-readr + r-rmarkdown + r-s4vectors + r-stringdb + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-martini/lilac.py b/prepare/r-martini/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-martini/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-martini/lilac.yaml b/prepare/r-martini/lilac.yaml new file mode 100644 index 0000000000..d002d2f431 --- /dev/null +++ b/prepare/r-martini/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +- r-rcpp +- r-rcppeigen +- r-snpstats +update_on: +- regex: martini_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/martini diff --git a/prepare/r-maser/PKGBUILD b/prepare/r-maser/PKGBUILD new file mode 100644 index 0000000000..d6e12e8db3 --- /dev/null +++ b/prepare/r-maser/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=maser +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mapping Alternative Splicing Events to pRoteins' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-data.table + r-dplyr + r-dt + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gviz + r-iranges + r-reshape2 + r-rtracklayer +) +optdepends=( + r-annotationhub + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-maser/lilac.py b/prepare/r-maser/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-maser/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-maser/lilac.yaml b/prepare/r-maser/lilac.yaml new file mode 100644 index 0000000000..70a25166df --- /dev/null +++ b/prepare/r-maser/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-data.table +- r-dplyr +- r-dt +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-gviz +- r-iranges +- r-reshape2 +- r-rtracklayer +update_on: +- regex: maser_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/maser diff --git a/prepare/r-masigpro/PKGBUILD b/prepare/r-masigpro/PKGBUILD new file mode 100644 index 0000000000..8b46722174 --- /dev/null +++ b/prepare/r-masigpro/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=maSigPro +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Significant Gene Expression Profile Differences in Time Course Gene Expression Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-mclust + r-venn +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-masigpro/lilac.py b/prepare/r-masigpro/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-masigpro/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-masigpro/lilac.yaml b/prepare/r-masigpro/lilac.yaml new file mode 100644 index 0000000000..4095066a6b --- /dev/null +++ b/prepare/r-masigpro/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-mclust +- r-venn +update_on: +- regex: maSigPro_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/maSigPro diff --git a/prepare/r-maskbad/PKGBUILD b/prepare/r-maskbad/PKGBUILD new file mode 100644 index 0000000000..c2c34ad0bb --- /dev/null +++ b/prepare/r-maskbad/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=maskBAD +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Masking probes with binding affinity differences' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-gcrma +) +optdepends=( + r-hgu95av2cdf + r-hgu95av2probe +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-maskbad/lilac.py b/prepare/r-maskbad/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-maskbad/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-maskbad/lilac.yaml b/prepare/r-maskbad/lilac.yaml new file mode 100644 index 0000000000..947b6c121e --- /dev/null +++ b/prepare/r-maskbad/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-gcrma +update_on: +- regex: maskBAD_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/maskBAD diff --git a/prepare/r-mass/PKGBUILD b/prepare/r-mass/PKGBUILD new file mode 100644 index 0000000000..26e16309af --- /dev/null +++ b/prepare/r-mass/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MASS +_pkgver=7.3-54 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Support Functions and Datasets for Venables and Ripley's MASS" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-lattice + r-nlme + r-nnet + r-survival +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mass/lilac.py b/prepare/r-mass/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mass/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mass/lilac.yaml b/prepare/r-mass/lilac.yaml new file mode 100644 index 0000000000..41104158f1 --- /dev/null +++ b/prepare/r-mass/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: MASS_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MASS diff --git a/prepare/r-massarray/PKGBUILD b/prepare/r-massarray/PKGBUILD new file mode 100644 index 0000000000..1c91622e87 --- /dev/null +++ b/prepare/r-massarray/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MassArray +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analytical Tools for MassArray Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-massarray/lilac.py b/prepare/r-massarray/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-massarray/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-massarray/lilac.yaml b/prepare/r-massarray/lilac.yaml new file mode 100644 index 0000000000..ff8f4b9752 --- /dev/null +++ b/prepare/r-massarray/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: MassArray_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MassArray diff --git a/prepare/r-massir/PKGBUILD b/prepare/r-massir/PKGBUILD new file mode 100644 index 0000000000..7bcce3f10a --- /dev/null +++ b/prepare/r-massir/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=massiR +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='massiR: MicroArray Sample Sex Identifier' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-diptest + r-gplots +) +optdepends=( + r-biocgenerics + r-biomart + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-massir/lilac.py b/prepare/r-massir/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-massir/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-massir/lilac.yaml b/prepare/r-massir/lilac.yaml new file mode 100644 index 0000000000..266265ce49 --- /dev/null +++ b/prepare/r-massir/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-diptest +- r-gplots +update_on: +- regex: massiR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/massiR diff --git a/prepare/r-massspecwavelet/PKGBUILD b/prepare/r-massspecwavelet/PKGBUILD new file mode 100644 index 0000000000..d63880e9e9 --- /dev/null +++ b/prepare/r-massspecwavelet/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MassSpecWavelet +_pkgver=1.60.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mass spectrum processing by wavelet-based algorithms' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-waveslim +) +optdepends=( + r-catools + r-xcms +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-massspecwavelet/lilac.py b/prepare/r-massspecwavelet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-massspecwavelet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-massspecwavelet/lilac.yaml b/prepare/r-massspecwavelet/lilac.yaml new file mode 100644 index 0000000000..6ef60f26c9 --- /dev/null +++ b/prepare/r-massspecwavelet/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-waveslim +update_on: +- regex: MassSpecWavelet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MassSpecWavelet diff --git a/prepare/r-mast/PKGBUILD b/prepare/r-mast/PKGBUILD new file mode 100644 index 0000000000..e62a43cc18 --- /dev/null +++ b/prepare/r-mast/PKGBUILD @@ -0,0 +1,64 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MAST +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Model-based Analysis of Single Cell Transcriptomics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-biobase + r-biocgenerics + r-data.table + r-ggplot2 + r-plyr + r-progress + r-reshape2 + r-s4vectors + r-singlecellexperiment + r-stringr + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-blme + r-car + r-delayedarray + r-dplyr + r-gdata + r-ggally + r-gseabase + r-hdf5array + r-knitr + r-lattice + r-limma + r-lme4 + r-matrix + r-nmf + r-numderiv + r-rcolorbrewer + r-rmarkdown + r-roxygen2 + r-rsvd + r-scater + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene + r-zinbwave +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mast/lilac.py b/prepare/r-mast/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mast/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mast/lilac.yaml b/prepare/r-mast/lilac.yaml new file mode 100644 index 0000000000..d705a9201b --- /dev/null +++ b/prepare/r-mast/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-biobase +- r-biocgenerics +- r-data.table +- r-ggplot2 +- r-plyr +- r-progress +- r-reshape2 +- r-s4vectors +- r-singlecellexperiment +- r-stringr +- r-summarizedexperiment +update_on: +- regex: MAST_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MAST diff --git a/prepare/r-matchbox/PKGBUILD b/prepare/r-matchbox/PKGBUILD new file mode 100644 index 0000000000..bb38cfad44 --- /dev/null +++ b/prepare/r-matchbox/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=matchBox +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-matchbox/lilac.py b/prepare/r-matchbox/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-matchbox/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-matchbox/lilac.yaml b/prepare/r-matchbox/lilac.yaml new file mode 100644 index 0000000000..2e82ebbf4d --- /dev/null +++ b/prepare/r-matchbox/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: matchBox_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/matchBox diff --git a/prepare/r-matching/PKGBUILD b/prepare/r-matching/PKGBUILD new file mode 100644 index 0000000000..5fbdf82aa6 --- /dev/null +++ b/prepare/r-matching/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Matching +_pkgver=4.9-11 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multivariate and Propensity Score Matching with Balance Optimization' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-parallel + r-rbounds + r-rgenoud +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-matching/lilac.py b/prepare/r-matching/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-matching/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-matching/lilac.yaml b/prepare/r-matching/lilac.yaml new file mode 100644 index 0000000000..21301c07cc --- /dev/null +++ b/prepare/r-matching/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Matching_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Matching diff --git a/prepare/r-matchingr/PKGBUILD b/prepare/r-matchingr/PKGBUILD new file mode 100644 index 0000000000..16a69e7eb2 --- /dev/null +++ b/prepare/r-matchingr/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=matchingR +_pkgver=1.3.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Matching Algorithms in R and C++' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-matchingr/lilac.py b/prepare/r-matchingr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-matchingr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-matchingr/lilac.yaml b/prepare/r-matchingr/lilac.yaml new file mode 100644 index 0000000000..44f70fd187 --- /dev/null +++ b/prepare/r-matchingr/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: matchingR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=matchingR diff --git a/prepare/r-mathjaxr/PKGBUILD b/prepare/r-mathjaxr/PKGBUILD new file mode 100644 index 0000000000..e4142a6299 --- /dev/null +++ b/prepare/r-mathjaxr/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mathjaxr +_pkgver=1.4-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Using 'Mathjax' in Rd Files" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-js +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mathjaxr/lilac.py b/prepare/r-mathjaxr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mathjaxr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mathjaxr/lilac.yaml b/prepare/r-mathjaxr/lilac.yaml new file mode 100644 index 0000000000..3369e34a35 --- /dev/null +++ b/prepare/r-mathjaxr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: mathjaxr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mathjaxr diff --git a/prepare/r-matlab/PKGBUILD b/prepare/r-matlab/PKGBUILD new file mode 100644 index 0000000000..ef6b77253b --- /dev/null +++ b/prepare/r-matlab/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=matlab +_pkgver=1.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MATLAB emulation package' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-matlab/lilac.py b/prepare/r-matlab/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-matlab/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-matlab/lilac.yaml b/prepare/r-matlab/lilac.yaml new file mode 100644 index 0000000000..589611d694 --- /dev/null +++ b/prepare/r-matlab/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: matlab_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=matlab diff --git a/prepare/r-matrix.utils/PKGBUILD b/prepare/r-matrix.utils/PKGBUILD new file mode 100644 index 0000000000..076306984b --- /dev/null +++ b/prepare/r-matrix.utils/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Matrix.utils +_pkgver=0.9.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data.frame-Like Operations on Sparse and Dense Matrix Objects' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-grr +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-matrix.utils/lilac.py b/prepare/r-matrix.utils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-matrix.utils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-matrix.utils/lilac.yaml b/prepare/r-matrix.utils/lilac.yaml new file mode 100644 index 0000000000..160f894bc0 --- /dev/null +++ b/prepare/r-matrix.utils/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-grr +update_on: +- regex: Matrix.utils_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Matrix.utils diff --git a/prepare/r-matrixcalc/PKGBUILD b/prepare/r-matrixcalc/PKGBUILD new file mode 100644 index 0000000000..a43d449328 --- /dev/null +++ b/prepare/r-matrixcalc/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=matrixcalc +_pkgver=1.0-5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Collection of Functions for Matrix Calculations' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-matrixcalc/lilac.py b/prepare/r-matrixcalc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-matrixcalc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-matrixcalc/lilac.yaml b/prepare/r-matrixcalc/lilac.yaml new file mode 100644 index 0000000000..8f3c8faabc --- /dev/null +++ b/prepare/r-matrixcalc/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: matrixcalc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=matrixcalc diff --git a/prepare/r-matrixcorrelation/PKGBUILD b/prepare/r-matrixcorrelation/PKGBUILD new file mode 100644 index 0000000000..0113754c34 --- /dev/null +++ b/prepare/r-matrixcorrelation/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MatrixCorrelation +_pkgver=0.9.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Matrix Correlation Coefficients' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-plotrix + r-pracma + r-progress + r-rcpp + r-rcpparmadillo + r-rspectra +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-matrixcorrelation/lilac.py b/prepare/r-matrixcorrelation/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-matrixcorrelation/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-matrixcorrelation/lilac.yaml b/prepare/r-matrixcorrelation/lilac.yaml new file mode 100644 index 0000000000..9c7823931a --- /dev/null +++ b/prepare/r-matrixcorrelation/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-plotrix +- r-pracma +- r-progress +- r-rcpp +- r-rcpparmadillo +- r-rspectra +update_on: +- regex: MatrixCorrelation_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MatrixCorrelation diff --git a/prepare/r-matrixextra/PKGBUILD b/prepare/r-matrixextra/PKGBUILD new file mode 100644 index 0000000000..349d92bbda --- /dev/null +++ b/prepare/r-matrixextra/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MatrixExtra +_pkgver=0.1.9-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Extra Methods for Sparse Matrices' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-float + r-rcpp + r-rhpcblasctl +) +optdepends=( + r-data.table + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-matrixextra/lilac.py b/prepare/r-matrixextra/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-matrixextra/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-matrixextra/lilac.yaml b/prepare/r-matrixextra/lilac.yaml new file mode 100644 index 0000000000..2d95c05da6 --- /dev/null +++ b/prepare/r-matrixextra/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-float +- r-rcpp +- r-rhpcblasctl +update_on: +- regex: MatrixExtra_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MatrixExtra diff --git a/prepare/r-matrixgenerics/PKGBUILD b/prepare/r-matrixgenerics/PKGBUILD new file mode 100644 index 0000000000..ffe32661ec --- /dev/null +++ b/prepare/r-matrixgenerics/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MatrixGenerics +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-matrixstats +) +optdepends=( + r-delayedmatrixstats + r-sparsematrixstats + r-summarizedexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-matrixgenerics/lilac.py b/prepare/r-matrixgenerics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-matrixgenerics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-matrixgenerics/lilac.yaml b/prepare/r-matrixgenerics/lilac.yaml new file mode 100644 index 0000000000..387bed2990 --- /dev/null +++ b/prepare/r-matrixgenerics/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-matrixstats +update_on: +- regex: MatrixGenerics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MatrixGenerics diff --git a/prepare/r-matrixmodels/PKGBUILD b/prepare/r-matrixmodels/PKGBUILD new file mode 100644 index 0000000000..07b3bb3c49 --- /dev/null +++ b/prepare/r-matrixmodels/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MatrixModels +_pkgver=0.5-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Modelling with Sparse and Dense Matrices' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-matrixmodels/lilac.py b/prepare/r-matrixmodels/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-matrixmodels/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-matrixmodels/lilac.yaml b/prepare/r-matrixmodels/lilac.yaml new file mode 100644 index 0000000000..46e665a41a --- /dev/null +++ b/prepare/r-matrixmodels/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: MatrixModels_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MatrixModels diff --git a/prepare/r-matrixqcvis/PKGBUILD b/prepare/r-matrixqcvis/PKGBUILD new file mode 100644 index 0000000000..77b6d00da6 --- /dev/null +++ b/prepare/r-matrixqcvis/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MatrixQCvis +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Shiny-based interactive data-quality exploration for omics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-complexheatmap + r-dplyr + r-ggplot2 + r-hmisc + r-htmlwidgets + r-impute + r-imputelcmd + r-limma + r-openxlsx + r-pcamethods + r-plotly + r-proda + r-rlang + r-rmarkdown + r-rtsne + r-s4vectors + r-shiny + r-shinydashboard + r-shinyhelper + r-shinyjs + r-summarizedexperiment + r-tibble + r-tidyr + r-umap + r-upsetr + r-vegan + r-vsn +) +optdepends=( + r-biocgenerics + r-biocstyle + r-hexbin + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-matrixqcvis/lilac.py b/prepare/r-matrixqcvis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-matrixqcvis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-matrixqcvis/lilac.yaml b/prepare/r-matrixqcvis/lilac.yaml new file mode 100644 index 0000000000..b382ddbdb7 --- /dev/null +++ b/prepare/r-matrixqcvis/lilac.yaml @@ -0,0 +1,36 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-complexheatmap +- r-dplyr +- r-ggplot2 +- r-hmisc +- r-htmlwidgets +- r-impute +- r-imputelcmd +- r-limma +- r-openxlsx +- r-pcamethods +- r-plotly +- r-proda +- r-rlang +- r-rmarkdown +- r-rtsne +- r-s4vectors +- r-shiny +- r-shinydashboard +- r-shinyhelper +- r-shinyjs +- r-summarizedexperiment +- r-tibble +- r-tidyr +- r-umap +- r-upsetr +- r-vegan +- r-vsn +update_on: +- regex: MatrixQCvis_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MatrixQCvis diff --git a/prepare/r-matrixrider/PKGBUILD b/prepare/r-matrixrider/PKGBUILD new file mode 100644 index 0000000000..82a864966c --- /dev/null +++ b/prepare/r-matrixrider/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MatrixRider +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Obtain total affinity and occupancies for binding site matrices on a given sequence' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-iranges + r-s4vectors + r-tfbstools + r-xvector +) +optdepends=( + r-biocgenerics + r-biocstyle + r-jaspar2014 + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-matrixrider/lilac.py b/prepare/r-matrixrider/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-matrixrider/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-matrixrider/lilac.yaml b/prepare/r-matrixrider/lilac.yaml new file mode 100644 index 0000000000..2c7612f458 --- /dev/null +++ b/prepare/r-matrixrider/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-iranges +- r-s4vectors +- r-tfbstools +- r-xvector +update_on: +- regex: MatrixRider_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MatrixRider diff --git a/prepare/r-matrixtests/PKGBUILD b/prepare/r-matrixtests/PKGBUILD new file mode 100644 index 0000000000..3233d9e6a8 --- /dev/null +++ b/prepare/r-matrixtests/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=matrixTests +_pkgver=0.1.9.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast Statistical Hypothesis Tests on Rows and Columns of Matrices' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-matrixstats +) +optdepends=( + r-car + r-cosinor + r-cosinor2 + r-moments + r-pmcmrplus + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-matrixtests/lilac.py b/prepare/r-matrixtests/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-matrixtests/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-matrixtests/lilac.yaml b/prepare/r-matrixtests/lilac.yaml new file mode 100644 index 0000000000..405bb41c32 --- /dev/null +++ b/prepare/r-matrixtests/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-matrixstats +update_on: +- regex: matrixTests_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=matrixTests diff --git a/prepare/r-matter/PKGBUILD b/prepare/r-matter/PKGBUILD new file mode 100644 index 0000000000..b2c0589612 --- /dev/null +++ b/prepare/r-matter/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=matter +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A framework for rapid prototyping with file-based data structures' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biglm + r-biocgenerics + r-biocparallel + r-digest + r-irlba + r-protgenerics +) +optdepends=( + r-biocstyle + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-matter/lilac.py b/prepare/r-matter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-matter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-matter/lilac.yaml b/prepare/r-matter/lilac.yaml new file mode 100644 index 0000000000..2b227243e7 --- /dev/null +++ b/prepare/r-matter/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biglm +- r-biocgenerics +- r-biocparallel +- r-digest +- r-irlba +- r-protgenerics +update_on: +- regex: matter_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/matter diff --git a/prepare/r-maxlik/PKGBUILD b/prepare/r-maxlik/PKGBUILD new file mode 100644 index 0000000000..0f4091c99c --- /dev/null +++ b/prepare/r-maxlik/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=maxLik +_pkgver=1.5-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Maximum Likelihood Estimation and Related Tools' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-generics + r-misctools + r-sandwich +) +optdepends=( + r-clue + r-dlm + r-mass + r-plot3d + r-tibble + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-maxlik/lilac.py b/prepare/r-maxlik/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-maxlik/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-maxlik/lilac.yaml b/prepare/r-maxlik/lilac.yaml new file mode 100644 index 0000000000..e4736abd52 --- /dev/null +++ b/prepare/r-maxlik/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-generics +- r-misctools +- r-sandwich +update_on: +- regex: maxLik_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=maxLik diff --git a/prepare/r-maxstat/PKGBUILD b/prepare/r-maxstat/PKGBUILD new file mode 100644 index 0000000000..5346243fcb --- /dev/null +++ b/prepare/r-maxstat/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=maxstat +_pkgver=0.7-25 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Maximally Selected Rank Statistics' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-exactranktests + r-mvtnorm +) +optdepends=( + r-survival + r-th.data +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-maxstat/lilac.py b/prepare/r-maxstat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-maxstat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-maxstat/lilac.yaml b/prepare/r-maxstat/lilac.yaml new file mode 100644 index 0000000000..dea07d25bd --- /dev/null +++ b/prepare/r-maxstat/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-exactranktests +- r-mvtnorm +update_on: +- regex: maxstat_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=maxstat diff --git a/prepare/r-mba/PKGBUILD b/prepare/r-mba/PKGBUILD new file mode 100644 index 0000000000..cf811f5b65 --- /dev/null +++ b/prepare/r-mba/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MBA +_pkgver=0.0-9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multilevel B-Spline Approximation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bh +) +optdepends=( + r-sp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mba/lilac.py b/prepare/r-mba/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mba/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mba/lilac.yaml b/prepare/r-mba/lilac.yaml new file mode 100644 index 0000000000..372b2b9773 --- /dev/null +++ b/prepare/r-mba/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +update_on: +- regex: MBA_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MBA diff --git a/prepare/r-mbamethyl/PKGBUILD b/prepare/r-mbamethyl/PKGBUILD new file mode 100644 index 0000000000..c18421bee2 --- /dev/null +++ b/prepare/r-mbamethyl/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MBAmethyl +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Model-based analysis of DNA methylation data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mbamethyl/lilac.py b/prepare/r-mbamethyl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mbamethyl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mbamethyl/lilac.yaml b/prepare/r-mbamethyl/lilac.yaml new file mode 100644 index 0000000000..3ed9642471 --- /dev/null +++ b/prepare/r-mbamethyl/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: MBAmethyl_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MBAmethyl diff --git a/prepare/r-mbased/PKGBUILD b/prepare/r-mbased/PKGBUILD new file mode 100644 index 0000000000..928d256426 --- /dev/null +++ b/prepare/r-mbased/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MBASED +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biocparallel + r-genomicranges + r-runit + r-summarizedexperiment +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mbased/lilac.py b/prepare/r-mbased/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mbased/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mbased/lilac.yaml b/prepare/r-mbased/lilac.yaml new file mode 100644 index 0000000000..ce31023a98 --- /dev/null +++ b/prepare/r-mbased/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-genomicranges +- r-runit +- r-summarizedexperiment +update_on: +- regex: MBASED_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MBASED diff --git a/prepare/r-mbcb/PKGBUILD b/prepare/r-mbcb/PKGBUILD new file mode 100644 index 0000000000..6c4249ed0a --- /dev/null +++ b/prepare/r-mbcb/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MBCB +_pkgver=1.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MBCB (Model-based Background Correction for Beadarray)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-preprocesscore + r-tcltk2 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mbcb/lilac.py b/prepare/r-mbcb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mbcb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mbcb/lilac.yaml b/prepare/r-mbcb/lilac.yaml new file mode 100644 index 0000000000..10fefba270 --- /dev/null +++ b/prepare/r-mbcb/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-preprocesscore +- r-tcltk2 +update_on: +- regex: MBCB_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MBCB diff --git a/prepare/r-mbest/PKGBUILD b/prepare/r-mbest/PKGBUILD new file mode 100644 index 0000000000..828366d8af --- /dev/null +++ b/prepare/r-mbest/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mbest +_pkgver=0.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Moment-Based Estimation for Hierarchical Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-abind + r-bigmemory + r-foreach + r-lme4 + r-logging +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mbest/lilac.py b/prepare/r-mbest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mbest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mbest/lilac.yaml b/prepare/r-mbest/lilac.yaml new file mode 100644 index 0000000000..4dfaf8dd08 --- /dev/null +++ b/prepare/r-mbest/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-bigmemory +- r-foreach +- r-lme4 +- r-logging +update_on: +- regex: mbest_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mbest diff --git a/prepare/r-mbkmeans/PKGBUILD b/prepare/r-mbkmeans/PKGBUILD new file mode 100644 index 0000000000..6dacd4faf9 --- /dev/null +++ b/prepare/r-mbkmeans/PKGBUILD @@ -0,0 +1,52 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=mbkmeans +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mini-batch K-means Clustering for Single-Cell RNA-seq' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-beachmat + r-benchmarkme + r-biocparallel + r-clusterr + r-delayedarray + r-rcpp + r-rcpparmadillo + r-rhdf5lib + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-beachmat + r-biocstyle + r-bluster + r-delayedmatrixstats + r-hdf5array + r-knitr + r-rhdf5lib + r-rmarkdown + r-scater + r-tenxpbmcdata + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mbkmeans/lilac.py b/prepare/r-mbkmeans/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mbkmeans/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mbkmeans/lilac.yaml b/prepare/r-mbkmeans/lilac.yaml new file mode 100644 index 0000000000..3b2aed450c --- /dev/null +++ b/prepare/r-mbkmeans/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beachmat +- r-benchmarkme +- r-biocparallel +- r-clusterr +- r-delayedarray +- r-rcpp +- r-rcpparmadillo +- r-rhdf5lib +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: mbkmeans_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mbkmeans diff --git a/prepare/r-mboost/PKGBUILD b/prepare/r-mboost/PKGBUILD new file mode 100644 index 0000000000..73b021f68e --- /dev/null +++ b/prepare/r-mboost/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mboost +_pkgver=2.9-5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Model-Based Boosting' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-nnls + r-partykit + r-quadprog + r-stabs +) +optdepends=( + r-bayesx + r-fields + r-gbm + r-kangar00 + r-mass + r-mlbench + r-nnet + r-randomforest + r-rcolorbrewer + r-rpart + r-testthat + r-th.data +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mboost/lilac.py b/prepare/r-mboost/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mboost/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mboost/lilac.yaml b/prepare/r-mboost/lilac.yaml new file mode 100644 index 0000000000..03f7bc12b6 --- /dev/null +++ b/prepare/r-mboost/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-nnls +- r-partykit +- r-quadprog +- r-stabs +update_on: +- regex: mboost_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mboost diff --git a/prepare/r-mbpcr/PKGBUILD b/prepare/r-mbpcr/PKGBUILD new file mode 100644 index 0000000000..4940b3af65 --- /dev/null +++ b/prepare/r-mbpcr/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mBPCR +_pkgver=1.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian Piecewise Constant Regression for DNA copy number estimation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-gwastools + r-oligoclasses +) +optdepends=( + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mbpcr/lilac.py b/prepare/r-mbpcr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mbpcr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mbpcr/lilac.yaml b/prepare/r-mbpcr/lilac.yaml new file mode 100644 index 0000000000..370d864a8f --- /dev/null +++ b/prepare/r-mbpcr/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-gwastools +- r-oligoclasses +update_on: +- regex: mBPCR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mBPCR diff --git a/prepare/r-mbqn/PKGBUILD b/prepare/r-mbqn/PKGBUILD new file mode 100644 index 0000000000..7b317b4cab --- /dev/null +++ b/prepare/r-mbqn/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MBQN +_pkgver=2.5.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mean/Median-balanced quantile normalization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocfilecache + r-ggplot2 + r-limma + r-paireddata + r-preprocesscore + r-rappdirs + r-rcurl + r-rpx + r-summarizedexperiment + r-xml2 +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mbqn/lilac.py b/prepare/r-mbqn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mbqn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mbqn/lilac.yaml b/prepare/r-mbqn/lilac.yaml new file mode 100644 index 0000000000..ab510da153 --- /dev/null +++ b/prepare/r-mbqn/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-ggplot2 +- r-limma +- r-paireddata +- r-preprocesscore +- r-rappdirs +- r-rcurl +- r-rpx +- r-summarizedexperiment +- r-xml2 +update_on: +- regex: MBQN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MBQN diff --git a/prepare/r-mbttest/PKGBUILD b/prepare/r-mbttest/PKGBUILD new file mode 100644 index 0000000000..9f60f70711 --- /dev/null +++ b/prepare/r-mbttest/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MBttest +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multiple Beta t-Tests' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-gplots + r-gtools +) +optdepends=( + r-biocgenerics + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mbttest/lilac.py b/prepare/r-mbttest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mbttest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mbttest/lilac.yaml b/prepare/r-mbttest/lilac.yaml new file mode 100644 index 0000000000..ce15e3dbca --- /dev/null +++ b/prepare/r-mbttest/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gplots +- r-gtools +update_on: +- regex: MBttest_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MBttest diff --git a/prepare/r-mcbiclust/PKGBUILD b/prepare/r-mcbiclust/PKGBUILD new file mode 100644 index 0000000000..d48bd869ea --- /dev/null +++ b/prepare/r-mcbiclust/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MCbiclust +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Massive correlating biclusters for gene expression data and associated methods' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocparallel + r-ggally + r-ggplot2 + r-go.db + r-org.hs.eg.db + r-scales + r-wgcna +) +optdepends=( + r-biocstyle + r-devtools + r-dplyr + r-gplots + r-gprofiler + r-gsva + r-knitr + r-mass + r-pander + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mcbiclust/lilac.py b/prepare/r-mcbiclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mcbiclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mcbiclust/lilac.yaml b/prepare/r-mcbiclust/lilac.yaml new file mode 100644 index 0000000000..d8a4064d8e --- /dev/null +++ b/prepare/r-mcbiclust/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocparallel +- r-ggally +- r-ggplot2 +- r-go.db +- r-org.hs.eg.db +- r-scales +- r-wgcna +update_on: +- regex: MCbiclust_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MCbiclust diff --git a/prepare/r-mcbiopi/PKGBUILD b/prepare/r-mcbiopi/PKGBUILD new file mode 100644 index 0000000000..39f7edb2ea --- /dev/null +++ b/prepare/r-mcbiopi/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mcbiopi +_pkgver=1.1.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Matrix Computation Based Identification of Prime Implicants' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mcbiopi/lilac.py b/prepare/r-mcbiopi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mcbiopi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mcbiopi/lilac.yaml b/prepare/r-mcbiopi/lilac.yaml new file mode 100644 index 0000000000..fe780efbb6 --- /dev/null +++ b/prepare/r-mcbiopi/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: mcbiopi_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mcbiopi diff --git a/prepare/r-mcl/PKGBUILD b/prepare/r-mcl/PKGBUILD new file mode 100644 index 0000000000..38c6458d39 --- /dev/null +++ b/prepare/r-mcl/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MCL +_pkgver=1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Markov Cluster Algorithm' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-expm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mcl/lilac.py b/prepare/r-mcl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mcl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mcl/lilac.yaml b/prepare/r-mcl/lilac.yaml new file mode 100644 index 0000000000..14d3fbaef4 --- /dev/null +++ b/prepare/r-mcl/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-expm +update_on: +- regex: MCL_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MCL diff --git a/prepare/r-mclust/PKGBUILD b/prepare/r-mclust/PKGBUILD new file mode 100644 index 0000000000..6f63a0afbd --- /dev/null +++ b/prepare/r-mclust/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mclust +_pkgver=5.4.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-geometry + r-knitr + r-mass + r-mix + r-rmarkdown +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mclust/lilac.py b/prepare/r-mclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mclust/lilac.yaml b/prepare/r-mclust/lilac.yaml new file mode 100644 index 0000000000..8dc4be9f79 --- /dev/null +++ b/prepare/r-mclust/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: mclust_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mclust diff --git a/prepare/r-mcmc/PKGBUILD b/prepare/r-mcmc/PKGBUILD new file mode 100644 index 0000000000..71fd0b77fc --- /dev/null +++ b/prepare/r-mcmc/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mcmc +_pkgver=0.9-7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Markov Chain Monte Carlo' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-iso + r-xtable +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mcmc/lilac.py b/prepare/r-mcmc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mcmc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mcmc/lilac.yaml b/prepare/r-mcmc/lilac.yaml new file mode 100644 index 0000000000..e4191cff0a --- /dev/null +++ b/prepare/r-mcmc/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: mcmc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mcmc diff --git a/prepare/r-mcmcglmm/PKGBUILD b/prepare/r-mcmcglmm/PKGBUILD new file mode 100644 index 0000000000..89ab5298d0 --- /dev/null +++ b/prepare/r-mcmcglmm/PKGBUILD @@ -0,0 +1,38 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=MCMCglmm +_pkgver=2.32 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MCMC Generalised Linear Mixed Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-coda + r-corpcor + r-cubature + r-tensora +) +optdepends=( + r-combinat + r-mvtnorm + r-orthopolynom + r-rgl +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mcmcglmm/lilac.py b/prepare/r-mcmcglmm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mcmcglmm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mcmcglmm/lilac.yaml b/prepare/r-mcmcglmm/lilac.yaml new file mode 100644 index 0000000000..f9c8eb5d2f --- /dev/null +++ b/prepare/r-mcmcglmm/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-coda +- r-corpcor +- r-cubature +- r-tensora +update_on: +- regex: MCMCglmm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MCMCglmm diff --git a/prepare/r-mcmcpack/PKGBUILD b/prepare/r-mcmcpack/PKGBUILD new file mode 100644 index 0000000000..f3224c8ceb --- /dev/null +++ b/prepare/r-mcmcpack/PKGBUILD @@ -0,0 +1,30 @@ +# system requirements: gcc (>= 4.0) +# Maintainer: Guoyi Zhang + +_pkgname=MCMCpack +_pkgver=1.6-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Markov Chain Monte Carlo (MCMC) Package' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-coda + r-mcmc + r-quantreg +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mcmcpack/lilac.py b/prepare/r-mcmcpack/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mcmcpack/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mcmcpack/lilac.yaml b/prepare/r-mcmcpack/lilac.yaml new file mode 100644 index 0000000000..cac05123b6 --- /dev/null +++ b/prepare/r-mcmcpack/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-coda +- r-mcmc +- r-quantreg +update_on: +- regex: MCMCpack_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MCMCpack diff --git a/prepare/r-mcmcprecision/PKGBUILD b/prepare/r-mcmcprecision/PKGBUILD new file mode 100644 index 0000000000..bcd83facd2 --- /dev/null +++ b/prepare/r-mcmcprecision/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MCMCprecision +_pkgver=0.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Precision of Discrete Parameters in Transdimensional MCMC' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-combinat + r-rcpp + r-rcpparmadillo + r-rcppeigen + r-rcppprogress +) +optdepends=( + r-r.rsp + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mcmcprecision/lilac.py b/prepare/r-mcmcprecision/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mcmcprecision/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mcmcprecision/lilac.yaml b/prepare/r-mcmcprecision/lilac.yaml new file mode 100644 index 0000000000..6e684abb4c --- /dev/null +++ b/prepare/r-mcmcprecision/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-combinat +- r-rcpp +- r-rcpparmadillo +- r-rcppeigen +- r-rcppprogress +update_on: +- regex: MCMCprecision_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MCMCprecision diff --git a/prepare/r-mco/PKGBUILD b/prepare/r-mco/PKGBUILD new file mode 100644 index 0000000000..b4aaca4ccb --- /dev/null +++ b/prepare/r-mco/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mco +_pkgver=1.15.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multiple Criteria Optimization Algorithms and Related Functions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-scatterplot3d + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mco/lilac.py b/prepare/r-mco/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mco/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mco/lilac.yaml b/prepare/r-mco/lilac.yaml new file mode 100644 index 0000000000..49a0c91455 --- /dev/null +++ b/prepare/r-mco/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: mco_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mco diff --git a/prepare/r-mcsea/PKGBUILD b/prepare/r-mcsea/PKGBUILD new file mode 100644 index 0000000000..62a31d431c --- /dev/null +++ b/prepare/r-mcsea/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mCSEA +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methylated CpGs Set Enrichment Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-fgsea + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-gviz + r-homo.sapiens + r-iranges + r-limma + r-mcseadata + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biobase + r-biocgenerics + r-biocstyle + r-flowsorted.blood.450k + r-knitr + r-leukemiaseset + r-minfi + r-minfidata + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mcsea/lilac.py b/prepare/r-mcsea/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mcsea/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mcsea/lilac.yaml b/prepare/r-mcsea/lilac.yaml new file mode 100644 index 0000000000..edf101af35 --- /dev/null +++ b/prepare/r-mcsea/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-fgsea +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-gviz +- r-homo.sapiens +- r-iranges +- r-limma +- r-mcseadata +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: mCSEA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mCSEA diff --git a/prepare/r-mcseadata/PKGBUILD b/prepare/r-mcseadata/PKGBUILD new file mode 100644 index 0000000000..727c6fb869 --- /dev/null +++ b/prepare/r-mcseadata/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mCSEAdata +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data package for mCSEA package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mcseadata/lilac.py b/prepare/r-mcseadata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mcseadata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mcseadata/lilac.yaml b/prepare/r-mcseadata/lilac.yaml new file mode 100644 index 0000000000..d248ab46a5 --- /dev/null +++ b/prepare/r-mcseadata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: mCSEAdata_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mCSEAdata diff --git a/prepare/r-mdp/PKGBUILD b/prepare/r-mdp/PKGBUILD new file mode 100644 index 0000000000..d8d03432c9 --- /dev/null +++ b/prepare/r-mdp/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mdp +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-gridextra +) +optdepends=( + r-biocmanager + r-fgsea + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mdp/lilac.py b/prepare/r-mdp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mdp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mdp/lilac.yaml b/prepare/r-mdp/lilac.yaml new file mode 100644 index 0000000000..19b79ae371 --- /dev/null +++ b/prepare/r-mdp/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gridextra +update_on: +- regex: mdp_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mdp diff --git a/prepare/r-mdqc/PKGBUILD b/prepare/r-mdqc/PKGBUILD new file mode 100644 index 0000000000..0a143ae351 --- /dev/null +++ b/prepare/r-mdqc/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mdqc +_pkgver=1.56.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mahalanobis Distance Quality Control for microarrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mdqc/lilac.py b/prepare/r-mdqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mdqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mdqc/lilac.yaml b/prepare/r-mdqc/lilac.yaml new file mode 100644 index 0000000000..a8816cb7b2 --- /dev/null +++ b/prepare/r-mdqc/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: mdqc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mdqc diff --git a/prepare/r-mdts/PKGBUILD b/prepare/r-mdts/PKGBUILD new file mode 100644 index 0000000000..7fd76de092 --- /dev/null +++ b/prepare/r-mdts/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MDTS +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detection of de novo deletion in targeted sequencing trios' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-dnacopy + r-genomicalignments + r-genomicranges + r-iranges + r-rsamtools + r-stringr +) +optdepends=( + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mdts/lilac.py b/prepare/r-mdts/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mdts/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mdts/lilac.yaml b/prepare/r-mdts/lilac.yaml new file mode 100644 index 0000000000..94239a4239 --- /dev/null +++ b/prepare/r-mdts/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-dnacopy +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-rsamtools +- r-stringr +update_on: +- regex: MDTS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MDTS diff --git a/prepare/r-meal/PKGBUILD b/prepare/r-meal/PKGBUILD new file mode 100644 index 0000000000..25cc4bf3e2 --- /dev/null +++ b/prepare/r-meal/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MEAL +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Perform methylation analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-genomicranges + r-ggplot2 + r-gviz + r-iranges + r-isva + r-limma + r-matrixstats + r-minfi + r-missmethyl + r-multidataset + r-permute + r-s4vectors + r-smartsva + r-summarizedexperiment + r-vegan +) +optdepends=( + r-biocstyle + r-brgedata + r-illuminahumanmethylation450kanno.ilmn12.hg19 + r-illuminahumanmethylationepicanno.ilm10b2.hg19 + r-knitr + r-minfidata + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-meal/lilac.py b/prepare/r-meal/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-meal/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-meal/lilac.yaml b/prepare/r-meal/lilac.yaml new file mode 100644 index 0000000000..209b920bfc --- /dev/null +++ b/prepare/r-meal/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-genomicranges +- r-ggplot2 +- r-gviz +- r-iranges +- r-isva +- r-limma +- r-matrixstats +- r-minfi +- r-missmethyl +- r-multidataset +- r-permute +- r-s4vectors +- r-smartsva +- r-summarizedexperiment +- r-vegan +update_on: +- regex: MEAL_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MEAL diff --git a/prepare/r-measurementerror.cor/PKGBUILD b/prepare/r-measurementerror.cor/PKGBUILD new file mode 100644 index 0000000000..2d78fd2d01 --- /dev/null +++ b/prepare/r-measurementerror.cor/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MeasurementError.cor +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Measurement Error model estimate for correlation coefficient' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-measurementerror.cor/lilac.py b/prepare/r-measurementerror.cor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-measurementerror.cor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-measurementerror.cor/lilac.yaml b/prepare/r-measurementerror.cor/lilac.yaml new file mode 100644 index 0000000000..a37e6a3197 --- /dev/null +++ b/prepare/r-measurementerror.cor/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: MeasurementError.cor_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MeasurementError.cor diff --git a/prepare/r-meat/PKGBUILD b/prepare/r-meat/PKGBUILD new file mode 100644 index 0000000000..f6bda54bab --- /dev/null +++ b/prepare/r-meat/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MEAT +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Muscle Epigenetic Age Test' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-dynamictreecut + r-glmnet + r-impute + r-minfi + r-rpmm + r-stringr + r-summarizedexperiment + r-tibble + r-watermelon +) +optdepends=( + r-biocstyle + r-knitr + r-markdown + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-meat/lilac.py b/prepare/r-meat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-meat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-meat/lilac.yaml b/prepare/r-meat/lilac.yaml new file mode 100644 index 0000000000..e8e38bbdef --- /dev/null +++ b/prepare/r-meat/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-dynamictreecut +- r-glmnet +- r-impute +- r-minfi +- r-rpmm +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-watermelon +update_on: +- regex: MEAT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MEAT diff --git a/prepare/r-meb/PKGBUILD b/prepare/r-meb/PKGBUILD new file mode 100644 index 0000000000..13b5275b4c --- /dev/null +++ b/prepare/r-meb/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MEB +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A normalization-invariant minimum enclosing ball method to detect differentially expressed genes for RNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-e1071 + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-meb/lilac.py b/prepare/r-meb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-meb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-meb/lilac.yaml b/prepare/r-meb/lilac.yaml new file mode 100644 index 0000000000..8958cef9c6 --- /dev/null +++ b/prepare/r-meb/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-e1071 +- r-summarizedexperiment +update_on: +- regex: MEB_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MEB diff --git a/prepare/r-medips/PKGBUILD b/prepare/r-medips/PKGBUILD new file mode 100644 index 0000000000..778c35647f --- /dev/null +++ b/prepare/r-medips/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MEDIPS +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='DNA IP-seq data analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-biostrings + r-bsgenome + r-dnacopy + r-edger + r-genomicranges + r-gtools + r-iranges + r-preprocesscore + r-rsamtools + r-rtracklayer +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-medipsdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-medips/lilac.py b/prepare/r-medips/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-medips/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-medips/lilac.yaml b/prepare/r-medips/lilac.yaml new file mode 100644 index 0000000000..db85a3420e --- /dev/null +++ b/prepare/r-medips/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-biostrings +- r-bsgenome +- r-dnacopy +- r-edger +- r-genomicranges +- r-gtools +- r-iranges +- r-preprocesscore +- r-rsamtools +- r-rtracklayer +update_on: +- regex: MEDIPS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MEDIPS diff --git a/prepare/r-medme/PKGBUILD b/prepare/r-medme/PKGBUILD new file mode 100644 index 0000000000..f5ae266b13 --- /dev/null +++ b/prepare/r-medme/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MEDME +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Modelling Experimental Data from MeDIP Enrichment' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-drc +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg18 + r-bsgenome.mmusculus.ucsc.mm9 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-medme/lilac.py b/prepare/r-medme/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-medme/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-medme/lilac.yaml b/prepare/r-medme/lilac.yaml new file mode 100644 index 0000000000..27cb7d0fd0 --- /dev/null +++ b/prepare/r-medme/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-drc +update_on: +- regex: MEDME_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MEDME diff --git a/prepare/r-mefa/PKGBUILD b/prepare/r-mefa/PKGBUILD new file mode 100644 index 0000000000..24276fb072 --- /dev/null +++ b/prepare/r-mefa/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mefa +_pkgver=3.2-8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multivariate Data Handling in Ecology and Biogeography' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-mass + r-matrix + r-mefa4 + r-vegan +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mefa/lilac.py b/prepare/r-mefa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mefa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mefa/lilac.yaml b/prepare/r-mefa/lilac.yaml new file mode 100644 index 0000000000..efdfa3640e --- /dev/null +++ b/prepare/r-mefa/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: mefa_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mefa diff --git a/prepare/r-megadepth/PKGBUILD b/prepare/r-megadepth/PKGBUILD new file mode 100644 index 0000000000..e2ec4e74a5 --- /dev/null +++ b/prepare/r-megadepth/PKGBUILD @@ -0,0 +1,47 @@ +# system requirements: megadepth() +# Maintainer: Guoyi Zhang + +_pkgname=megadepth +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='megadepth: BigWig and BAM related utilities' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-cmdfun + r-dplyr + r-fs + r-genomicranges + r-magrittr + r-readr + r-xfun +) +optdepends=( + r-biocstyle + r-covr + r-derfinder + r-genomeinfodb + r-knitr + r-refmanager + r-rmarkdown + r-rtracklayer + r-sessioninfo + r-testthat + r-tools +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-megadepth/lilac.py b/prepare/r-megadepth/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-megadepth/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-megadepth/lilac.yaml b/prepare/r-megadepth/lilac.yaml new file mode 100644 index 0000000000..cf2fecd9b4 --- /dev/null +++ b/prepare/r-megadepth/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cmdfun +- r-dplyr +- r-fs +- r-genomicranges +- r-magrittr +- r-readr +- r-xfun +update_on: +- regex: megadepth_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/megadepth diff --git a/prepare/r-meigor/PKGBUILD b/prepare/r-meigor/PKGBUILD new file mode 100644 index 0000000000..594f1772bd --- /dev/null +++ b/prepare/r-meigor/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MEIGOR +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MEIGO - MEtaheuristics for bIoinformatics Global Optimization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cnorode + r-desolve + r-rsolnp + r-snowfall +) +optdepends=( + r-cellnoptr + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-meigor/lilac.py b/prepare/r-meigor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-meigor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-meigor/lilac.yaml b/prepare/r-meigor/lilac.yaml new file mode 100644 index 0000000000..fc166e9b01 --- /dev/null +++ b/prepare/r-meigor/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cnorode +- r-desolve +- r-rsolnp +- r-snowfall +update_on: +- regex: MEIGOR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MEIGOR diff --git a/prepare/r-melissa/PKGBUILD b/prepare/r-melissa/PKGBUILD new file mode 100644 index 0000000000..efb7cb9aa7 --- /dev/null +++ b/prepare/r-melissa/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Melissa +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian clustering and imputationa of single cell methylomes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-biocstyle + r-bprmeth + r-cowplot + r-data.table + r-doparallel + r-foreach + r-genomicranges + r-ggplot2 + r-magrittr + r-matrixcalc + r-mclust + r-mcmcpack + r-mvtnorm + r-rocr + r-truncnorm +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-melissa/lilac.py b/prepare/r-melissa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-melissa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-melissa/lilac.yaml b/prepare/r-melissa/lilac.yaml new file mode 100644 index 0000000000..7fe59f985f --- /dev/null +++ b/prepare/r-melissa/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biocstyle +- r-bprmeth +- r-cowplot +- r-data.table +- r-doparallel +- r-foreach +- r-genomicranges +- r-ggplot2 +- r-magrittr +- r-matrixcalc +- r-mclust +- r-mcmcpack +- r-mvtnorm +- r-rocr +- r-truncnorm +update_on: +- regex: Melissa_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Melissa diff --git a/prepare/r-memes/PKGBUILD b/prepare/r-memes/PKGBUILD new file mode 100644 index 0000000000..2dd76e7721 --- /dev/null +++ b/prepare/r-memes/PKGBUILD @@ -0,0 +1,60 @@ +# system requirements: Meme Suite (v5.3.3 or above) +# Maintainer: Guoyi Zhang + +_pkgname=memes +_pkgver=1.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='motif matching, comparison, and de novo discovery using the MEME Suite' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biostrings + r-cmdfun + r-dplyr + r-genomicranges + r-ggplot2 + r-ggseqlogo + r-magrittr + r-matrixstats + r-patchwork + r-processx + r-purrr + r-readr + r-rlang + r-tibble + r-tidyr + r-universalmotif + r-usethis + r-xml2 +) +optdepends=( + r-bsgenome.dmelanogaster.ucsc.dm3 + r-bsgenome.dmelanogaster.ucsc.dm6 + r-covr + r-cowplot + r-forcats + r-knitr + r-motifdb + r-pheatmap + r-plyranges + r-pmcmrplus + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-memes/lilac.py b/prepare/r-memes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-memes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-memes/lilac.yaml b/prepare/r-memes/lilac.yaml new file mode 100644 index 0000000000..2de45944b6 --- /dev/null +++ b/prepare/r-memes/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-cmdfun +- r-dplyr +- r-genomicranges +- r-ggplot2 +- r-ggseqlogo +- r-magrittr +- r-matrixstats +- r-patchwork +- r-processx +- r-purrr +- r-readr +- r-rlang +- r-tibble +- r-tidyr +- r-universalmotif +- r-usethis +- r-xml2 +update_on: +- regex: memes_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/memes diff --git a/prepare/r-memuse/PKGBUILD b/prepare/r-memuse/PKGBUILD new file mode 100644 index 0000000000..2870e5e4a1 --- /dev/null +++ b/prepare/r-memuse/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=memuse +_pkgver=4.2-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Memory Estimation Utilities' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-memuse/lilac.py b/prepare/r-memuse/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-memuse/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-memuse/lilac.yaml b/prepare/r-memuse/lilac.yaml new file mode 100644 index 0000000000..1b485e0a25 --- /dev/null +++ b/prepare/r-memuse/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: memuse_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=memuse diff --git a/prepare/r-mergeomics/PKGBUILD b/prepare/r-mergeomics/PKGBUILD new file mode 100644 index 0000000000..a5cdabd12e --- /dev/null +++ b/prepare/r-mergeomics/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Mergeomics +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integrative network analysis of omics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mergeomics/lilac.py b/prepare/r-mergeomics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mergeomics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mergeomics/lilac.yaml b/prepare/r-mergeomics/lilac.yaml new file mode 100644 index 0000000000..ef4cbae19c --- /dev/null +++ b/prepare/r-mergeomics/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Mergeomics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Mergeomics diff --git a/prepare/r-meshdbi/PKGBUILD b/prepare/r-meshdbi/PKGBUILD new file mode 100644 index 0000000000..6fdfc243f7 --- /dev/null +++ b/prepare/r-meshdbi/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MeSHDbi +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='DBI to construct MeSH-related package from sqlite file' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biobase + r-rsqlite +) +optdepends=( + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-meshdbi/lilac.py b/prepare/r-meshdbi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-meshdbi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-meshdbi/lilac.yaml b/prepare/r-meshdbi/lilac.yaml new file mode 100644 index 0000000000..a256fd5d0e --- /dev/null +++ b/prepare/r-meshdbi/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-rsqlite +update_on: +- regex: MeSHDbi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MeSHDbi diff --git a/prepare/r-meshes/PKGBUILD b/prepare/r-meshes/PKGBUILD new file mode 100644 index 0000000000..9559010cb6 --- /dev/null +++ b/prepare/r-meshes/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=meshes +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MeSH Enrichment and Semantic analyses' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-annotationhub + r-dose + r-enrichplot + r-gosemsim + r-meshdbi + r-yulab.utils +) +optdepends=( + r-knitr + r-prettydoc + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-meshes/lilac.py b/prepare/r-meshes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-meshes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-meshes/lilac.yaml b/prepare/r-meshes/lilac.yaml new file mode 100644 index 0000000000..4bfe715812 --- /dev/null +++ b/prepare/r-meshes/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-dose +- r-enrichplot +- r-gosemsim +- r-meshdbi +- r-yulab.utils +update_on: +- regex: meshes_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/meshes diff --git a/prepare/r-meshr/PKGBUILD b/prepare/r-meshr/PKGBUILD new file mode 100644 index 0000000000..ef72ef5a2a --- /dev/null +++ b/prepare/r-meshr/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=meshr +_pkgver=2.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for conducting enrichment analysis of MeSH' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biocstyle + r-category + r-fdrtool + r-knitr + r-markdown + r-meshdbi + r-rmarkdown + r-rsqlite + r-s4vectors +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-meshr/lilac.py b/prepare/r-meshr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-meshr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-meshr/lilac.yaml b/prepare/r-meshr/lilac.yaml new file mode 100644 index 0000000000..a8d9efedde --- /dev/null +++ b/prepare/r-meshr/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocstyle +- r-category +- r-fdrtool +- r-knitr +- r-markdown +- r-meshdbi +- r-rmarkdown +- r-rsqlite +- r-s4vectors +update_on: +- regex: meshr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/meshr diff --git a/prepare/r-meskit/PKGBUILD b/prepare/r-meskit/PKGBUILD new file mode 100644 index 0000000000..12ae2cb67c --- /dev/null +++ b/prepare/r-meskit/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MesKit +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-ape + r-biostrings + r-circlize + r-complexheatmap + r-cowplot + r-data.table + r-dplyr + r-ggplot2 + r-ggrepel + r-ggridges + r-iranges + r-mclust + r-phangorn + r-pracma + r-rcolorbrewer + r-s4vectors + r-tidyr +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg19 + r-clusterprofiler + r-knitr + r-org.hs.eg.db + r-rmarkdown + r-shiny + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-meskit/lilac.py b/prepare/r-meskit/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-meskit/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-meskit/lilac.yaml b/prepare/r-meskit/lilac.yaml new file mode 100644 index 0000000000..304a2f0da8 --- /dev/null +++ b/prepare/r-meskit/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-ape +- r-biostrings +- r-circlize +- r-complexheatmap +- r-cowplot +- r-data.table +- r-dplyr +- r-ggplot2 +- r-ggrepel +- r-ggridges +- r-iranges +- r-mclust +- r-phangorn +- r-pracma +- r-rcolorbrewer +- r-s4vectors +- r-tidyr +update_on: +- regex: MesKit_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MesKit diff --git a/prepare/r-mess/PKGBUILD b/prepare/r-mess/PKGBUILD new file mode 100644 index 0000000000..c0d37f01aa --- /dev/null +++ b/prepare/r-mess/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MESS +_pkgver=0.5.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Miscellaneous Esoteric Statistical Scripts' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-geem + r-geepack + r-ggformula + r-ggplot2 + r-glmnet + r-kinship2 + r-mvtnorm + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-knitr + r-lme4 + r-magrittr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mess/lilac.py b/prepare/r-mess/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mess/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mess/lilac.yaml b/prepare/r-mess/lilac.yaml new file mode 100644 index 0000000000..4e4dda7a41 --- /dev/null +++ b/prepare/r-mess/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-geem +- r-geepack +- r-ggformula +- r-ggplot2 +- r-glmnet +- r-kinship2 +- r-mvtnorm +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: MESS_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MESS diff --git a/prepare/r-messina/PKGBUILD b/prepare/r-messina/PKGBUILD new file mode 100644 index 0000000000..cf878c286b --- /dev/null +++ b/prepare/r-messina/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=messina +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('EPL') +depends=( + r + r-foreach + r-ggplot2 + r-plyr + r-rcpp +) +optdepends=( + r-antiprofilesdata + r-biobase + r-biocstyle + r-domc + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-messina/lilac.py b/prepare/r-messina/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-messina/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-messina/lilac.yaml b/prepare/r-messina/lilac.yaml new file mode 100644 index 0000000000..89b51a454c --- /dev/null +++ b/prepare/r-messina/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-foreach +- r-ggplot2 +- r-plyr +- r-rcpp +update_on: +- regex: messina_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/messina diff --git a/prepare/r-metab/PKGBUILD b/prepare/r-metab/PKGBUILD new file mode 100644 index 0000000000..afb81912ae --- /dev/null +++ b/prepare/r-metab/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Metab +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-pander + r-svdialogs + r-xcms +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metab/lilac.py b/prepare/r-metab/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metab/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metab/lilac.yaml b/prepare/r-metab/lilac.yaml new file mode 100644 index 0000000000..1dd570e558 --- /dev/null +++ b/prepare/r-metab/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-pander +- r-svdialogs +- r-xcms +update_on: +- regex: Metab_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Metab diff --git a/prepare/r-metabcombiner/PKGBUILD b/prepare/r-metabcombiner/PKGBUILD new file mode 100644 index 0000000000..9fc04021c9 --- /dev/null +++ b/prepare/r-metabcombiner/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=metabCombiner +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Method for Combining LC-MS Metabolomics Feature Measurements' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-caret + r-dplyr + r-matrixstats + r-rlang + r-s4vectors + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metabcombiner/lilac.py b/prepare/r-metabcombiner/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metabcombiner/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metabcombiner/lilac.yaml b/prepare/r-metabcombiner/lilac.yaml new file mode 100644 index 0000000000..5c150aa8a3 --- /dev/null +++ b/prepare/r-metabcombiner/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-caret +- r-dplyr +- r-matrixstats +- r-rlang +- r-s4vectors +- r-tidyr +update_on: +- regex: metabCombiner_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/metabCombiner diff --git a/prepare/r-metabocoreutils/PKGBUILD b/prepare/r-metabocoreutils/PKGBUILD new file mode 100644 index 0000000000..18ab114d5f --- /dev/null +++ b/prepare/r-metabocoreutils/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MetaboCoreUtils +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Core Utils for Metabolomics Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-mscoreutils + r-stringr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metabocoreutils/lilac.py b/prepare/r-metabocoreutils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metabocoreutils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metabocoreutils/lilac.yaml b/prepare/r-metabocoreutils/lilac.yaml new file mode 100644 index 0000000000..1b7f537557 --- /dev/null +++ b/prepare/r-metabocoreutils/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mscoreutils +- r-stringr +update_on: +- regex: MetaboCoreUtils_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MetaboCoreUtils diff --git a/prepare/r-metabolomicsworkbenchr/PKGBUILD b/prepare/r-metabolomicsworkbenchr/PKGBUILD new file mode 100644 index 0000000000..213cf42826 --- /dev/null +++ b/prepare/r-metabolomicsworkbenchr/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=metabolomicsWorkbenchR +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Metabolomics Workbench in R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-httr + r-jsonlite + r-multiassayexperiment + r-struct + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-covr + r-grid + r-hdf5array + r-knitr + r-pmp + r-png + r-rmarkdown + r-structtoolbox + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metabolomicsworkbenchr/lilac.py b/prepare/r-metabolomicsworkbenchr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metabolomicsworkbenchr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metabolomicsworkbenchr/lilac.yaml b/prepare/r-metabolomicsworkbenchr/lilac.yaml new file mode 100644 index 0000000000..d7bfa22783 --- /dev/null +++ b/prepare/r-metabolomicsworkbenchr/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-httr +- r-jsonlite +- r-multiassayexperiment +- r-struct +- r-summarizedexperiment +update_on: +- regex: metabolomicsWorkbenchR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/metabolomicsWorkbenchR diff --git a/prepare/r-metabomxtr/PKGBUILD b/prepare/r-metabomxtr/PKGBUILD new file mode 100644 index 0000000000..838b300f5e --- /dev/null +++ b/prepare/r-metabomxtr/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=metabomxtr +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A package to run mixture models for truncated metabolomics data with normal or lognormal distributions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocparallel + r-formula + r-ggplot2 + r-multtest + r-optimx + r-plyr +) +optdepends=( + r-reshape2 + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metabomxtr/lilac.py b/prepare/r-metabomxtr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metabomxtr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metabomxtr/lilac.yaml b/prepare/r-metabomxtr/lilac.yaml new file mode 100644 index 0000000000..1c13a39c4c --- /dev/null +++ b/prepare/r-metabomxtr/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocparallel +- r-formula +- r-ggplot2 +- r-multtest +- r-optimx +- r-plyr +update_on: +- regex: metabomxtr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/metabomxtr diff --git a/prepare/r-metabosignal/PKGBUILD b/prepare/r-metabosignal/PKGBUILD new file mode 100644 index 0000000000..a9e8e57991 --- /dev/null +++ b/prepare/r-metabosignal/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MetaboSignal +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biomart + r-ensdb.hsapiens.v75 + r-hpar + r-igraph + r-kegggraph + r-keggrest + r-mwastools + r-mygene + r-org.hs.eg.db + r-rcurl +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metabosignal/lilac.py b/prepare/r-metabosignal/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metabosignal/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metabosignal/lilac.yaml b/prepare/r-metabosignal/lilac.yaml new file mode 100644 index 0000000000..489b0a10d9 --- /dev/null +++ b/prepare/r-metabosignal/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biomart +- r-ensdb.hsapiens.v75 +- r-hpar +- r-igraph +- r-kegggraph +- r-keggrest +- r-mwastools +- r-mygene +- r-org.hs.eg.db +- r-rcurl +update_on: +- regex: MetaboSignal_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MetaboSignal diff --git a/prepare/r-metacca/PKGBUILD b/prepare/r-metacca/PKGBUILD new file mode 100644 index 0000000000..e0f609b189 --- /dev/null +++ b/prepare/r-metacca/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=metaCCA +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metacca/lilac.py b/prepare/r-metacca/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metacca/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metacca/lilac.yaml b/prepare/r-metacca/lilac.yaml new file mode 100644 index 0000000000..c9da705fac --- /dev/null +++ b/prepare/r-metacca/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: metaCCA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/metaCCA diff --git a/prepare/r-metacycle/PKGBUILD b/prepare/r-metacycle/PKGBUILD new file mode 100644 index 0000000000..d86cdf3541 --- /dev/null +++ b/prepare/r-metacycle/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MetaCycle +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Evaluate Periodicity in Large Scale Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-gnm +) +optdepends=( + r-knitr + r-parallel + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metacycle/lilac.py b/prepare/r-metacycle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metacycle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metacycle/lilac.yaml b/prepare/r-metacycle/lilac.yaml new file mode 100644 index 0000000000..79819a60e0 --- /dev/null +++ b/prepare/r-metacycle/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gnm +update_on: +- regex: MetaCycle_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MetaCycle diff --git a/prepare/r-metacyto/PKGBUILD b/prepare/r-metacyto/PKGBUILD new file mode 100644 index 0000000000..a6045da40c --- /dev/null +++ b/prepare/r-metacyto/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MetaCyto +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MetaCyto: A package for meta-analysis of cytometry data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-fastcluster + r-flowcore + r-flowsom + r-ggplot2 + r-metafor + r-tidyr +) +optdepends=( + r-dplyr + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metacyto/lilac.py b/prepare/r-metacyto/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metacyto/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metacyto/lilac.yaml b/prepare/r-metacyto/lilac.yaml new file mode 100644 index 0000000000..679144b229 --- /dev/null +++ b/prepare/r-metacyto/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fastcluster +- r-flowcore +- r-flowsom +- r-ggplot2 +- r-metafor +- r-tidyr +update_on: +- regex: MetaCyto_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MetaCyto diff --git a/prepare/r-metafor/PKGBUILD b/prepare/r-metafor/PKGBUILD new file mode 100644 index 0000000000..da2b589cd0 --- /dev/null +++ b/prepare/r-metafor/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=metafor +_pkgver=3.0-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Meta-Analysis Package for R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mathjaxr + r-pbapply +) +optdepends=( + r-ape + r-biasedurn + r-boot + r-compquadform + r-crayon + r-dfoptim + r-epi + r-glmmadaptive + r-gsl + r-lme4 + r-minqa + r-multcomp + r-mvtnorm + r-nloptr + r-numderiv + r-optimparallel + r-r.rsp + r-rmarkdown + r-sp + r-survival + r-testthat + r-ucminf +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metafor/lilac.py b/prepare/r-metafor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metafor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metafor/lilac.yaml b/prepare/r-metafor/lilac.yaml new file mode 100644 index 0000000000..cb51327ec4 --- /dev/null +++ b/prepare/r-metafor/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mathjaxr +- r-pbapply +update_on: +- regex: metafor_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=metafor diff --git a/prepare/r-metagene/PKGBUILD b/prepare/r-metagene/PKGBUILD new file mode 100644 index 0000000000..99e9e08121 --- /dev/null +++ b/prepare/r-metagene/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=metagene +_pkgver=2.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A package to produce metagene plots' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-data.table + r-ensdb.hsapiens.v86 + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-gplots + r-iranges + r-magrittr + r-matrixstats + r-mustat + r-purrr + r-r6 + r-rsamtools + r-rtracklayer + r-stringr +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit + r-similarpeak + r-similarpeak +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metagene/lilac.py b/prepare/r-metagene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metagene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metagene/lilac.yaml b/prepare/r-metagene/lilac.yaml new file mode 100644 index 0000000000..c960682120 --- /dev/null +++ b/prepare/r-metagene/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-data.table +- r-ensdb.hsapiens.v86 +- r-ensembldb +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-gplots +- r-iranges +- r-magrittr +- r-matrixstats +- r-mustat +- r-purrr +- r-r6 +- r-rsamtools +- r-rtracklayer +- r-stringr +update_on: +- regex: metagene_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/metagene diff --git a/prepare/r-metagene2/PKGBUILD b/prepare/r-metagene2/PKGBUILD new file mode 100644 index 0000000000..3c459aacb2 --- /dev/null +++ b/prepare/r-metagene2/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=metagene2 +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A package to produce metagene plots' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-data.table + r-dplyr + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-magrittr + r-purrr + r-r6 + r-reshape2 + r-rsamtools + r-rtracklayer +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metagene2/lilac.py b/prepare/r-metagene2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metagene2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metagene2/lilac.yaml b/prepare/r-metagene2/lilac.yaml new file mode 100644 index 0000000000..071adcaa27 --- /dev/null +++ b/prepare/r-metagene2/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-data.table +- r-dplyr +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-magrittr +- r-purrr +- r-r6 +- r-reshape2 +- r-rsamtools +- r-rtracklayer +update_on: +- regex: metagene2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/metagene2 diff --git a/prepare/r-metagenomeseq/PKGBUILD b/prepare/r-metagenomeseq/PKGBUILD new file mode 100644 index 0000000000..cbba2d3354 --- /dev/null +++ b/prepare/r-metagenomeseq/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=metagenomeSeq +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical analysis for sparse high-throughput sequencing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-foreach + r-glmnet + r-gplots + r-limma + r-matrixstats + r-rcolorbrewer + r-wrench +) +optdepends=( + r-annotate + r-biocgenerics + r-biomformat + r-gss + r-ihw + r-interactivedisplay + r-knitr + r-testthat + r-vegan +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metagenomeseq/lilac.py b/prepare/r-metagenomeseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metagenomeseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metagenomeseq/lilac.yaml b/prepare/r-metagenomeseq/lilac.yaml new file mode 100644 index 0000000000..c0271b3758 --- /dev/null +++ b/prepare/r-metagenomeseq/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-foreach +- r-glmnet +- r-gplots +- r-limma +- r-matrixstats +- r-rcolorbrewer +- r-wrench +update_on: +- regex: metagenomeSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/metagenomeSeq diff --git a/prepare/r-metahdep/PKGBUILD b/prepare/r-metahdep/PKGBUILD new file mode 100644 index 0000000000..c0c6f29c0b --- /dev/null +++ b/prepare/r-metahdep/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=metahdep +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Hierarchical Dependence in Meta-Analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-affyplm +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metahdep/lilac.py b/prepare/r-metahdep/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metahdep/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metahdep/lilac.yaml b/prepare/r-metahdep/lilac.yaml new file mode 100644 index 0000000000..876cbb8494 --- /dev/null +++ b/prepare/r-metahdep/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: metahdep_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/metahdep diff --git a/prepare/r-metama/PKGBUILD b/prepare/r-metama/PKGBUILD new file mode 100644 index 0000000000..acdc46c2ac --- /dev/null +++ b/prepare/r-metama/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=metaMA +_pkgver=3.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Meta-analysis for MicroArrays' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-limma + r-smvar +) +optdepends=( + r-annaffy + r-geoquery + r-hgu133a.db + r-hgu133plus2.db + r-hgu95av2.db + r-org.hs.eg.db + r-venndiagram +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metama/lilac.py b/prepare/r-metama/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metama/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metama/lilac.yaml b/prepare/r-metama/lilac.yaml new file mode 100644 index 0000000000..2e5e8d1303 --- /dev/null +++ b/prepare/r-metama/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-limma +- r-smvar +update_on: +- regex: metaMA_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=metaMA diff --git a/prepare/r-metams/PKGBUILD b/prepare/r-metams/PKGBUILD new file mode 100644 index 0000000000..f6fb9c34d4 --- /dev/null +++ b/prepare/r-metams/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=metaMS +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MS-based metabolomics annotation pipeline' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-camera + r-robustbase + r-xcms +) +optdepends=( + r-metamsdata + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metams/lilac.py b/prepare/r-metams/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metams/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metams/lilac.yaml b/prepare/r-metams/lilac.yaml new file mode 100644 index 0000000000..283e17959b --- /dev/null +++ b/prepare/r-metams/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-camera +- r-robustbase +- r-xcms +update_on: +- regex: metaMS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/metaMS diff --git a/prepare/r-metaneighbor/PKGBUILD b/prepare/r-metaneighbor/PKGBUILD new file mode 100644 index 0000000000..62268a61fa --- /dev/null +++ b/prepare/r-metaneighbor/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MetaNeighbor +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Single cell replicability analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-beanplot + r-dplyr + r-ggplot2 + r-gplots + r-igraph + r-matrixstats + r-rcolorbrewer + r-singlecellexperiment + r-summarizedexperiment + r-tibble + r-tidyr +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat + r-upsetr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metaneighbor/lilac.py b/prepare/r-metaneighbor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metaneighbor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metaneighbor/lilac.yaml b/prepare/r-metaneighbor/lilac.yaml new file mode 100644 index 0000000000..111fb93541 --- /dev/null +++ b/prepare/r-metaneighbor/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beanplot +- r-dplyr +- r-ggplot2 +- r-gplots +- r-igraph +- r-matrixstats +- r-rcolorbrewer +- r-singlecellexperiment +- r-summarizedexperiment +- r-tibble +- r-tidyr +update_on: +- regex: MetaNeighbor_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MetaNeighbor diff --git a/prepare/r-metap/PKGBUILD b/prepare/r-metap/PKGBUILD new file mode 100644 index 0000000000..9d01c470d9 --- /dev/null +++ b/prepare/r-metap/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=metap +_pkgver=1.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Meta-Analysis of Significance Values' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mathjaxr + r-mutoss + r-rdpack + r-tfisher +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metap/lilac.py b/prepare/r-metap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metap/lilac.yaml b/prepare/r-metap/lilac.yaml new file mode 100644 index 0000000000..1b7a815f55 --- /dev/null +++ b/prepare/r-metap/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mathjaxr +- r-mutoss +- r-rdpack +- r-tfisher +update_on: +- regex: metap_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=metap diff --git a/prepare/r-metapod/PKGBUILD b/prepare/r-metapod/PKGBUILD new file mode 100644 index 0000000000..9c73b31a78 --- /dev/null +++ b/prepare/r-metapod/PKGBUILD @@ -0,0 +1,34 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=metapod +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Meta-Analyses on P-Values of Differential Analyses' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metapod/lilac.py b/prepare/r-metapod/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metapod/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metapod/lilac.yaml b/prepare/r-metapod/lilac.yaml new file mode 100644 index 0000000000..fe2f51cc2e --- /dev/null +++ b/prepare/r-metapod/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: metapod_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/metapod diff --git a/prepare/r-metapone/PKGBUILD b/prepare/r-metapone/PKGBUILD new file mode 100644 index 0000000000..a3d16d0a36 --- /dev/null +++ b/prepare/r-metapone/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=metapone +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Conducts pathway test of metabolomics data using a weighted permutation test' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-fields + r-markdown +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metapone/lilac.py b/prepare/r-metapone/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metapone/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metapone/lilac.yaml b/prepare/r-metapone/lilac.yaml new file mode 100644 index 0000000000..0f2c354888 --- /dev/null +++ b/prepare/r-metapone/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-fields +- r-markdown +update_on: +- regex: metapone_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/metapone diff --git a/prepare/r-metaseq/PKGBUILD b/prepare/r-metaseq/PKGBUILD new file mode 100644 index 0000000000..5f06964eac --- /dev/null +++ b/prepare/r-metaseq/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=metaSeq +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Meta-analysis of RNA-Seq count data in multiple studies' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-noiseq + r-rcpp + r-snow +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metaseq/lilac.py b/prepare/r-metaseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metaseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metaseq/lilac.yaml b/prepare/r-metaseq/lilac.yaml new file mode 100644 index 0000000000..2d197c9b87 --- /dev/null +++ b/prepare/r-metaseq/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-noiseq +- r-rcpp +- r-snow +update_on: +- regex: metaSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/metaSeq diff --git a/prepare/r-metaseqr2/PKGBUILD b/prepare/r-metaseqr2/PKGBUILD new file mode 100644 index 0000000000..5afe78a0db --- /dev/null +++ b/prepare/r-metaseqr2/PKGBUILD @@ -0,0 +1,79 @@ +# Maintainer: Guoyi Zhang + +_pkgname=metaseqR2 +_pkgver=1.6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-absseq + r-bayseq + r-biobase + r-biocgenerics + r-biocparallel + r-biomart + r-biostrings + r-corrplot + r-deseq2 + r-dss + r-dt + r-edaseq + r-edger + r-genefilter + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-gplots + r-harmonicmeanp + r-heatmaply + r-htmltools + r-httr + r-iranges + r-jsonlite + r-limma + r-locfit + r-log4r + r-magrittr + r-nbpseq + r-pander + r-qvalue + r-rmarkdown + r-rmdformats + r-rsamtools + r-rsqlite + r-rtracklayer + r-s4vectors + r-stringr + r-summarizedexperiment + r-survcomp + r-venndiagram + r-vsn + r-yaml + r-zoo +) +optdepends=( + r-biocmanager + r-bsgenome + r-knitr + r-rmysql + r-runit + r-tcc +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metaseqr2/lilac.py b/prepare/r-metaseqr2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metaseqr2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metaseqr2/lilac.yaml b/prepare/r-metaseqr2/lilac.yaml new file mode 100644 index 0000000000..837afdb47b --- /dev/null +++ b/prepare/r-metaseqr2/lilac.yaml @@ -0,0 +1,54 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-absseq +- r-bayseq +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-biomart +- r-biostrings +- r-corrplot +- r-deseq2 +- r-dss +- r-dt +- r-edaseq +- r-edger +- r-genefilter +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-gplots +- r-harmonicmeanp +- r-heatmaply +- r-htmltools +- r-httr +- r-iranges +- r-jsonlite +- r-limma +- r-locfit +- r-log4r +- r-magrittr +- r-nbpseq +- r-pander +- r-qvalue +- r-rmarkdown +- r-rmdformats +- r-rsamtools +- r-rsqlite +- r-rtracklayer +- r-s4vectors +- r-stringr +- r-summarizedexperiment +- r-survcomp +- r-venndiagram +- r-vsn +- r-yaml +- r-zoo +update_on: +- regex: metaseqR2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/metaseqR2 diff --git a/prepare/r-metavizr/PKGBUILD b/prepare/r-metavizr/PKGBUILD new file mode 100644 index 0000000000..0dfc57257c --- /dev/null +++ b/prepare/r-metavizr/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=metavizr +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Interface to the metaviz web app for interactive metagenomics data analysis and visualization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-data.table + r-digest + r-epivizr + r-epivizrdata + r-epivizrserver + r-epivizrstandalone + r-genomeinfodb + r-httr + r-metagenomeseq + r-phyloseq + r-vegan +) +optdepends=( + r-biocstyle + r-etec16s + r-experimenthub + r-gss + r-knitr + r-matrixstats + r-msd16s + r-rmarkdown + r-testthat + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metavizr/lilac.py b/prepare/r-metavizr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metavizr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metavizr/lilac.yaml b/prepare/r-metavizr/lilac.yaml new file mode 100644 index 0000000000..77f5353a1f --- /dev/null +++ b/prepare/r-metavizr/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-data.table +- r-digest +- r-epivizr +- r-epivizrdata +- r-epivizrserver +- r-epivizrstandalone +- r-genomeinfodb +- r-httr +- r-metagenomeseq +- r-phyloseq +- r-vegan +update_on: +- regex: metavizr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/metavizr diff --git a/prepare/r-metavolcanor/PKGBUILD b/prepare/r-metavolcanor/PKGBUILD new file mode 100644 index 0000000000..a7b60c141a --- /dev/null +++ b/prepare/r-metavolcanor/PKGBUILD @@ -0,0 +1,47 @@ + +_pkgname=MetaVolcanoR +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-dplyr + r-tidyr + r-plotly + r-ggplot2 + r-cowplot + r-metafor + r-metap + r-rlang + r-topconfects + r-htmlwidgets +) +makedepends=( + git + tar +) +optdepends=( + r-knitr + r-markdown + r-rmakrdown + r-testthat + ) +source=("git+https://git.bioconductor.org/packages/${_pkgname}.git") +sha256sums=('SKIP') + +build() { + tar -zcvf ${_pkgname}.tar.gz ${_pkgname} + R CMD INSTALL ${_pkgname}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metavolcanor/lilac.py b/prepare/r-metavolcanor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metavolcanor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metavolcanor/lilac.yaml b/prepare/r-metavolcanor/lilac.yaml new file mode 100644 index 0000000000..7bb304981d --- /dev/null +++ b/prepare/r-metavolcanor/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-dplyr +- r-tidyr +- r-plotly +- r-ggplot2 +- r-cowplot +- r-metafor +- r-metap +- r-rlang +- r-topconfects +- r-htmlwidgets +update_on: +- regex: Version(\d+.\d+.\d+) + source: regex + url: https://bioconductor.org/packages/MetaVolcanoR diff --git a/prepare/r-metcirc/PKGBUILD b/prepare/r-metcirc/PKGBUILD new file mode 100644 index 0000000000..dea231b850 --- /dev/null +++ b/prepare/r-metcirc/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MetCirc +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Navigating mass spectral similarity in high-resolution MS/MS metabolomics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-amap + r-circlize + r-ggplot2 + r-msnbase + r-s4vectors + r-scales + r-shiny +) +optdepends=( + r-biocgenerics + r-graphics + r-grdevices + r-knitr + r-methods + r-stats + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metcirc/lilac.py b/prepare/r-metcirc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metcirc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metcirc/lilac.yaml b/prepare/r-metcirc/lilac.yaml new file mode 100644 index 0000000000..4c54ae4648 --- /dev/null +++ b/prepare/r-metcirc/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-amap +- r-circlize +- r-ggplot2 +- r-msnbase +- r-s4vectors +- r-scales +- r-shiny +update_on: +- regex: MetCirc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MetCirc diff --git a/prepare/r-methcp/PKGBUILD b/prepare/r-methcp/PKGBUILD new file mode 100644 index 0000000000..f01fe06bb8 --- /dev/null +++ b/prepare/r-methcp/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MethCP +_pkgver=1.7.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential methylation anlsysis for bisulfite sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-bsseq + r-dnacopy + r-dss + r-genomeinfodb + r-genomicranges + r-iranges + r-methylkit + r-s4vectors +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methcp/lilac.py b/prepare/r-methcp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methcp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methcp/lilac.yaml b/prepare/r-methcp/lilac.yaml new file mode 100644 index 0000000000..5b4a0cc981 --- /dev/null +++ b/prepare/r-methcp/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-bsseq +- r-dnacopy +- r-dss +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-methylkit +- r-s4vectors +update_on: +- regex: MethCP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MethCP diff --git a/prepare/r-methimpute/PKGBUILD b/prepare/r-methimpute/PKGBUILD new file mode 100644 index 0000000000..d8dc86d2cf --- /dev/null +++ b/prepare/r-methimpute/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=methimpute +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Imputation-guided re-construction of complete methylomes from WGBS data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-data.table + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-minpack.lm + r-rcpp + r-reshape2 +) +optdepends=( + r-biocstyle + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methimpute/lilac.py b/prepare/r-methimpute/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methimpute/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methimpute/lilac.yaml b/prepare/r-methimpute/lilac.yaml new file mode 100644 index 0000000000..d05624a257 --- /dev/null +++ b/prepare/r-methimpute/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-data.table +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-minpack.lm +- r-rcpp +- r-reshape2 +update_on: +- regex: methimpute_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/methimpute diff --git a/prepare/r-methinheritsim/PKGBUILD b/prepare/r-methinheritsim/PKGBUILD new file mode 100644 index 0000000000..06fb145a03 --- /dev/null +++ b/prepare/r-methinheritsim/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=methInheritSim +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Simulating Whole-Genome Inherited Bisulphite Sequencing Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-genomeinfodb + r-genomicranges + r-iranges + r-methylkit + r-msm + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-methylinheritance + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methinheritsim/lilac.py b/prepare/r-methinheritsim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methinheritsim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methinheritsim/lilac.yaml b/prepare/r-methinheritsim/lilac.yaml new file mode 100644 index 0000000000..7033dccd09 --- /dev/null +++ b/prepare/r-methinheritsim/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-methylkit +- r-msm +- r-s4vectors +update_on: +- regex: methInheritSim_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/methInheritSim diff --git a/prepare/r-methped/PKGBUILD b/prepare/r-methped/PKGBUILD new file mode 100644 index 0000000000..98d45cae45 --- /dev/null +++ b/prepare/r-methped/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MethPed +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-randomforest +) +optdepends=( + r-biocstyle + r-impute + r-knitr + r-markdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methped/lilac.py b/prepare/r-methped/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methped/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methped/lilac.yaml b/prepare/r-methped/lilac.yaml new file mode 100644 index 0000000000..7d0ec61ee5 --- /dev/null +++ b/prepare/r-methped/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-randomforest +update_on: +- regex: MethPed_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MethPed diff --git a/prepare/r-methreg/PKGBUILD b/prepare/r-methreg/PKGBUILD new file mode 100644 index 0000000000..9a50f3b856 --- /dev/null +++ b/prepare/r-methreg/PKGBUILD @@ -0,0 +1,70 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MethReg +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assessing the regulatory potential of DNA methylation regions or sites on gene transcription' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-delayedarray + r-dplyr + r-genomicranges + r-ggplot2 + r-ggpubr + r-iranges + r-plyr + r-progress + r-pscl + r-readr + r-rlang + r-s4vectors + r-sesamedata + r-sfsmisc + r-stringr + r-summarizedexperiment + r-tibble + r-tidyr +) +optdepends=( + r-biocfilecache + r-biocstyle + r-biomart + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.hsapiens.ucsc.hg38 + r-doparallel + r-dorothea + r-downloader + r-htmltools + r-jaspar2020 + r-jpeg + r-knitr + r-matrixstats + r-motifmatchr + r-parallel + r-png + r-r.utils + r-reshape2 + r-rmarkdown + r-sesame + r-stager + r-testthat + r-tfbstools + r-viper +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methreg/lilac.py b/prepare/r-methreg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methreg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methreg/lilac.yaml b/prepare/r-methreg/lilac.yaml new file mode 100644 index 0000000000..398a8d4726 --- /dev/null +++ b/prepare/r-methreg/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-delayedarray +- r-dplyr +- r-genomicranges +- r-ggplot2 +- r-ggpubr +- r-iranges +- r-plyr +- r-progress +- r-pscl +- r-readr +- r-rlang +- r-s4vectors +- r-sesamedata +- r-sfsmisc +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-tidyr +update_on: +- regex: MethReg_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MethReg diff --git a/prepare/r-methrix/PKGBUILD b/prepare/r-methrix/PKGBUILD new file mode 100644 index 0000000000..950f9fc066 --- /dev/null +++ b/prepare/r-methrix/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=methrix +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast and efficient summarization of generic bedGraph files from Bisufite sequencing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-bsgenome + r-data.table + r-delayedarray + r-delayedmatrixstats + r-genomicranges + r-ggplot2 + r-hdf5array + r-iranges + r-matrixstats + r-rtracklayer + r-summarizedexperiment +) +optdepends=( + r-biostrings + r-bsgenome.mmusculus.ucsc.mm9 + r-bsseq + r-dss + r-genomeinfodb + r-genomicscores + r-knitr + r-mafdb.1kgenomes.phase3.grch38 + r-mafdb.1kgenomes.phase3.hs37d5 + r-plotly + r-rcolorbrewer + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methrix/lilac.py b/prepare/r-methrix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methrix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methrix/lilac.yaml b/prepare/r-methrix/lilac.yaml new file mode 100644 index 0000000000..db931dde54 --- /dev/null +++ b/prepare/r-methrix/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +- r-data.table +- r-delayedarray +- r-delayedmatrixstats +- r-genomicranges +- r-ggplot2 +- r-hdf5array +- r-iranges +- r-matrixstats +- r-rtracklayer +- r-summarizedexperiment +update_on: +- regex: methrix_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/methrix diff --git a/prepare/r-methtargetedngs/PKGBUILD b/prepare/r-methtargetedngs/PKGBUILD new file mode 100644 index 0000000000..094de67ab6 --- /dev/null +++ b/prepare/r-methtargetedngs/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: HMMER3 +# Maintainer: Guoyi Zhang + +_pkgname=MethTargetedNGS +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Perform Methylation Analysis on Next Generation Sequencing Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-gplots + r-seqinr + r-stringr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methtargetedngs/lilac.py b/prepare/r-methtargetedngs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methtargetedngs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methtargetedngs/lilac.yaml b/prepare/r-methtargetedngs/lilac.yaml new file mode 100644 index 0000000000..d313471f63 --- /dev/null +++ b/prepare/r-methtargetedngs/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-gplots +- r-seqinr +- r-stringr +update_on: +- regex: MethTargetedNGS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MethTargetedNGS diff --git a/prepare/r-methylaid/PKGBUILD b/prepare/r-methylaid/PKGBUILD new file mode 100644 index 0000000000..3979803983 --- /dev/null +++ b/prepare/r-methylaid/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MethylAid +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visual and interactive quality control of large Illumina DNA Methylation array data sets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-ggplot2 + r-gridbase + r-hexbin + r-matrixstats + r-minfi + r-rcolorbrewer + r-shiny + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-methylaiddata + r-minfidata + r-minfidataepic + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methylaid/lilac.py b/prepare/r-methylaid/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methylaid/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methylaid/lilac.yaml b/prepare/r-methylaid/lilac.yaml new file mode 100644 index 0000000000..8f72d0b3b5 --- /dev/null +++ b/prepare/r-methylaid/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-ggplot2 +- r-gridbase +- r-hexbin +- r-matrixstats +- r-minfi +- r-rcolorbrewer +- r-shiny +- r-summarizedexperiment +update_on: +- regex: MethylAid_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MethylAid diff --git a/prepare/r-methylcc/PKGBUILD b/prepare/r-methylcc/PKGBUILD new file mode 100644 index 0000000000..db8b18a01f --- /dev/null +++ b/prepare/r-methylcc/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=methylCC +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimate the cell composition of whole blood in DNA methylation samples' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CCPL:by-nc-sa') +depends=( + r + r-biobase + r-bsseq + r-bumphunter + r-dplyr + r-flowsorted.blood.450k + r-genefilter + r-genomicranges + r-illuminahumanmethylation450kanno.ilmn12.hg19 + r-illuminahumanmethylation450kmanifest + r-iranges + r-magrittr + r-minfi + r-plyranges + r-quadprog + r-s4vectors +) +optdepends=( + r-biocgenerics + r-biocstyle + r-ggplot2 + r-knitr + r-rmarkdown + r-testthat + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methylcc/lilac.py b/prepare/r-methylcc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methylcc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methylcc/lilac.yaml b/prepare/r-methylcc/lilac.yaml new file mode 100644 index 0000000000..2df850e772 --- /dev/null +++ b/prepare/r-methylcc/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-bsseq +- r-bumphunter +- r-dplyr +- r-flowsorted.blood.450k +- r-genefilter +- r-genomicranges +- r-illuminahumanmethylation450kanno.ilmn12.hg19 +- r-illuminahumanmethylation450kmanifest +- r-iranges +- r-magrittr +- r-minfi +- r-plyranges +- r-quadprog +- r-s4vectors +update_on: +- regex: methylCC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/methylCC diff --git a/prepare/r-methylclock/PKGBUILD b/prepare/r-methylclock/PKGBUILD new file mode 100644 index 0000000000..59c1aed9e6 --- /dev/null +++ b/prepare/r-methylclock/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=methylclock +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methylclock - DNA methylation-based clocks' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-devtools + r-dplyr + r-dynamictreecut + r-experimenthub + r-ggplot2 + r-ggpmisc + r-ggpubr + r-impute + r-methylclockdata + r-minfi + r-performanceanalytics + r-preprocesscore + r-quadprog + r-rcpp + r-rpmm + r-tibble + r-tidyr + r-tidyverse +) +optdepends=( + r-biocstyle + r-geoquery + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methylclock/lilac.py b/prepare/r-methylclock/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methylclock/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methylclock/lilac.yaml b/prepare/r-methylclock/lilac.yaml new file mode 100644 index 0000000000..57322d55bd --- /dev/null +++ b/prepare/r-methylclock/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-devtools +- r-dplyr +- r-dynamictreecut +- r-experimenthub +- r-ggplot2 +- r-ggpmisc +- r-ggpubr +- r-impute +- r-methylclockdata +- r-minfi +- r-performanceanalytics +- r-preprocesscore +- r-quadprog +- r-rcpp +- r-rpmm +- r-tibble +- r-tidyr +- r-tidyverse +update_on: +- regex: methylclock_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/methylclock diff --git a/prepare/r-methylclockdata/PKGBUILD b/prepare/r-methylclockdata/PKGBUILD new file mode 100644 index 0000000000..cbf02b1e6b --- /dev/null +++ b/prepare/r-methylclockdata/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=methylclockData +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data for methylclock package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-experimenthub + r-experimenthubdata +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methylclockdata/lilac.py b/prepare/r-methylclockdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methylclockdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methylclockdata/lilac.yaml b/prepare/r-methylclockdata/lilac.yaml new file mode 100644 index 0000000000..34bc2764a9 --- /dev/null +++ b/prepare/r-methylclockdata/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-experimenthub +- r-experimenthubdata +update_on: +- regex: methylclockData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/methylclockData diff --git a/prepare/r-methylgsa/PKGBUILD b/prepare/r-methylgsa/PKGBUILD new file mode 100644 index 0000000000..1a15e09e4f --- /dev/null +++ b/prepare/r-methylgsa/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=methylGSA +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Set Analysis Using the Outcome of Differential Methylation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocparallel + r-clusterprofiler + r-ggplot2 + r-go.db + r-illuminahumanmethylation450kanno.ilmn12.hg19 + r-illuminahumanmethylationepicanno.ilm10b4.hg19 + r-missmethyl + r-org.hs.eg.db + r-reactome.db + r-robustrankaggreg + r-shiny + r-stringr +) +optdepends=( + r-enrichplot + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methylgsa/lilac.py b/prepare/r-methylgsa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methylgsa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methylgsa/lilac.yaml b/prepare/r-methylgsa/lilac.yaml new file mode 100644 index 0000000000..8529437193 --- /dev/null +++ b/prepare/r-methylgsa/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocparallel +- r-clusterprofiler +- r-ggplot2 +- r-go.db +- r-illuminahumanmethylation450kanno.ilmn12.hg19 +- r-illuminahumanmethylationepicanno.ilm10b4.hg19 +- r-missmethyl +- r-org.hs.eg.db +- r-reactome.db +- r-robustrankaggreg +- r-shiny +- r-stringr +update_on: +- regex: methylGSA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/methylGSA diff --git a/prepare/r-methylinheritance/PKGBUILD b/prepare/r-methylinheritance/PKGBUILD new file mode 100644 index 0000000000..4dcdf7ed70 --- /dev/null +++ b/prepare/r-methylinheritance/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=methylInheritance +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-genomicranges + r-ggplot2 + r-gridextra + r-iranges + r-methylkit + r-rebus + r-s4vectors +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-methinheritsim + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methylinheritance/lilac.py b/prepare/r-methylinheritance/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methylinheritance/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methylinheritance/lilac.yaml b/prepare/r-methylinheritance/lilac.yaml new file mode 100644 index 0000000000..0d0bc3744a --- /dev/null +++ b/prepare/r-methylinheritance/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-genomicranges +- r-ggplot2 +- r-gridextra +- r-iranges +- r-methylkit +- r-rebus +- r-s4vectors +update_on: +- regex: methylInheritance_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/methylInheritance diff --git a/prepare/r-methylkit/PKGBUILD b/prepare/r-methylkit/PKGBUILD new file mode 100644 index 0000000000..bb8db8289f --- /dev/null +++ b/prepare/r-methylkit/PKGBUILD @@ -0,0 +1,51 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=methylKit +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='DNA methylation analysis from high-throughput bisulfite sequencing results' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-data.table + r-emdbook + r-fastseg + r-genomeinfodb + r-genomicranges + r-gtools + r-iranges + r-limma + r-mclust + r-qvalue + r-r.utils + r-rcpp + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-zlibbioc +) +optdepends=( + r-biocmanager + r-genomation + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methylkit/lilac.py b/prepare/r-methylkit/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methylkit/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methylkit/lilac.yaml b/prepare/r-methylkit/lilac.yaml new file mode 100644 index 0000000000..a025edb1e1 --- /dev/null +++ b/prepare/r-methylkit/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-emdbook +- r-fastseg +- r-genomeinfodb +- r-genomicranges +- r-gtools +- r-iranges +- r-limma +- r-mclust +- r-qvalue +- r-r.utils +- r-rcpp +- r-rhtslib +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-zlibbioc +update_on: +- regex: methylKit_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/methylKit diff --git a/prepare/r-methylmix/PKGBUILD b/prepare/r-methylmix/PKGBUILD new file mode 100644 index 0000000000..7415156103 --- /dev/null +++ b/prepare/r-methylmix/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MethylMix +_pkgver=2.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MethylMix: Identifying methylation driven cancer genes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-digest + r-foreach + r-ggplot2 + r-impute + r-limma + r-r.matlab + r-rcolorbrewer + r-rcurl + r-rpmm +) +optdepends=( + r-biocstyle + r-doparallel + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methylmix/lilac.py b/prepare/r-methylmix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methylmix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methylmix/lilac.yaml b/prepare/r-methylmix/lilac.yaml new file mode 100644 index 0000000000..54162ff2b9 --- /dev/null +++ b/prepare/r-methylmix/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-digest +- r-foreach +- r-ggplot2 +- r-impute +- r-limma +- r-r.matlab +- r-rcolorbrewer +- r-rcurl +- r-rpmm +update_on: +- regex: MethylMix_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MethylMix diff --git a/prepare/r-methylmnm/PKGBUILD b/prepare/r-methylmnm/PKGBUILD new file mode 100644 index 0000000000..aeeb803836 --- /dev/null +++ b/prepare/r-methylmnm/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=methylMnM +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='detect different methylation level (DMR)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-edger + r-statmod +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methylmnm/lilac.py b/prepare/r-methylmnm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methylmnm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methylmnm/lilac.yaml b/prepare/r-methylmnm/lilac.yaml new file mode 100644 index 0000000000..b7c11266dc --- /dev/null +++ b/prepare/r-methylmnm/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-edger +- r-statmod +update_on: +- regex: methylMnM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/methylMnM diff --git a/prepare/r-methylpipe/PKGBUILD b/prepare/r-methylpipe/PKGBUILD new file mode 100644 index 0000000000..ba6a8b9fe7 --- /dev/null +++ b/prepare/r-methylpipe/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=methylPipe +_pkgver=1.27.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Base resolution DNA methylation data analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-data.table + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-gplots + r-gviz + r-iranges + r-marray + r-rsamtools + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg18 + r-knitr + r-methylseekr + r-txdb.hsapiens.ucsc.hg18.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methylpipe/lilac.py b/prepare/r-methylpipe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methylpipe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methylpipe/lilac.yaml b/prepare/r-methylpipe/lilac.yaml new file mode 100644 index 0000000000..6b18058590 --- /dev/null +++ b/prepare/r-methylpipe/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-data.table +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-gplots +- r-gviz +- r-iranges +- r-marray +- r-rsamtools +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: methylPipe_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/methylPipe diff --git a/prepare/r-methylscaper/PKGBUILD b/prepare/r-methylscaper/PKGBUILD new file mode 100644 index 0000000000..4f9b8255f1 --- /dev/null +++ b/prepare/r-methylscaper/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=methylscaper +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization of Methylation Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-biostrings + r-data.table + r-rfast + r-seqinr + r-seriation + r-shiny + r-shinyfiles + r-shinyjs + r-summarizedexperiment +) +optdepends=( + r-devtools + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methylscaper/lilac.py b/prepare/r-methylscaper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methylscaper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methylscaper/lilac.yaml b/prepare/r-methylscaper/lilac.yaml new file mode 100644 index 0000000000..d5a4c4ff92 --- /dev/null +++ b/prepare/r-methylscaper/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-biostrings +- r-data.table +- r-rfast +- r-seqinr +- r-seriation +- r-shiny +- r-shinyfiles +- r-shinyjs +- r-summarizedexperiment +update_on: +- regex: methylscaper_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/methylscaper diff --git a/prepare/r-methylseekr/PKGBUILD b/prepare/r-methylseekr/PKGBUILD new file mode 100644 index 0000000000..ca18b7de0b --- /dev/null +++ b/prepare/r-methylseekr/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MethylSeekR +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Segmentation of Bis-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bsgenome + r-geneplotter + r-genomicranges + r-iranges + r-mhsmm + r-rtracklayer +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg18 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methylseekr/lilac.py b/prepare/r-methylseekr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methylseekr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methylseekr/lilac.yaml b/prepare/r-methylseekr/lilac.yaml new file mode 100644 index 0000000000..c5ac371010 --- /dev/null +++ b/prepare/r-methylseekr/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +- r-geneplotter +- r-genomicranges +- r-iranges +- r-mhsmm +- r-rtracklayer +update_on: +- regex: MethylSeekR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MethylSeekR diff --git a/prepare/r-methylsig/PKGBUILD b/prepare/r-methylsig/PKGBUILD new file mode 100644 index 0000000000..d3f97b0706 --- /dev/null +++ b/prepare/r-methylsig/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=methylSig +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MethylSig: Differential Methylation Testing for WGBS and RRBS Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bsseq + r-delayedarray + r-delayedmatrixstats + r-dss + r-genomeinfodb + r-genomicranges + r-iranges + r-s4vectors +) +optdepends=( + r-biocstyle + r-bsseqdata + r-covr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methylsig/lilac.py b/prepare/r-methylsig/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methylsig/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methylsig/lilac.yaml b/prepare/r-methylsig/lilac.yaml new file mode 100644 index 0000000000..e8c37d18ae --- /dev/null +++ b/prepare/r-methylsig/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsseq +- r-delayedarray +- r-delayedmatrixstats +- r-dss +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-s4vectors +update_on: +- regex: methylSig_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/methylSig diff --git a/prepare/r-methylumi/PKGBUILD b/prepare/r-methylumi/PKGBUILD new file mode 100644 index 0000000000..2c290e49d9 --- /dev/null +++ b/prepare/r-methylumi/PKGBUILD @@ -0,0 +1,61 @@ +# Maintainer: Guoyi Zhang + +_pkgname=methylumi +_pkgver=2.40.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Handle Illumina methylation data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-fdb.infiniummethylation.hg19 + r-genefilter + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-illuminaio + r-iranges + r-matrixstats + r-minfi + r-reshape2 + r-s4vectors + r-scales + r-summarizedexperiment +) +optdepends=( + r-biostrings + r-fdb.infiniummethylation.hg18 + r-homo.sapiens + r-illuminahumanmethylation450kanno.ilmn12.hg19 + r-knitr + r-lattice + r-limma + r-lumi + r-mass + r-matrixstats + r-parallel + r-rtracklayer + r-sqn + r-tcgamethylation450k + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-methylumi/lilac.py b/prepare/r-methylumi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-methylumi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-methylumi/lilac.yaml b/prepare/r-methylumi/lilac.yaml new file mode 100644 index 0000000000..f89e620142 --- /dev/null +++ b/prepare/r-methylumi/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-fdb.infiniummethylation.hg19 +- r-genefilter +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-illuminaio +- r-iranges +- r-matrixstats +- r-minfi +- r-reshape2 +- r-s4vectors +- r-scales +- r-summarizedexperiment +update_on: +- regex: methylumi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/methylumi diff --git a/prepare/r-metid/PKGBUILD b/prepare/r-metid/PKGBUILD new file mode 100644 index 0000000000..9393a6569f --- /dev/null +++ b/prepare/r-metid/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MetID +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Network-based prioritization of putative metabolite IDs' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-chemminer + r-devtools + r-igraph + r-stringr +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metid/lilac.py b/prepare/r-metid/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metid/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metid/lilac.yaml b/prepare/r-metid/lilac.yaml new file mode 100644 index 0000000000..1c6815a4d6 --- /dev/null +++ b/prepare/r-metid/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-chemminer +- r-devtools +- r-igraph +- r-stringr +update_on: +- regex: MetID_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MetID diff --git a/prepare/r-metnet/PKGBUILD b/prepare/r-metnet/PKGBUILD new file mode 100644 index 0000000000..b93a695548 --- /dev/null +++ b/prepare/r-metnet/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MetNet +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Inferring metabolic networks from untargeted high-resolution mass spectrometry data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-bnlearn + r-dplyr + r-genie3 + r-ggplot2 + r-mpmi + r-parmigene + r-ppcor + r-psych + r-rlang + r-s4vectors + r-stabs + r-summarizedexperiment + r-tibble + r-tidyr +) +optdepends=( + r-biocgenerics + r-biocstyle + r-glmnet + r-igraph + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metnet/lilac.py b/prepare/r-metnet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metnet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metnet/lilac.yaml b/prepare/r-metnet/lilac.yaml new file mode 100644 index 0000000000..a018d4d312 --- /dev/null +++ b/prepare/r-metnet/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-bnlearn +- r-dplyr +- r-genie3 +- r-ggplot2 +- r-mpmi +- r-parmigene +- r-ppcor +- r-psych +- r-rlang +- r-s4vectors +- r-stabs +- r-summarizedexperiment +- r-tibble +- r-tidyr +update_on: +- regex: MetNet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MetNet diff --git a/prepare/r-metr/PKGBUILD b/prepare/r-metr/PKGBUILD new file mode 100644 index 0000000000..a5426d1932 --- /dev/null +++ b/prepare/r-metr/PKGBUILD @@ -0,0 +1,64 @@ +# Maintainer: Guoyi Zhang + +_pkgname=metR +_pkgver=0.11.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Easier Analysis of Meteorological Fields' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-checkmate + r-data.table + r-digest + r-fields + r-formula + r-formula.tools + r-ggplot2 + r-gtable + r-isoband + r-lubridate + r-memoise + r-plyr + r-purrr + r-rcurl + r-scales + r-sp + r-stringr +) +optdepends=( + r-covr + r-gridextra + r-here + r-irlba + r-knitr + r-kriging + r-maps + r-maptools + r-ncdf4 + r-pkgdown + r-proj4 + r-raster + r-reshape2 + r-rgdal + r-rmarkdown + r-testthat + r-udunits2 + r-vdiffr + r-viridis +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-metr/lilac.py b/prepare/r-metr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-metr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-metr/lilac.yaml b/prepare/r-metr/lilac.yaml new file mode 100644 index 0000000000..840c381541 --- /dev/null +++ b/prepare/r-metr/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-checkmate +- r-data.table +- r-digest +- r-fields +- r-formula +- r-formula.tools +- r-ggplot2 +- r-gtable +- r-isoband +- r-lubridate +- r-memoise +- r-plyr +- r-purrr +- r-rcurl +- r-scales +- r-sp +- r-stringr +update_on: +- regex: metR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=metR diff --git a/prepare/r-mfa/PKGBUILD b/prepare/r-mfa/PKGBUILD new file mode 100644 index 0000000000..49d2aa6447 --- /dev/null +++ b/prepare/r-mfa/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mfa +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-coda + r-dplyr + r-ggmcmc + r-ggplot2 + r-magrittr + r-mcmcglmm + r-mcmcpack + r-rcpp + r-tibble +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mfa/lilac.py b/prepare/r-mfa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mfa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mfa/lilac.yaml b/prepare/r-mfa/lilac.yaml new file mode 100644 index 0000000000..f67c685755 --- /dev/null +++ b/prepare/r-mfa/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-coda +- r-dplyr +- r-ggmcmc +- r-ggplot2 +- r-magrittr +- r-mcmcglmm +- r-mcmcpack +- r-rcpp +- r-tibble +update_on: +- regex: mfa_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mfa diff --git a/prepare/r-mfuzz/PKGBUILD b/prepare/r-mfuzz/PKGBUILD new file mode 100644 index 0000000000..bbc1ca86ec --- /dev/null +++ b/prepare/r-mfuzz/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Mfuzz +_pkgver=2.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Soft clustering of time series gene expression data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-e1071 + r-tkwidgets +) +optdepends=( + r-marray +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mfuzz/lilac.py b/prepare/r-mfuzz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mfuzz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mfuzz/lilac.yaml b/prepare/r-mfuzz/lilac.yaml new file mode 100644 index 0000000000..7a00ff820b --- /dev/null +++ b/prepare/r-mfuzz/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-e1071 +- r-tkwidgets +update_on: +- regex: Mfuzz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Mfuzz diff --git a/prepare/r-mgfm/PKGBUILD b/prepare/r-mgfm/PKGBUILD new file mode 100644 index 0000000000..0726cc0d88 --- /dev/null +++ b/prepare/r-mgfm/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MGFM +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Marker Gene Finder in Microarray gene expression data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotate + r-annotationdbi +) +optdepends=( + r-hgu133a.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mgfm/lilac.py b/prepare/r-mgfm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mgfm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mgfm/lilac.yaml b/prepare/r-mgfm/lilac.yaml new file mode 100644 index 0000000000..393bda0ded --- /dev/null +++ b/prepare/r-mgfm/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +update_on: +- regex: MGFM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MGFM diff --git a/prepare/r-mgfr/PKGBUILD b/prepare/r-mgfr/PKGBUILD new file mode 100644 index 0000000000..b128b3e44e --- /dev/null +++ b/prepare/r-mgfr/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MGFR +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Marker Gene Finder in RNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotate + r-biomart +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mgfr/lilac.py b/prepare/r-mgfr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mgfr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mgfr/lilac.yaml b/prepare/r-mgfr/lilac.yaml new file mode 100644 index 0000000000..e0520c95d5 --- /dev/null +++ b/prepare/r-mgfr/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-biomart +update_on: +- regex: MGFR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MGFR diff --git a/prepare/r-mglm/PKGBUILD b/prepare/r-mglm/PKGBUILD new file mode 100644 index 0000000000..f3c384da62 --- /dev/null +++ b/prepare/r-mglm/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MGLM +_pkgver=0.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multivariate Response Generalized Linear Models' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-ggplot2 + r-knitr + r-plyr + r-reshape2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mglm/lilac.py b/prepare/r-mglm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mglm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mglm/lilac.yaml b/prepare/r-mglm/lilac.yaml new file mode 100644 index 0000000000..615e411222 --- /dev/null +++ b/prepare/r-mglm/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: MGLM_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MGLM diff --git a/prepare/r-mgsa/PKGBUILD b/prepare/r-mgsa/PKGBUILD new file mode 100644 index 0000000000..38628c46c4 --- /dev/null +++ b/prepare/r-mgsa/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mgsa +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Model-based gene set analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-gplots +) +optdepends=( + r-dbi + r-go.db + r-rsqlite + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mgsa/lilac.py b/prepare/r-mgsa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mgsa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mgsa/lilac.yaml b/prepare/r-mgsa/lilac.yaml new file mode 100644 index 0000000000..d39501e109 --- /dev/null +++ b/prepare/r-mgsa/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gplots +update_on: +- regex: mgsa_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mgsa diff --git a/prepare/r-mgsub/PKGBUILD b/prepare/r-mgsub/PKGBUILD new file mode 100644 index 0000000000..139c8c76e9 --- /dev/null +++ b/prepare/r-mgsub/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mgsub +_pkgver=1.7.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Safe, Multiple, Simultaneous String Substitution' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mgsub/lilac.py b/prepare/r-mgsub/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mgsub/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mgsub/lilac.yaml b/prepare/r-mgsub/lilac.yaml new file mode 100644 index 0000000000..1b9e38ae40 --- /dev/null +++ b/prepare/r-mgsub/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: mgsub_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mgsub diff --git a/prepare/r-mgsz/PKGBUILD b/prepare/r-mgsz/PKGBUILD new file mode 100644 index 0000000000..ac14281c96 --- /dev/null +++ b/prepare/r-mgsz/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mGSZ +_pkgver=1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene set analysis based on GSZ-scoring function and asymptotic p-value' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-gsa + r-ismev + r-limma +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mgsz/lilac.py b/prepare/r-mgsz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mgsz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mgsz/lilac.yaml b/prepare/r-mgsz/lilac.yaml new file mode 100644 index 0000000000..7ae32ae7fc --- /dev/null +++ b/prepare/r-mgsz/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-gsa +- r-ismev +- r-limma +update_on: +- regex: mGSZ_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mGSZ diff --git a/prepare/r-mhsmm/PKGBUILD b/prepare/r-mhsmm/PKGBUILD new file mode 100644 index 0000000000..f53d6daafa --- /dev/null +++ b/prepare/r-mhsmm/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mhsmm +_pkgver=0.4.16 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Inference for Hidden Markov and Semi-Markov Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mvtnorm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mhsmm/lilac.py b/prepare/r-mhsmm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mhsmm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mhsmm/lilac.yaml b/prepare/r-mhsmm/lilac.yaml new file mode 100644 index 0000000000..1a1dbafbb3 --- /dev/null +++ b/prepare/r-mhsmm/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mvtnorm +update_on: +- regex: mhsmm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mhsmm diff --git a/prepare/r-mia/PKGBUILD b/prepare/r-mia/PKGBUILD new file mode 100644 index 0000000000..bd19ef7558 --- /dev/null +++ b/prepare/r-mia/PKGBUILD @@ -0,0 +1,63 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mia +_pkgver=1.2.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Microbiome analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ape + r-biocgenerics + r-biocparallel + r-biostrings + r-decipher + r-decontam + r-delayedarray + r-delayedmatrixstats + r-dirichletmultinomial + r-dplyr + r-iranges + r-multiassayexperiment + r-rlang + r-s4vectors + r-scater + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-tibble + r-tidyr + r-treesummarizedexperiment + r-vegan +) +optdepends=( + r-ade4 + r-biocstyle + r-biomformat + r-dada2 + r-knitr + r-microbiomedatasets + r-patchwork + r-phyloseq + r-reldist + r-rmarkdown + r-stringr + r-testthat + r-yaml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mia/lilac.py b/prepare/r-mia/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mia/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mia/lilac.yaml b/prepare/r-mia/lilac.yaml new file mode 100644 index 0000000000..b2c023d2be --- /dev/null +++ b/prepare/r-mia/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-decipher +- r-decontam +- r-delayedarray +- r-delayedmatrixstats +- r-dirichletmultinomial +- r-dplyr +- r-iranges +- r-multiassayexperiment +- r-rlang +- r-s4vectors +- r-scater +- r-scuttle +- r-singlecellexperiment +- r-summarizedexperiment +- r-tibble +- r-tidyr +- r-treesummarizedexperiment +- r-vegan +update_on: +- regex: mia_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mia diff --git a/prepare/r-miasim/PKGBUILD b/prepare/r-miasim/PKGBUILD new file mode 100644 index 0000000000..2059fefe76 --- /dev/null +++ b/prepare/r-miasim/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miaSim +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Microbiome Data Simulation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-desolve + r-powerlaw + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-miasim/lilac.py b/prepare/r-miasim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-miasim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-miasim/lilac.yaml b/prepare/r-miasim/lilac.yaml new file mode 100644 index 0000000000..4e34aca25f --- /dev/null +++ b/prepare/r-miasim/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-desolve +- r-powerlaw +- r-summarizedexperiment +update_on: +- regex: miaSim_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/miaSim diff --git a/prepare/r-miaviz/PKGBUILD b/prepare/r-miaviz/PKGBUILD new file mode 100644 index 0000000000..5fe61ec87f --- /dev/null +++ b/prepare/r-miaviz/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miaViz +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Microbiome Analysis Plotting and Visualization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ape + r-biocgenerics + r-biocparallel + r-delayedarray + r-dirichletmultinomial + r-dplyr + r-ggnewscale + r-ggplot2 + r-ggraph + r-ggtree + r-mia + r-purrr + r-rlang + r-s4vectors + r-scater + r-summarizedexperiment + r-tibble + r-tidygraph + r-tidyr + r-tidytree + r-treesummarizedexperiment + r-viridis +) +optdepends=( + r-biocstyle + r-knitr + r-microbiomedatasets + r-patchwork + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-miaviz/lilac.py b/prepare/r-miaviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-miaviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-miaviz/lilac.yaml b/prepare/r-miaviz/lilac.yaml new file mode 100644 index 0000000000..d03358a337 --- /dev/null +++ b/prepare/r-miaviz/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-biocgenerics +- r-biocparallel +- r-delayedarray +- r-dirichletmultinomial +- r-dplyr +- r-ggnewscale +- r-ggplot2 +- r-ggraph +- r-ggtree +- r-mia +- r-purrr +- r-rlang +- r-s4vectors +- r-scater +- r-summarizedexperiment +- r-tibble +- r-tidygraph +- r-tidyr +- r-tidytree +- r-treesummarizedexperiment +- r-viridis +update_on: +- regex: miaViz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/miaViz diff --git a/prepare/r-mice/PKGBUILD b/prepare/r-mice/PKGBUILD new file mode 100644 index 0000000000..c7b8fbea8a --- /dev/null +++ b/prepare/r-mice/PKGBUILD @@ -0,0 +1,56 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=mice +_pkgver=3.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multivariate Imputation by Chained Equations' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-broom + r-cpp11 + r-dplyr + r-generics + r-rcpp + r-rlang + r-tidyr + r-withr +) +optdepends=( + r-broom.mixed + r-decor + r-glmnet + r-haven + r-knitr + r-lme4 + r-lmtest + r-mass + r-metafor + r-miceadds + r-mitml + r-nnet + r-pan + r-randomforest + r-ranger + r-rmarkdown + r-rpart + r-survival + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mice/lilac.py b/prepare/r-mice/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mice/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mice/lilac.yaml b/prepare/r-mice/lilac.yaml new file mode 100644 index 0000000000..93b2a3b22d --- /dev/null +++ b/prepare/r-mice/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-broom +- r-cpp11 +- r-dplyr +- r-generics +- r-rcpp +- r-rlang +- r-tidyr +- r-withr +update_on: +- regex: mice_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mice diff --git a/prepare/r-michip/PKGBUILD b/prepare/r-michip/PKGBUILD new file mode 100644 index 0000000000..ece74cbdd9 --- /dev/null +++ b/prepare/r-michip/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MiChip +_pkgver=1.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MiChip Parsing and Summarizing Functions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-michip/lilac.py b/prepare/r-michip/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-michip/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-michip/lilac.yaml b/prepare/r-michip/lilac.yaml new file mode 100644 index 0000000000..da06fc182f --- /dev/null +++ b/prepare/r-michip/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: MiChip_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MiChip diff --git a/prepare/r-microbenchmark/PKGBUILD b/prepare/r-microbenchmark/PKGBUILD new file mode 100644 index 0000000000..fcd85e9173 --- /dev/null +++ b/prepare/r-microbenchmark/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: On a Unix-alike, one of the C functionsmach_absolute_time (macOS), clock_gettime or gethrtime. If noneof these is found, the obsolescent POSIX function gettimeofdaywill be tried. +# Maintainer: Guoyi Zhang + +_pkgname=microbenchmark +_pkgver=1.4.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Accurate Timing Functions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +optdepends=( + r-ggplot2 + r-multcomp + r-runit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-microbenchmark/lilac.py b/prepare/r-microbenchmark/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-microbenchmark/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-microbenchmark/lilac.yaml b/prepare/r-microbenchmark/lilac.yaml new file mode 100644 index 0000000000..b1ac3ac348 --- /dev/null +++ b/prepare/r-microbenchmark/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: microbenchmark_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=microbenchmark diff --git a/prepare/r-microbiome/PKGBUILD b/prepare/r-microbiome/PKGBUILD new file mode 100644 index 0000000000..1463ed0add --- /dev/null +++ b/prepare/r-microbiome/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=microbiome +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Microbiome Analytics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-dplyr + r-ggplot2 + r-phyloseq + r-reshape2 + r-rtsne + r-scales + r-tibble + r-tidyr + r-vegan +) +optdepends=( + r-biocgenerics + r-biocstyle + r-cairo + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-microbiome/lilac.py b/prepare/r-microbiome/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-microbiome/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-microbiome/lilac.yaml b/prepare/r-microbiome/lilac.yaml new file mode 100644 index 0000000000..95f7c305ae --- /dev/null +++ b/prepare/r-microbiome/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-phyloseq +- r-reshape2 +- r-rtsne +- r-scales +- r-tibble +- r-tidyr +- r-vegan +update_on: +- regex: microbiome_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/microbiome diff --git a/prepare/r-microbiomedasim/PKGBUILD b/prepare/r-microbiomedasim/PKGBUILD new file mode 100644 index 0000000000..d0e13f5188 --- /dev/null +++ b/prepare/r-microbiomedasim/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=microbiomeDASim +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Microbiome Differential Abundance Simulation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-ggplot2 + r-metagenomeseq + r-mvtnorm + r-pbapply + r-phyloseq + r-tmvtnorm +) +optdepends=( + r-devtools + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-microbiomedasim/lilac.py b/prepare/r-microbiomedasim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-microbiomedasim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-microbiomedasim/lilac.yaml b/prepare/r-microbiomedasim/lilac.yaml new file mode 100644 index 0000000000..076eb75c1c --- /dev/null +++ b/prepare/r-microbiomedasim/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-ggplot2 +- r-metagenomeseq +- r-mvtnorm +- r-pbapply +- r-phyloseq +- r-tmvtnorm +update_on: +- regex: microbiomeDASim_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/microbiomeDASim diff --git a/prepare/r-microbiomeexplorer/PKGBUILD b/prepare/r-microbiomeexplorer/PKGBUILD new file mode 100644 index 0000000000..aef9c25ad2 --- /dev/null +++ b/prepare/r-microbiomeexplorer/PKGBUILD @@ -0,0 +1,62 @@ +# Maintainer: Guoyi Zhang + +_pkgname=microbiomeExplorer +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Microbiome Exploration App' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-biomformat + r-broom + r-car + r-deseq2 + r-dplyr + r-dt + r-forcats + r-heatmaply + r-knitr + r-limma + r-lubridate + r-magrittr + r-matrixstats + r-metagenomeseq + r-plotly + r-purrr + r-rcolorbrewer + r-readr + r-reshape2 + r-rlang + r-rmarkdown + r-shiny + r-shinycssloaders + r-shinydashboard + r-shinyjs + r-shinywidgets + r-stringr + r-tibble + r-tidyr + r-vegan +) +optdepends=( + r-testthat + r-v8 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-microbiomeexplorer/lilac.py b/prepare/r-microbiomeexplorer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-microbiomeexplorer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-microbiomeexplorer/lilac.yaml b/prepare/r-microbiomeexplorer/lilac.yaml new file mode 100644 index 0000000000..0fb6c01782 --- /dev/null +++ b/prepare/r-microbiomeexplorer/lilac.yaml @@ -0,0 +1,40 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biomformat +- r-broom +- r-car +- r-deseq2 +- r-dplyr +- r-dt +- r-forcats +- r-heatmaply +- r-knitr +- r-limma +- r-lubridate +- r-magrittr +- r-matrixstats +- r-metagenomeseq +- r-plotly +- r-purrr +- r-rcolorbrewer +- r-readr +- r-reshape2 +- r-rlang +- r-rmarkdown +- r-shiny +- r-shinycssloaders +- r-shinydashboard +- r-shinyjs +- r-shinywidgets +- r-stringr +- r-tibble +- r-tidyr +- r-vegan +update_on: +- regex: microbiomeExplorer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/microbiomeExplorer diff --git a/prepare/r-microbiomemarker/PKGBUILD b/prepare/r-microbiomemarker/PKGBUILD new file mode 100644 index 0000000000..2fa682cdad --- /dev/null +++ b/prepare/r-microbiomemarker/PKGBUILD @@ -0,0 +1,68 @@ +# Maintainer: Guoyi Zhang + +_pkgname=microbiomeMarker +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='microbiome biomarker analysis toolkit' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-aldex2 + r-ancombc + r-biobase + r-biocgenerics + r-biomformat + r-biostrings + r-caret + r-coin + r-complexheatmap + r-deseq2 + r-dplyr + r-edger + r-ggplot2 + r-ggsignif + r-ggtree + r-iranges + r-limma + r-magrittr + r-metagenomeseq + r-multtest + r-patchwork + r-phyloseq + r-plotroc + r-purrr + r-rlang + r-s4vectors + r-tibble + r-tidyr + r-tidytree + r-yaml +) +optdepends=( + r-biocstyle + r-covr + r-e1071 + r-glmnet + r-kernlab + r-knitr + r-matrix + r-ranger + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-microbiomemarker/lilac.py b/prepare/r-microbiomemarker/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-microbiomemarker/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-microbiomemarker/lilac.yaml b/prepare/r-microbiomemarker/lilac.yaml new file mode 100644 index 0000000000..357812f73d --- /dev/null +++ b/prepare/r-microbiomemarker/lilac.yaml @@ -0,0 +1,39 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aldex2 +- r-ancombc +- r-biobase +- r-biocgenerics +- r-biomformat +- r-biostrings +- r-caret +- r-coin +- r-complexheatmap +- r-deseq2 +- r-dplyr +- r-edger +- r-ggplot2 +- r-ggsignif +- r-ggtree +- r-iranges +- r-limma +- r-magrittr +- r-metagenomeseq +- r-multtest +- r-patchwork +- r-phyloseq +- r-plotroc +- r-purrr +- r-rlang +- r-s4vectors +- r-tibble +- r-tidyr +- r-tidytree +- r-yaml +update_on: +- regex: microbiomeMarker_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/microbiomeMarker diff --git a/prepare/r-microbiomeprofiler/PKGBUILD b/prepare/r-microbiomeprofiler/PKGBUILD new file mode 100644 index 0000000000..96ceb98fd3 --- /dev/null +++ b/prepare/r-microbiomeprofiler/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MicrobiomeProfiler +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R/shiny package for microbiome functional enrichment analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-clusterprofiler + r-config + r-dt + r-enrichplot + r-ggplot2 + r-golem + r-htmltools + r-magrittr + r-shiny + r-shinycustomloader + r-shinywidgets +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-microbiomeprofiler/lilac.py b/prepare/r-microbiomeprofiler/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-microbiomeprofiler/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-microbiomeprofiler/lilac.yaml b/prepare/r-microbiomeprofiler/lilac.yaml new file mode 100644 index 0000000000..a5c7c84084 --- /dev/null +++ b/prepare/r-microbiomeprofiler/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clusterprofiler +- r-config +- r-dt +- r-enrichplot +- r-ggplot2 +- r-golem +- r-htmltools +- r-magrittr +- r-shiny +- r-shinycustomloader +- r-shinywidgets +update_on: +- regex: MicrobiomeProfiler_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MicrobiomeProfiler diff --git a/prepare/r-microbiotaprocess/PKGBUILD b/prepare/r-microbiotaprocess/PKGBUILD new file mode 100644 index 0000000000..a5140d1ea6 --- /dev/null +++ b/prepare/r-microbiotaprocess/PKGBUILD @@ -0,0 +1,82 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MicrobiotaProcess +_pkgver=1.6.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='an R package for analysis, visualization and biomarker discovery of microbiome' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-biostrings + r-coin + r-dplyr + r-dtplyr + r-foreach + r-ggplot2 + r-ggrepel + r-ggsignif + r-ggstar + r-ggtree + r-ggtreeextra + r-magrittr + r-patchwork + r-pillar + r-rlang + r-summarizedexperiment + r-tibble + r-tidyr + r-tidyselect + r-tidytree + r-treeio + r-vegan + r-zoo +) +optdepends=( + r-aplot + r-biomformat + r-cli + r-corrr + r-decipher + r-forcats + r-ggalluvial + r-ggh4x + r-gghalves + r-ggnewscale + r-ggside + r-ggupset + r-ggvenndiagram + r-glue + r-knitr + r-nlme + r-phangorn + r-phyloseq + r-picante + r-plyr + r-prettydoc + r-purrr + r-randomforest + r-rmarkdown + r-s4vectors + r-scales + r-seqmagick + r-testthat + r-withr + r-yaml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-microbiotaprocess/lilac.py b/prepare/r-microbiotaprocess/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-microbiotaprocess/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-microbiotaprocess/lilac.yaml b/prepare/r-microbiotaprocess/lilac.yaml new file mode 100644 index 0000000000..0a8ac2b183 --- /dev/null +++ b/prepare/r-microbiotaprocess/lilac.yaml @@ -0,0 +1,33 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-biostrings +- r-coin +- r-dplyr +- r-dtplyr +- r-foreach +- r-ggplot2 +- r-ggrepel +- r-ggsignif +- r-ggstar +- r-ggtree +- r-ggtreeextra +- r-magrittr +- r-patchwork +- r-pillar +- r-rlang +- r-summarizedexperiment +- r-tibble +- r-tidyr +- r-tidyselect +- r-tidytree +- r-treeio +- r-vegan +- r-zoo +update_on: +- regex: MicrobiotaProcess_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MicrobiotaProcess diff --git a/prepare/r-microrna/PKGBUILD b/prepare/r-microrna/PKGBUILD new file mode 100644 index 0000000000..3569761104 --- /dev/null +++ b/prepare/r-microrna/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=microRNA +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data and functions for dealing with microRNAs' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-microrna/lilac.py b/prepare/r-microrna/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-microrna/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-microrna/lilac.yaml b/prepare/r-microrna/lilac.yaml new file mode 100644 index 0000000000..2f5663415f --- /dev/null +++ b/prepare/r-microrna/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +update_on: +- regex: microRNA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/microRNA diff --git a/prepare/r-midashla/PKGBUILD b/prepare/r-midashla/PKGBUILD new file mode 100644 index 0000000000..2bf36d073f --- /dev/null +++ b/prepare/r-midashla/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=midasHLA +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R package for immunogenomics data handling and association analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-assertthat + r-broom + r-dplyr + r-formattable + r-hardyweinberg + r-kableextra + r-knitr + r-magrittr + r-multiassayexperiment + r-qdaptools + r-rlang + r-s4vectors + r-stringi + r-summarizedexperiment + r-tibble +) +optdepends=( + r-broom.mixed + r-cowplot + r-devtools + r-ggplot2 + r-ggpubr + r-rmarkdown + r-seqinr + r-survival + r-testthat + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENCE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-midashla/lilac.py b/prepare/r-midashla/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-midashla/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-midashla/lilac.yaml b/prepare/r-midashla/lilac.yaml new file mode 100644 index 0000000000..594c32dcc3 --- /dev/null +++ b/prepare/r-midashla/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-broom +- r-dplyr +- r-formattable +- r-hardyweinberg +- r-kableextra +- r-knitr +- r-magrittr +- r-multiassayexperiment +- r-qdaptools +- r-rlang +- r-s4vectors +- r-stringi +- r-summarizedexperiment +- r-tibble +update_on: +- regex: midasHLA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/midasHLA diff --git a/prepare/r-migsa/PKGBUILD b/prepare/r-migsa/PKGBUILD new file mode 100644 index 0000000000..96d5bb008d --- /dev/null +++ b/prepare/r-migsa/PKGBUILD @@ -0,0 +1,61 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MIGSA +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Massive and Integrative Gene Set Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-data.table + r-edger + r-futile.logger + r-ggdendro + r-ggplot2 + r-go.db + r-gostats + r-graph + r-gseabase + r-ismev + r-jsonlite + r-limma + r-matrixstats + r-org.hs.eg.db + r-rbgl + r-reshape2 + r-rgraphviz + r-vegan +) +optdepends=( + r-biocstyle + r-breastcancermainz + r-breastcancernki + r-breastcancertransbig + r-breastcancerunt + r-breastcancerupp + r-breastcancervdx + r-knitr + r-mgsz + r-migsadata + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-migsa/lilac.py b/prepare/r-migsa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-migsa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-migsa/lilac.yaml b/prepare/r-migsa/lilac.yaml new file mode 100644 index 0000000000..f2e4a20914 --- /dev/null +++ b/prepare/r-migsa/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-data.table +- r-edger +- r-futile.logger +- r-ggdendro +- r-ggplot2 +- r-go.db +- r-gostats +- r-graph +- r-gseabase +- r-ismev +- r-jsonlite +- r-limma +- r-matrixstats +- r-org.hs.eg.db +- r-rbgl +- r-reshape2 +- r-rgraphviz +- r-vegan +update_on: +- regex: MIGSA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MIGSA diff --git a/prepare/r-milor/PKGBUILD b/prepare/r-milor/PKGBUILD new file mode 100644 index 0000000000..b54caefe08 --- /dev/null +++ b/prepare/r-milor/PKGBUILD @@ -0,0 +1,66 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miloR +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential neighbourhood abundance testing on a graph' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocneighbors + r-biocparallel + r-biocsingular + r-cowplot + r-dplyr + r-edger + r-ggbeeswarm + r-ggplot2 + r-ggraph + r-ggrepel + r-gtools + r-igraph + r-irlba + r-limma + r-matrixstats + r-patchwork + r-rcolorbrewer + r-s4vectors + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-covr + r-curl + r-graphics + r-knitr + r-magick + r-mass + r-mousegastrulationdata + r-mvtnorm + r-rcurl + r-rmarkdown + r-scater + r-scran + r-testthat + r-uwot +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-milor/lilac.py b/prepare/r-milor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-milor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-milor/lilac.yaml b/prepare/r-milor/lilac.yaml new file mode 100644 index 0000000000..9bd28712a9 --- /dev/null +++ b/prepare/r-milor/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocneighbors +- r-biocparallel +- r-biocsingular +- r-cowplot +- r-dplyr +- r-edger +- r-ggbeeswarm +- r-ggplot2 +- r-ggraph +- r-ggrepel +- r-gtools +- r-igraph +- r-irlba +- r-limma +- r-matrixstats +- r-patchwork +- r-rcolorbrewer +- r-s4vectors +- r-singlecellexperiment +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-tidyr +update_on: +- regex: miloR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/miloR diff --git a/prepare/r-mimager/PKGBUILD b/prepare/r-mimager/PKGBUILD new file mode 100644 index 0000000000..7df59bdc8c --- /dev/null +++ b/prepare/r-mimager/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mimager +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='mimager: The Microarray Imager' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-affy + r-affyplm + r-biobase + r-biocgenerics + r-dbi + r-gtable + r-oligo + r-oligoclasses + r-preprocesscore + r-s4vectors + r-scales +) +optdepends=( + r-abind + r-affydata + r-biocstyle + r-hgu95av2cdf + r-knitr + r-lintr + r-matrix + r-oligodata + r-pd.hugene.1.0.st.v1 + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mimager/lilac.py b/prepare/r-mimager/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mimager/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mimager/lilac.yaml b/prepare/r-mimager/lilac.yaml new file mode 100644 index 0000000000..6452a3cc28 --- /dev/null +++ b/prepare/r-mimager/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-affyplm +- r-biobase +- r-biocgenerics +- r-dbi +- r-gtable +- r-oligo +- r-oligoclasses +- r-preprocesscore +- r-s4vectors +- r-scales +update_on: +- regex: mimager_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mimager diff --git a/prepare/r-mimosa/PKGBUILD b/prepare/r-mimosa/PKGBUILD new file mode 100644 index 0000000000..c86da651f9 --- /dev/null +++ b/prepare/r-mimosa/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MIMOSA +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mixture Models for Single-Cell Assays' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-coda + r-data.table + r-dplyr + r-formula + r-ggplot2 + r-mcmcpack + r-modeest + r-plyr + r-pracma + r-rcpp + r-rcpparmadillo + r-reshape + r-rlang + r-scales + r-testthat + r-tidyr +) +optdepends=( + r-knitr + r-parallel +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mimosa/lilac.py b/prepare/r-mimosa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mimosa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mimosa/lilac.yaml b/prepare/r-mimosa/lilac.yaml new file mode 100644 index 0000000000..34f240a546 --- /dev/null +++ b/prepare/r-mimosa/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-coda +- r-data.table +- r-dplyr +- r-formula +- r-ggplot2 +- r-mcmcpack +- r-modeest +- r-plyr +- r-pracma +- r-rcpp +- r-rcpparmadillo +- r-reshape +- r-rlang +- r-scales +- r-testthat +- r-tidyr +update_on: +- regex: MIMOSA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MIMOSA diff --git a/prepare/r-mina/PKGBUILD b/prepare/r-mina/PKGBUILD new file mode 100644 index 0000000000..6912f5c6d4 --- /dev/null +++ b/prepare/r-mina/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mina +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Microbial community dIversity and Network Analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-apcluster + r-biganalytics + r-bigmemory + r-foreach + r-ggplot2 + r-hmisc + r-mcl + r-paralleldist + r-plyr + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-reshape2 + r-rspectra + r-stringr +) +optdepends=( + r-domc + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mina/lilac.py b/prepare/r-mina/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mina/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mina/lilac.yaml b/prepare/r-mina/lilac.yaml new file mode 100644 index 0000000000..2fa3924d75 --- /dev/null +++ b/prepare/r-mina/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-apcluster +- r-biganalytics +- r-bigmemory +- r-foreach +- r-ggplot2 +- r-hmisc +- r-mcl +- r-paralleldist +- r-plyr +- r-rcpp +- r-rcpparmadillo +- r-rcppparallel +- r-reshape2 +- r-rspectra +- r-stringr +update_on: +- regex: mina_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mina diff --git a/prepare/r-mineica/PKGBUILD b/prepare/r-mineica/PKGBUILD new file mode 100644 index 0000000000..7138aed662 --- /dev/null +++ b/prepare/r-mineica/PKGBUILD @@ -0,0 +1,66 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MineICA +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of an ICA decomposition obtained on genomics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-biomart + r-colorspace + r-fastica + r-foreach + r-fpc + r-ggplot2 + r-gostats + r-graph + r-gtools + r-hmisc + r-igraph + r-jade + r-lumi + r-lumihumanall.db + r-marray + r-mclust + r-plyr + r-rcolorbrewer + r-rgraphviz + r-scales + r-xtable +) +optdepends=( + r-biomart + r-breastcancermainz + r-breastcancertransbig + r-breastcancerupp + r-breastcancervdx + r-cluster + r-domc + r-future + r-future.apply + r-gostats + r-hgu133a.db + r-igraph + r-mclust +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mineica/lilac.py b/prepare/r-mineica/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mineica/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mineica/lilac.yaml b/prepare/r-mineica/lilac.yaml new file mode 100644 index 0000000000..ba92ef50b1 --- /dev/null +++ b/prepare/r-mineica/lilac.yaml @@ -0,0 +1,34 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-biomart +- r-colorspace +- r-fastica +- r-foreach +- r-fpc +- r-ggplot2 +- r-gostats +- r-graph +- r-gtools +- r-hmisc +- r-igraph +- r-jade +- r-lumi +- r-lumihumanall.db +- r-marray +- r-mclust +- r-plyr +- r-rcolorbrewer +- r-rgraphviz +- r-scales +- r-xtable +update_on: +- regex: MineICA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MineICA diff --git a/prepare/r-minerva/PKGBUILD b/prepare/r-minerva/PKGBUILD new file mode 100644 index 0000000000..7c8a167ff7 --- /dev/null +++ b/prepare/r-minerva/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=minerva +_pkgver=1.5.10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Maximal Information-Based Nonparametric Exploration for Variable Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-minerva/lilac.py b/prepare/r-minerva/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-minerva/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-minerva/lilac.yaml b/prepare/r-minerva/lilac.yaml new file mode 100644 index 0000000000..5693fb5834 --- /dev/null +++ b/prepare/r-minerva/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: minerva_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=minerva diff --git a/prepare/r-minet/PKGBUILD b/prepare/r-minet/PKGBUILD new file mode 100644 index 0000000000..378338ac27 --- /dev/null +++ b/prepare/r-minet/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=minet +_pkgver=3.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mutual Information NETworks' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-infotheo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-minet/lilac.py b/prepare/r-minet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-minet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-minet/lilac.yaml b/prepare/r-minet/lilac.yaml new file mode 100644 index 0000000000..f745332d96 --- /dev/null +++ b/prepare/r-minet/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-infotheo +update_on: +- regex: minet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/minet diff --git a/prepare/r-minfi/PKGBUILD b/prepare/r-minfi/PKGBUILD new file mode 100644 index 0000000000..7ad863a34f --- /dev/null +++ b/prepare/r-minfi/PKGBUILD @@ -0,0 +1,65 @@ +# Maintainer: Guoyi Zhang + +_pkgname=minfi +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analyze Illumina Infinium DNA methylation arrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-beanplot + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bumphunter + r-data.table + r-delayedarray + r-delayedmatrixstats + r-genefilter + r-genomeinfodb + r-genomicranges + r-geoquery + r-hdf5array + r-illuminaio + r-iranges + r-limma + r-mclust + r-nor1mix + r-preprocesscore + r-quadprog + r-rcolorbrewer + r-reshape + r-s4vectors + r-siggenes + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-digest + r-flowsorted.blood.450k + r-illuminahumanmethylation450kanno.ilmn12.hg19 + r-illuminahumanmethylation450kmanifest + r-knitr + r-minfidata + r-minfidataepic + r-rmarkdown + r-runit + r-tools +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-minfi/lilac.py b/prepare/r-minfi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-minfi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-minfi/lilac.yaml b/prepare/r-minfi/lilac.yaml new file mode 100644 index 0000000000..97a1ea6ae3 --- /dev/null +++ b/prepare/r-minfi/lilac.yaml @@ -0,0 +1,35 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beanplot +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bumphunter +- r-data.table +- r-delayedarray +- r-delayedmatrixstats +- r-genefilter +- r-genomeinfodb +- r-genomicranges +- r-geoquery +- r-hdf5array +- r-illuminaio +- r-iranges +- r-limma +- r-mclust +- r-nor1mix +- r-preprocesscore +- r-quadprog +- r-rcolorbrewer +- r-reshape +- r-s4vectors +- r-siggenes +- r-summarizedexperiment +update_on: +- regex: minfi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/minfi diff --git a/prepare/r-minimumdistance/PKGBUILD b/prepare/r-minimumdistance/PKGBUILD new file mode 100644 index 0000000000..c43f190b95 --- /dev/null +++ b/prepare/r-minimumdistance/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MinimumDistance +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Package for De Novo CNV Detection in Case-Parent Trios' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-data.table + r-dnacopy + r-ff + r-foreach + r-genomeinfodb + r-genomicranges + r-iranges + r-matrixgenerics + r-matrixstats + r-oligoclasses + r-s4vectors + r-summarizedexperiment + r-vanillaice +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg18 + r-bsgenome.hsapiens.ucsc.hg19 + r-dosnow + r-human610quadv1bcrlmm + r-runit + r-snow +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-minimumdistance/lilac.py b/prepare/r-minimumdistance/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-minimumdistance/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-minimumdistance/lilac.yaml b/prepare/r-minimumdistance/lilac.yaml new file mode 100644 index 0000000000..dd93cf669f --- /dev/null +++ b/prepare/r-minimumdistance/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-data.table +- r-dnacopy +- r-ff +- r-foreach +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-matrixgenerics +- r-matrixstats +- r-oligoclasses +- r-s4vectors +- r-summarizedexperiment +- r-vanillaice +update_on: +- regex: MinimumDistance_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MinimumDistance diff --git a/prepare/r-miniui/PKGBUILD b/prepare/r-miniui/PKGBUILD new file mode 100644 index 0000000000..9ce574181a --- /dev/null +++ b/prepare/r-miniui/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miniUI +_pkgver=0.1.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Shiny UI Widgets for Small Screens' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-htmltools + r-shiny +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-miniui/lilac.py b/prepare/r-miniui/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-miniui/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-miniui/lilac.yaml b/prepare/r-miniui/lilac.yaml new file mode 100644 index 0000000000..a946ce7f59 --- /dev/null +++ b/prepare/r-miniui/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-shiny +update_on: +- regex: miniUI_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=miniUI diff --git a/prepare/r-minpack.lm/PKGBUILD b/prepare/r-minpack.lm/PKGBUILD new file mode 100644 index 0000000000..d286d2e070 --- /dev/null +++ b/prepare/r-minpack.lm/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=minpack.lm +_pkgver=1.2-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Interface to the Levenberg-Marquardt Nonlinear Least-Squares Algorithm Found in MINPACK, Plus Support for Bounds' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-mass +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-minpack.lm/lilac.py b/prepare/r-minpack.lm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-minpack.lm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-minpack.lm/lilac.yaml b/prepare/r-minpack.lm/lilac.yaml new file mode 100644 index 0000000000..91d439d491 --- /dev/null +++ b/prepare/r-minpack.lm/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: minpack.lm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=minpack.lm diff --git a/prepare/r-minqa/PKGBUILD b/prepare/r-minqa/PKGBUILD new file mode 100644 index 0000000000..30d1734018 --- /dev/null +++ b/prepare/r-minqa/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=minqa +_pkgver=1.2.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Derivative-free optimization algorithms by quadratic approximation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-minqa/lilac.py b/prepare/r-minqa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-minqa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-minqa/lilac.yaml b/prepare/r-minqa/lilac.yaml new file mode 100644 index 0000000000..2257791019 --- /dev/null +++ b/prepare/r-minqa/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: minqa_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=minqa diff --git a/prepare/r-mipp/PKGBUILD b/prepare/r-mipp/PKGBUILD new file mode 100644 index 0000000000..b8e0d6a0df --- /dev/null +++ b/prepare/r-mipp/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MiPP +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Misclassification Penalized Posterior Classification' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-e1071 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mipp/lilac.py b/prepare/r-mipp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mipp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mipp/lilac.yaml b/prepare/r-mipp/lilac.yaml new file mode 100644 index 0000000000..57107e833c --- /dev/null +++ b/prepare/r-mipp/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-e1071 +update_on: +- regex: MiPP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MiPP diff --git a/prepare/r-miqc/PKGBUILD b/prepare/r-miqc/PKGBUILD new file mode 100644 index 0000000000..2d970ea28f --- /dev/null +++ b/prepare/r-miqc/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miQC +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Flexible, probabilistic metrics for quality control of scRNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-flexmix + r-ggplot2 + r-singlecellexperiment +) +optdepends=( + r-biocstyle + r-biomart + r-knitr + r-rmarkdown + r-scater + r-scrnaseq +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-miqc/lilac.py b/prepare/r-miqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-miqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-miqc/lilac.yaml b/prepare/r-miqc/lilac.yaml new file mode 100644 index 0000000000..6ba3ecdd9b --- /dev/null +++ b/prepare/r-miqc/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-flexmix +- r-ggplot2 +- r-singlecellexperiment +update_on: +- regex: miQC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/miQC diff --git a/prepare/r-mira/PKGBUILD b/prepare/r-mira/PKGBUILD new file mode 100644 index 0000000000..c5e72149f3 --- /dev/null +++ b/prepare/r-mira/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MIRA +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methylation-Based Inference of Regulatory Activity' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-bsseq + r-data.table + r-genomicranges + r-ggplot2 + r-iranges + r-s4vectors +) +optdepends=( + r-annotationhub + r-biocstyle + r-knitr + r-lola + r-parallel + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mira/lilac.py b/prepare/r-mira/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mira/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mira/lilac.yaml b/prepare/r-mira/lilac.yaml new file mode 100644 index 0000000000..729213ef1f --- /dev/null +++ b/prepare/r-mira/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-bsseq +- r-data.table +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-s4vectors +update_on: +- regex: MIRA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MIRA diff --git a/prepare/r-mirage/PKGBUILD b/prepare/r-mirage/PKGBUILD new file mode 100644 index 0000000000..cd4ad614ed --- /dev/null +++ b/prepare/r-mirage/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MiRaGE +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MiRNA Ranking by Gene Expression' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biobase + r-biocgenerics + r-biocmanager + r-s4vectors +) +optdepends=( + r-beadarrayexampledata + r-biomart + r-biostrings + r-bsgenome + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.mmusculus.ucsc.mm10 + r-genomicfeatures + r-genomicranges + r-humanstemcell + r-iranges + r-mirnatarget + r-seqinr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mirage/lilac.py b/prepare/r-mirage/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mirage/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mirage/lilac.yaml b/prepare/r-mirage/lilac.yaml new file mode 100644 index 0000000000..db42124015 --- /dev/null +++ b/prepare/r-mirage/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-biocmanager +- r-s4vectors +update_on: +- regex: MiRaGE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MiRaGE diff --git a/prepare/r-mirbase.db/PKGBUILD b/prepare/r-mirbase.db/PKGBUILD new file mode 100644 index 0000000000..2fe4cd1c76 --- /dev/null +++ b/prepare/r-mirbase.db/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mirbase.db +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='miRBase: the microRNA database' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-annotationdbi +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mirbase.db/lilac.py b/prepare/r-mirbase.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mirbase.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mirbase.db/lilac.yaml b/prepare/r-mirbase.db/lilac.yaml new file mode 100644 index 0000000000..d5a811b1c0 --- /dev/null +++ b/prepare/r-mirbase.db/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +update_on: +- regex: mirbase.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mirbase.db diff --git a/prepare/r-mirbaseconverter/PKGBUILD b/prepare/r-mirbaseconverter/PKGBUILD new file mode 100644 index 0000000000..e06f37d7f8 --- /dev/null +++ b/prepare/r-mirbaseconverter/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miRBaseConverter +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biocgenerics + r-knitr + r-rmarkdown + r-rtracklayer + r-runit + r-utils +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mirbaseconverter/lilac.py b/prepare/r-mirbaseconverter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mirbaseconverter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mirbaseconverter/lilac.yaml b/prepare/r-mirbaseconverter/lilac.yaml new file mode 100644 index 0000000000..3587fcd23b --- /dev/null +++ b/prepare/r-mirbaseconverter/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: miRBaseConverter_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/miRBaseConverter diff --git a/prepare/r-mirbaseversions.db/PKGBUILD b/prepare/r-mirbaseversions.db/PKGBUILD new file mode 100644 index 0000000000..87c06784c2 --- /dev/null +++ b/prepare/r-mirbaseversions.db/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miRBaseVersions.db +_pkgver=1.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Collection of mature miRNA names of 22 different miRBase release versions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-dbi + r-gtools + r-rsqlite +) +optdepends=( + r-annotate + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mirbaseversions.db/lilac.py b/prepare/r-mirbaseversions.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mirbaseversions.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mirbaseversions.db/lilac.yaml b/prepare/r-mirbaseversions.db/lilac.yaml new file mode 100644 index 0000000000..9c371ca841 --- /dev/null +++ b/prepare/r-mirbaseversions.db/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-dbi +- r-gtools +- r-rsqlite +update_on: +- regex: miRBaseVersions.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/miRBaseVersions.db diff --git a/prepare/r-mircomp/PKGBUILD b/prepare/r-mircomp/PKGBUILD new file mode 100644 index 0000000000..6b3a9b25a7 --- /dev/null +++ b/prepare/r-mircomp/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miRcomp +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools to assess and compare miRNA expression estimatation methods' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-mircompdata +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit + r-shiny +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mircomp/lilac.py b/prepare/r-mircomp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mircomp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mircomp/lilac.yaml b/prepare/r-mircomp/lilac.yaml new file mode 100644 index 0000000000..a74c2fee96 --- /dev/null +++ b/prepare/r-mircomp/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-mircompdata +update_on: +- regex: miRcomp_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/miRcomp diff --git a/prepare/r-mircompdata/PKGBUILD b/prepare/r-mircompdata/PKGBUILD new file mode 100644 index 0000000000..1edbc52e89 --- /dev/null +++ b/prepare/r-mircompdata/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miRcompData +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data used in the miRcomp package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mircompdata/lilac.py b/prepare/r-mircompdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mircompdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mircompdata/lilac.yaml b/prepare/r-mircompdata/lilac.yaml new file mode 100644 index 0000000000..252c950bbe --- /dev/null +++ b/prepare/r-mircompdata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: miRcompData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/miRcompData diff --git a/prepare/r-mirintegrator/PKGBUILD b/prepare/r-mirintegrator/PKGBUILD new file mode 100644 index 0000000000..243aebc0a5 --- /dev/null +++ b/prepare/r-mirintegrator/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mirIntegrator +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integrating microRNA expression into signaling pathways for pathway analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-ggplot2 + r-graph + r-org.hs.eg.db + r-rgraphviz + r-rontotools +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mirintegrator/lilac.py b/prepare/r-mirintegrator/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mirintegrator/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mirintegrator/lilac.yaml b/prepare/r-mirintegrator/lilac.yaml new file mode 100644 index 0000000000..e3552efe44 --- /dev/null +++ b/prepare/r-mirintegrator/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-ggplot2 +- r-graph +- r-org.hs.eg.db +- r-rgraphviz +- r-rontotools +update_on: +- regex: mirIntegrator_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mirIntegrator diff --git a/prepare/r-mirlab/PKGBUILD b/prepare/r-mirlab/PKGBUILD new file mode 100644 index 0000000000..ba38917ed9 --- /dev/null +++ b/prepare/r-mirlab/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miRLAB +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dry lab for exploring miRNA-mRNA relationships' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-category + r-ctc + r-dplyr + r-energy + r-entropy + r-glmnet + r-gostats + r-gplots + r-hmisc + r-httr + r-impute + r-invariantcausalprediction + r-limma + r-org.hs.eg.db + r-pcalg + r-rcurl + r-stringr + r-summarizedexperiment + r-tcgabiolinks +) +optdepends=( + r-annotationdbi + r-biocgenerics + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mirlab/lilac.py b/prepare/r-mirlab/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mirlab/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mirlab/lilac.yaml b/prepare/r-mirlab/lilac.yaml new file mode 100644 index 0000000000..8a949e1513 --- /dev/null +++ b/prepare/r-mirlab/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-category +- r-ctc +- r-dplyr +- r-energy +- r-entropy +- r-glmnet +- r-gostats +- r-gplots +- r-hmisc +- r-httr +- r-impute +- r-invariantcausalprediction +- r-limma +- r-org.hs.eg.db +- r-pcalg +- r-rcurl +- r-stringr +- r-summarizedexperiment +- r-tcgabiolinks +update_on: +- regex: miRLAB_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/miRLAB diff --git a/prepare/r-mirmine/PKGBUILD b/prepare/r-mirmine/PKGBUILD new file mode 100644 index 0000000000..dfc735566a --- /dev/null +++ b/prepare/r-mirmine/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miRmine +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data package with miRNA-seq datasets from miRmine database as RangedSummarizedExperiment' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-deseq2 + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mirmine/lilac.py b/prepare/r-mirmine/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mirmine/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mirmine/lilac.yaml b/prepare/r-mirmine/lilac.yaml new file mode 100644 index 0000000000..c25d538a29 --- /dev/null +++ b/prepare/r-mirmine/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-summarizedexperiment +update_on: +- regex: miRmine_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/miRmine diff --git a/prepare/r-mirnameconverter/PKGBUILD b/prepare/r-mirnameconverter/PKGBUILD new file mode 100644 index 0000000000..1b5a266ba6 --- /dev/null +++ b/prepare/r-mirnameconverter/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miRNAmeConverter +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Convert miRNA Names to Different miRBase Versions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-dbi + r-mirbaseversions.db + r-reshape2 +) +optdepends=( + r-knitr + r-methods + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mirnameconverter/lilac.py b/prepare/r-mirnameconverter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mirnameconverter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mirnameconverter/lilac.yaml b/prepare/r-mirnameconverter/lilac.yaml new file mode 100644 index 0000000000..36182fc37d --- /dev/null +++ b/prepare/r-mirnameconverter/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-dbi +- r-mirbaseversions.db +- r-reshape2 +update_on: +- regex: miRNAmeConverter_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/miRNAmeConverter diff --git a/prepare/r-mirnapath/PKGBUILD b/prepare/r-mirnapath/PKGBUILD new file mode 100644 index 0000000000..6283cb20f4 --- /dev/null +++ b/prepare/r-mirnapath/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miRNApath +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='miRNApath: Pathway Enrichment for miRNA Expression Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mirnapath/lilac.py b/prepare/r-mirnapath/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mirnapath/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mirnapath/lilac.yaml b/prepare/r-mirnapath/lilac.yaml new file mode 100644 index 0000000000..ab7e1adad0 --- /dev/null +++ b/prepare/r-mirnapath/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: miRNApath_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/miRNApath diff --git a/prepare/r-mirnatap.db/PKGBUILD b/prepare/r-mirnatap.db/PKGBUILD new file mode 100644 index 0000000000..d8d3946740 --- /dev/null +++ b/prepare/r-mirnatap.db/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miRNAtap.db +_pkgver=0.99.10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data for miRNAtap' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-dbi + r-mirnatap + r-rsqlite +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mirnatap.db/lilac.py b/prepare/r-mirnatap.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mirnatap.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mirnatap.db/lilac.yaml b/prepare/r-mirnatap.db/lilac.yaml new file mode 100644 index 0000000000..d8df838630 --- /dev/null +++ b/prepare/r-mirnatap.db/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-dbi +- r-mirnatap +- r-rsqlite +update_on: +- regex: miRNAtap.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/miRNAtap.db diff --git a/prepare/r-mirnatap/PKGBUILD b/prepare/r-mirnatap/PKGBUILD new file mode 100644 index 0000000000..3f941d8877 --- /dev/null +++ b/prepare/r-mirnatap/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miRNAtap +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='miRNAtap: microRNA Targets - Aggregated Predictions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-dbi + r-plyr + r-rsqlite + r-sqldf + r-stringr +) +optdepends=( + r-mirnatap.db + r-org.hs.eg.db + r-testthat + r-topgo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mirnatap/lilac.py b/prepare/r-mirnatap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mirnatap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mirnatap/lilac.yaml b/prepare/r-mirnatap/lilac.yaml new file mode 100644 index 0000000000..3d2270a82a --- /dev/null +++ b/prepare/r-mirnatap/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-dbi +- r-plyr +- r-rsqlite +- r-sqldf +- r-stringr +update_on: +- regex: miRNAtap_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/miRNAtap diff --git a/prepare/r-mirsm/PKGBUILD b/prepare/r-mirsm/PKGBUILD new file mode 100644 index 0000000000..c1bf6acdd5 --- /dev/null +++ b/prepare/r-mirsm/PKGBUILD @@ -0,0 +1,62 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miRSM +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Inferring miRNA sponge modules in heterogeneous data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bibitr + r-bicare + r-biclust + r-biobase + r-dbscan + r-dynamictreecut + r-energy + r-fabia + r-flashclust + r-gfa + r-gseabase + r-ibbig + r-igraph + r-isa2 + r-linkcomm + r-matrixcorrelation + r-mcl + r-mclust + r-mirsponger + r-nmf + r-org.hs.eg.db + r-pma + r-ppclust + r-rcpp + r-rqubic + r-s4vd + r-sombrero + r-subspace + r-summarizedexperiment + r-wgcna +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mirsm/lilac.py b/prepare/r-mirsm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mirsm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mirsm/lilac.yaml b/prepare/r-mirsm/lilac.yaml new file mode 100644 index 0000000000..808e261f49 --- /dev/null +++ b/prepare/r-mirsm/lilac.yaml @@ -0,0 +1,39 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bibitr +- r-bicare +- r-biclust +- r-biobase +- r-dbscan +- r-dynamictreecut +- r-energy +- r-fabia +- r-flashclust +- r-gfa +- r-gseabase +- r-ibbig +- r-igraph +- r-isa2 +- r-linkcomm +- r-matrixcorrelation +- r-mcl +- r-mclust +- r-mirsponger +- r-nmf +- r-org.hs.eg.db +- r-pma +- r-ppclust +- r-rcpp +- r-rqubic +- r-s4vd +- r-sombrero +- r-subspace +- r-summarizedexperiment +- r-wgcna +update_on: +- regex: miRSM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/miRSM diff --git a/prepare/r-mirsponger/PKGBUILD b/prepare/r-mirsponger/PKGBUILD new file mode 100644 index 0000000000..cecbfb5df2 --- /dev/null +++ b/prepare/r-mirsponger/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miRspongeR +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identification and analysis of miRNA sponge interaction networks and modules' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-clusterprofiler + r-corpcor + r-dose + r-igraph + r-linkcomm + r-mcl + r-org.hs.eg.db + r-rcpp + r-reactomepa + r-varhandle +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mirsponger/lilac.py b/prepare/r-mirsponger/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mirsponger/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mirsponger/lilac.yaml b/prepare/r-mirsponger/lilac.yaml new file mode 100644 index 0000000000..0ebe267ccc --- /dev/null +++ b/prepare/r-mirsponger/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clusterprofiler +- r-corpcor +- r-dose +- r-igraph +- r-linkcomm +- r-mcl +- r-org.hs.eg.db +- r-rcpp +- r-reactomepa +- r-varhandle +update_on: +- regex: miRspongeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/miRspongeR diff --git a/prepare/r-mirtarrnaseq/PKGBUILD b/prepare/r-mirtarrnaseq/PKGBUILD new file mode 100644 index 0000000000..ace21463c3 --- /dev/null +++ b/prepare/r-mirtarrnaseq/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mirTarRnaSeq +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='mirTarRnaSeq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-assertthat + r-catools + r-corrplot + r-data.table + r-dplyr + r-pheatmap + r-pscl + r-purrr + r-r.utils + r-reshape2 +) +optdepends=( + r-biocstyle + r-knitr + r-r.cache + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mirtarrnaseq/lilac.py b/prepare/r-mirtarrnaseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mirtarrnaseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mirtarrnaseq/lilac.yaml b/prepare/r-mirtarrnaseq/lilac.yaml new file mode 100644 index 0000000000..06e3beaddb --- /dev/null +++ b/prepare/r-mirtarrnaseq/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-catools +- r-corrplot +- r-data.table +- r-dplyr +- r-pheatmap +- r-pscl +- r-purrr +- r-r.utils +- r-reshape2 +update_on: +- regex: mirTarRnaSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mirTarRnaSeq diff --git a/prepare/r-misc3d/PKGBUILD b/prepare/r-misc3d/PKGBUILD new file mode 100644 index 0000000000..d357d228ed --- /dev/null +++ b/prepare/r-misc3d/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=misc3d +_pkgver=0.9-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Miscellaneous 3D Plots' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-mass + r-rgl + r-tkrplot +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-misc3d/lilac.py b/prepare/r-misc3d/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-misc3d/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-misc3d/lilac.yaml b/prepare/r-misc3d/lilac.yaml new file mode 100644 index 0000000000..122656ebbd --- /dev/null +++ b/prepare/r-misc3d/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: misc3d_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=misc3d diff --git a/prepare/r-misctools/PKGBUILD b/prepare/r-misctools/PKGBUILD new file mode 100644 index 0000000000..d25d8b396d --- /dev/null +++ b/prepare/r-misctools/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=miscTools +_pkgver=0.6-26 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Miscellaneous Tools and Utilities' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-digest +) +optdepends=( + r-ecdat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-misctools/lilac.py b/prepare/r-misctools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-misctools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-misctools/lilac.yaml b/prepare/r-misctools/lilac.yaml new file mode 100644 index 0000000000..1cd56f1eb8 --- /dev/null +++ b/prepare/r-misctools/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +update_on: +- regex: miscTools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=miscTools diff --git a/prepare/r-missforest/PKGBUILD b/prepare/r-missforest/PKGBUILD new file mode 100644 index 0000000000..25bb4cd335 --- /dev/null +++ b/prepare/r-missforest/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=missForest +_pkgver=1.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Nonparametric Missing Value Imputation using Random Forest' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-foreach + r-itertools + r-randomforest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-missforest/lilac.py b/prepare/r-missforest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-missforest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-missforest/lilac.yaml b/prepare/r-missforest/lilac.yaml new file mode 100644 index 0000000000..4bc0e0f570 --- /dev/null +++ b/prepare/r-missforest/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-foreach +- r-itertools +- r-randomforest +update_on: +- regex: missForest_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=missForest diff --git a/prepare/r-missmda/PKGBUILD b/prepare/r-missmda/PKGBUILD new file mode 100644 index 0000000000..bff960bb08 --- /dev/null +++ b/prepare/r-missmda/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=missMDA +_pkgver=1.18 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Handling Missing Values with Multivariate Data Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-doparallel + r-factominer + r-foreach + r-ggplot2 + r-mice + r-mvtnorm +) +optdepends=( + r-knitr + r-markdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-missmda/lilac.py b/prepare/r-missmda/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-missmda/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-missmda/lilac.yaml b/prepare/r-missmda/lilac.yaml new file mode 100644 index 0000000000..f1ba335f0e --- /dev/null +++ b/prepare/r-missmda/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-factominer +- r-foreach +- r-ggplot2 +- r-mice +- r-mvtnorm +update_on: +- regex: missMDA_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=missMDA diff --git a/prepare/r-missmethyl/PKGBUILD b/prepare/r-missmethyl/PKGBUILD new file mode 100644 index 0000000000..29bc9c062a --- /dev/null +++ b/prepare/r-missmethyl/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=missMethyl +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysing Illumina HumanMethylation BeadChip Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biasedurn + r-biobase + r-biocgenerics + r-genomicranges + r-go.db + r-illuminahumanmethylation450kanno.ilmn12.hg19 + r-illuminahumanmethylation450kmanifest + r-illuminahumanmethylationepicanno.ilm10b4.hg19 + r-illuminahumanmethylationepicmanifest + r-iranges + r-limma + r-methylumi + r-minfi + r-org.hs.eg.db + r-ruv + r-s4vectors + r-statmod + r-stringr + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-dmrcate + r-edger + r-experimenthub + r-knitr + r-minfidata + r-rmarkdown + r-tweedeseqcountdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-missmethyl/lilac.py b/prepare/r-missmethyl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-missmethyl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-missmethyl/lilac.yaml b/prepare/r-missmethyl/lilac.yaml new file mode 100644 index 0000000000..6a5c72a9e1 --- /dev/null +++ b/prepare/r-missmethyl/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biasedurn +- r-biobase +- r-biocgenerics +- r-genomicranges +- r-go.db +- r-illuminahumanmethylation450kanno.ilmn12.hg19 +- r-illuminahumanmethylation450kmanifest +- r-illuminahumanmethylationepicanno.ilm10b4.hg19 +- r-illuminahumanmethylationepicmanifest +- r-iranges +- r-limma +- r-methylumi +- r-minfi +- r-org.hs.eg.db +- r-ruv +- r-s4vectors +- r-statmod +- r-stringr +- r-summarizedexperiment +update_on: +- regex: missMethyl_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/missMethyl diff --git a/prepare/r-missrows/PKGBUILD b/prepare/r-missrows/PKGBUILD new file mode 100644 index 0000000000..d4c13a50e1 --- /dev/null +++ b/prepare/r-missrows/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=missRows +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Handling Missing Individuals in Multi-Omics Data Integration' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ggplot2 + r-gtools + r-multiassayexperiment + r-plyr + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-missrows/lilac.py b/prepare/r-missrows/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-missrows/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-missrows/lilac.yaml b/prepare/r-missrows/lilac.yaml new file mode 100644 index 0000000000..2882b629a7 --- /dev/null +++ b/prepare/r-missrows/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gtools +- r-multiassayexperiment +- r-plyr +- r-s4vectors +update_on: +- regex: missRows_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/missRows diff --git a/prepare/r-mistyr/PKGBUILD b/prepare/r-mistyr/PKGBUILD new file mode 100644 index 0000000000..d261ce8b0f --- /dev/null +++ b/prepare/r-mistyr/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mistyR +_pkgver=1.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multiview Intercellular SpaTial modeling framework' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-caret + r-deldir + r-digest + r-distances + r-dplyr + r-filelock + r-furrr + r-ggplot2 + r-purrr + r-r.utils + r-ranger + r-readr + r-rlang + r-rlist + r-stringr + r-tibble + r-tidyr + r-withr +) +optdepends=( + r-biocstyle + r-covr + r-future + r-igraph + r-knitr + r-matrix + r-progeny + r-rmarkdown + r-sctransform + r-singlecellexperiment + r-spatialexperiment + r-summarizedexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mistyr/lilac.py b/prepare/r-mistyr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mistyr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mistyr/lilac.yaml b/prepare/r-mistyr/lilac.yaml new file mode 100644 index 0000000000..1558734b0d --- /dev/null +++ b/prepare/r-mistyr/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-caret +- r-deldir +- r-digest +- r-distances +- r-dplyr +- r-filelock +- r-furrr +- r-ggplot2 +- r-purrr +- r-r.utils +- r-ranger +- r-readr +- r-rlang +- r-rlist +- r-stringr +- r-tibble +- r-tidyr +- r-withr +update_on: +- regex: mistyR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mistyR diff --git a/prepare/r-mitch/PKGBUILD b/prepare/r-mitch/PKGBUILD new file mode 100644 index 0000000000..40545e6edf --- /dev/null +++ b/prepare/r-mitch/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mitch +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multi-Contrast Gene Set Enrichment Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CCPL:by-nc-sa') +depends=( + r + r-beeswarm + r-echarts4r + r-ggally + r-ggplot2 + r-gplots + r-gridextra + r-knitr + r-plyr + r-reshape2 + r-rmarkdown +) +optdepends=( + r-stringi + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mitch/lilac.py b/prepare/r-mitch/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mitch/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mitch/lilac.yaml b/prepare/r-mitch/lilac.yaml new file mode 100644 index 0000000000..ba1e8e39d4 --- /dev/null +++ b/prepare/r-mitch/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beeswarm +- r-echarts4r +- r-ggally +- r-ggplot2 +- r-gplots +- r-gridextra +- r-knitr +- r-plyr +- r-reshape2 +- r-rmarkdown +update_on: +- regex: mitch_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mitch diff --git a/prepare/r-mitoclone2/PKGBUILD b/prepare/r-mitoclone2/PKGBUILD new file mode 100644 index 0000000000..a57b5da095 --- /dev/null +++ b/prepare/r-mitoclone2/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: GNU make, PhISCS (optional) +# Maintainer: Guoyi Zhang + +_pkgname=mitoClone2 +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-deepsnv + r-genomicranges + r-ggplot2 + r-pheatmap + r-reshape2 + r-rhtslib + r-s4vectors +) +optdepends=( + r-biostrings + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mitoclone2/lilac.py b/prepare/r-mitoclone2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mitoclone2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mitoclone2/lilac.yaml b/prepare/r-mitoclone2/lilac.yaml new file mode 100644 index 0000000000..48555bcb75 --- /dev/null +++ b/prepare/r-mitoclone2/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-deepsnv +- r-genomicranges +- r-ggplot2 +- r-pheatmap +- r-reshape2 +- r-rhtslib +- r-s4vectors +update_on: +- regex: mitoClone2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mitoClone2 diff --git a/prepare/r-mitools/PKGBUILD b/prepare/r-mitools/PKGBUILD new file mode 100644 index 0000000000..618e9acb94 --- /dev/null +++ b/prepare/r-mitools/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mitools +_pkgver=2.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Multiple Imputation of Missing Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dbi +) +optdepends=( + r-foreign + r-rodbc +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mitools/lilac.py b/prepare/r-mitools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mitools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mitools/lilac.yaml b/prepare/r-mitools/lilac.yaml new file mode 100644 index 0000000000..7b760124c5 --- /dev/null +++ b/prepare/r-mitools/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dbi +update_on: +- regex: mitools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mitools diff --git a/prepare/r-mixomics/PKGBUILD b/prepare/r-mixomics/PKGBUILD new file mode 100644 index 0000000000..543b9bd91e --- /dev/null +++ b/prepare/r-mixomics/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mixOmics +_pkgver=6.18.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Omics Data Integration Project' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-corpcor + r-dplyr + r-ellipse + r-ggplot2 + r-ggrepel + r-gridextra + r-igraph + r-matrixstats + r-rarpack + r-rcolorbrewer + r-reshape2 + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-rgl + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mixomics/lilac.py b/prepare/r-mixomics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mixomics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mixomics/lilac.yaml b/prepare/r-mixomics/lilac.yaml new file mode 100644 index 0000000000..cb47e904ba --- /dev/null +++ b/prepare/r-mixomics/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-corpcor +- r-dplyr +- r-ellipse +- r-ggplot2 +- r-ggrepel +- r-gridextra +- r-igraph +- r-matrixstats +- r-rarpack +- r-rcolorbrewer +- r-reshape2 +- r-tidyr +update_on: +- regex: mixOmics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mixOmics diff --git a/prepare/r-mixsmsn/PKGBUILD b/prepare/r-mixsmsn/PKGBUILD new file mode 100644 index 0000000000..3bd6f3f33e --- /dev/null +++ b/prepare/r-mixsmsn/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mixsmsn +_pkgver=1.1-10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fitting Finite Mixture of Scale Mixture of Skew-Normal Distributions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mvtnorm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mixsmsn/lilac.py b/prepare/r-mixsmsn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mixsmsn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mixsmsn/lilac.yaml b/prepare/r-mixsmsn/lilac.yaml new file mode 100644 index 0000000000..2407d3a2ab --- /dev/null +++ b/prepare/r-mixsmsn/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mvtnorm +update_on: +- regex: mixsmsn_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mixsmsn diff --git a/prepare/r-mixsqp/PKGBUILD b/prepare/r-mixsqp/PKGBUILD new file mode 100644 index 0000000000..9667e7e235 --- /dev/null +++ b/prepare/r-mixsqp/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mixsqp +_pkgver=0.3-43 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sequential Quadratic Programming for Fast Maximum-Likelihood Estimation of Mixture Proportions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-irlba + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-knitr + r-rebayes + r-rmarkdown + r-rmosek + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mixsqp/lilac.py b/prepare/r-mixsqp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mixsqp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mixsqp/lilac.yaml b/prepare/r-mixsqp/lilac.yaml new file mode 100644 index 0000000000..f869883572 --- /dev/null +++ b/prepare/r-mixsqp/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-irlba +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: mixsqp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mixsqp diff --git a/prepare/r-mixtools/PKGBUILD b/prepare/r-mixtools/PKGBUILD new file mode 100644 index 0000000000..57ded0cc4f --- /dev/null +++ b/prepare/r-mixtools/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mixtools +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Analyzing Finite Mixture Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-kernlab + r-segmented +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mixtools/lilac.py b/prepare/r-mixtools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mixtools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mixtools/lilac.yaml b/prepare/r-mixtools/lilac.yaml new file mode 100644 index 0000000000..bd9907a08b --- /dev/null +++ b/prepare/r-mixtools/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-kernlab +- r-segmented +update_on: +- regex: mixtools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mixtools diff --git a/prepare/r-mkmisc/PKGBUILD b/prepare/r-mkmisc/PKGBUILD new file mode 100644 index 0000000000..1341afe47e --- /dev/null +++ b/prepare/r-mkmisc/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MKmisc +_pkgver=1.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Miscellaneous Functions from M. Kohl' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-ggplot2 + r-limma + r-rcolorbrewer + r-robustbase + r-scales +) +optdepends=( + r-amelia + r-doparallel + r-exactranktests + r-foreach + r-gplots + r-knitr + r-parallel + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mkmisc/lilac.py b/prepare/r-mkmisc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mkmisc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mkmisc/lilac.yaml b/prepare/r-mkmisc/lilac.yaml new file mode 100644 index 0000000000..9fa8107565 --- /dev/null +++ b/prepare/r-mkmisc/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-limma +- r-rcolorbrewer +- r-robustbase +- r-scales +update_on: +- regex: MKmisc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MKmisc diff --git a/prepare/r-mlapi/PKGBUILD b/prepare/r-mlapi/PKGBUILD new file mode 100644 index 0000000000..981f6699da --- /dev/null +++ b/prepare/r-mlapi/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mlapi +_pkgver=0.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Abstract Classes for Building 'scikit-learn' Like API" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-r6 +) +optdepends=( + r-knitr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mlapi/lilac.py b/prepare/r-mlapi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mlapi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mlapi/lilac.yaml b/prepare/r-mlapi/lilac.yaml new file mode 100644 index 0000000000..da3f39fabe --- /dev/null +++ b/prepare/r-mlapi/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-r6 +update_on: +- regex: mlapi_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mlapi diff --git a/prepare/r-mlbench/PKGBUILD b/prepare/r-mlbench/PKGBUILD new file mode 100644 index 0000000000..14b0f3114b --- /dev/null +++ b/prepare/r-mlbench/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mlbench +_pkgver=2.1-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Machine Learning Benchmark Problems' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-lattice +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mlbench/lilac.py b/prepare/r-mlbench/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mlbench/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mlbench/lilac.yaml b/prepare/r-mlbench/lilac.yaml new file mode 100644 index 0000000000..cf048045a2 --- /dev/null +++ b/prepare/r-mlbench/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: mlbench_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mlbench diff --git a/prepare/r-mlinterfaces/PKGBUILD b/prepare/r-mlinterfaces/PKGBUILD new file mode 100644 index 0000000000..6de2f8bf4c --- /dev/null +++ b/prepare/r-mlinterfaces/PKGBUILD @@ -0,0 +1,67 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MLInterfaces +_pkgver=1.74.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Uniform interfaces to R machine learning procedures for data in Bioconductor containers' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-annotate + r-biobase + r-biocgenerics + r-fpc + r-gbm + r-gdata + r-genefilter + r-ggvis + r-hwriter + r-magrittr + r-mlbench + r-pls + r-rcolorbrewer + r-rcpp + r-sfsmisc + r-shiny + r-threejs +) +optdepends=( + r-ada + r-all + r-caret + r-class + r-e1071 + r-golubesets + r-gpls + r-hgu95av2.db + r-hu6800.db + r-ipred + r-keggorthology + r-kernlab + r-klar + r-lattice + r-mboost + r-nnet + r-pamr + r-parallel + r-party + r-randomforest + r-som + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mlinterfaces/lilac.py b/prepare/r-mlinterfaces/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mlinterfaces/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mlinterfaces/lilac.yaml b/prepare/r-mlinterfaces/lilac.yaml new file mode 100644 index 0000000000..70d9cd3c47 --- /dev/null +++ b/prepare/r-mlinterfaces/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-biobase +- r-biocgenerics +- r-fpc +- r-gbm +- r-gdata +- r-genefilter +- r-ggvis +- r-hwriter +- r-magrittr +- r-mlbench +- r-pls +- r-rcolorbrewer +- r-rcpp +- r-sfsmisc +- r-shiny +- r-threejs +update_on: +- regex: MLInterfaces_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MLInterfaces diff --git a/prepare/r-mlmetrics/PKGBUILD b/prepare/r-mlmetrics/PKGBUILD new file mode 100644 index 0000000000..6ba98b35fd --- /dev/null +++ b/prepare/r-mlmetrics/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MLmetrics +_pkgver=1.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Machine Learning Evaluation Metrics' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rocr +) +optdepends=( + r-e1071 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mlmetrics/lilac.py b/prepare/r-mlmetrics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mlmetrics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mlmetrics/lilac.yaml b/prepare/r-mlmetrics/lilac.yaml new file mode 100644 index 0000000000..dc10bbd480 --- /dev/null +++ b/prepare/r-mlmetrics/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rocr +update_on: +- regex: MLmetrics_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MLmetrics diff --git a/prepare/r-mlp/PKGBUILD b/prepare/r-mlp/PKGBUILD new file mode 100644 index 0000000000..f599f77124 --- /dev/null +++ b/prepare/r-mlp/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MLP +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mean Log P Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-gplots +) +optdepends=( + r-annotate + r-go.db + r-gostats + r-graph + r-keggrest + r-limma + r-mouse4302.db + r-org.cf.eg.db + r-org.hs.eg.db + r-org.mm.eg.db + r-org.rn.eg.db + r-reactome.db + r-rgraphviz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mlp/lilac.py b/prepare/r-mlp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mlp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mlp/lilac.yaml b/prepare/r-mlp/lilac.yaml new file mode 100644 index 0000000000..06ab134c9e --- /dev/null +++ b/prepare/r-mlp/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-gplots +update_on: +- regex: MLP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MLP diff --git a/prepare/r-mlr/PKGBUILD b/prepare/r-mlr/PKGBUILD new file mode 100644 index 0000000000..9635de4460 --- /dev/null +++ b/prepare/r-mlr/PKGBUILD @@ -0,0 +1,150 @@ +# system requirements: gdal (optional), geos (optional), proj (optional),udunits (optional), gsl (optional), gmp (optional), glu(optional), jags (optional), mpfr (optional), openmpi(optional) +# Maintainer: Guoyi Zhang + +_pkgname=mlr +_pkgver=2.19.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Machine Learning in R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-backports + r-bbmisc + r-checkmate + r-data.table + r-ggplot2 + r-parallelmap + r-paramhelpers + r-stringi + r-xml +) +optdepends=( + r-ada + r-adabag + r-bartmachine + r-batchtools + r-bit64 + r-brnn + r-bst + r-c50 + r-care + r-caret + r-class + r-clue + r-cluster + r-clusterr + r-clustersim + r-cmaes + r-cowplot + r-crs + r-cubist + r-deepnet + r-dicekriging + r-discriminer + r-e1071 + r-earth + r-elasticnet + r-emoa + r-evtree + r-extratrees + r-fda.usc + r-fdboost + r-fnn + r-forecast + r-fpc + r-frbs + r-fselector + r-fselectorrcpp + r-gbm + r-gensa + r-ggpubr + r-glmnet + r-gpfit + r-h2o + r-hmisc + r-irace + r-kernlab + r-kknn + r-klar + r-knitr + r-lagp + r-liblinear + r-lintr + r-mass + r-mboost + r-mco + r-mda + r-memoise + r-mlbench + r-mldr + r-mlrmbo + r-mmpf + r-modeltools + r-mrmre + r-neuralnet + r-nnet + r-nodeharvest + r-numderiv + r-pamr + r-pander + r-party + r-pec + r-penalized + r-pls + r-pmcmrplus + r-praznik + r-randomforest + r-randomforestsrc + r-ranger + r-rappdirs + r-refund + r-rex + r-rferns + r-rgenoud + r-rknn + r-rmarkdown + r-rmpi + r-rocr + r-rotationforest + r-rpart + r-rrf + r-rrlda + r-rsm + r-rsnns + r-rucrdtw + r-rweka + r-sda + r-sf + r-smoof + r-snow + r-sparselda + r-stepplr + r-survauc + r-svglite + r-swarmsvm + r-testthat + r-tgp + r-th.data + r-tidyr + r-tsfeatures + r-vdiffr + r-wavelets + r-xgboost +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mlr/lilac.py b/prepare/r-mlr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mlr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mlr/lilac.yaml b/prepare/r-mlr/lilac.yaml new file mode 100644 index 0000000000..064bbeaf0f --- /dev/null +++ b/prepare/r-mlr/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-backports +- r-bbmisc +- r-checkmate +- r-data.table +- r-ggplot2 +- r-parallelmap +- r-paramhelpers +- r-stringi +- r-xml +update_on: +- regex: mlr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mlr diff --git a/prepare/r-mlseq/PKGBUILD b/prepare/r-mlseq/PKGBUILD new file mode 100644 index 0000000000..ec609da9bb --- /dev/null +++ b/prepare/r-mlseq/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MLSeq +_pkgver=2.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Machine Learning Interface for RNA-Seq Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-caret + r-deseq2 + r-edger + r-foreach + r-ggplot2 + r-limma + r-pamr + r-plyr + r-sseq + r-summarizedexperiment + r-testthat + r-venndiagram + r-xtable +) +optdepends=( + r-e1071 + r-kernlab + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mlseq/lilac.py b/prepare/r-mlseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mlseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mlseq/lilac.yaml b/prepare/r-mlseq/lilac.yaml new file mode 100644 index 0000000000..ac8a4a246e --- /dev/null +++ b/prepare/r-mlseq/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-caret +- r-deseq2 +- r-edger +- r-foreach +- r-ggplot2 +- r-limma +- r-pamr +- r-plyr +- r-sseq +- r-summarizedexperiment +- r-testthat +- r-venndiagram +- r-xtable +update_on: +- regex: MLSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MLSeq diff --git a/prepare/r-mltools/PKGBUILD b/prepare/r-mltools/PKGBUILD new file mode 100644 index 0000000000..dfd0410325 --- /dev/null +++ b/prepare/r-mltools/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mltools +_pkgver=0.3.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Machine Learning Tools' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-data.table +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mltools/lilac.py b/prepare/r-mltools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mltools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mltools/lilac.yaml b/prepare/r-mltools/lilac.yaml new file mode 100644 index 0000000000..0b3e3cc52c --- /dev/null +++ b/prepare/r-mltools/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +update_on: +- regex: mltools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mltools diff --git a/prepare/r-mmappr2/PKGBUILD b/prepare/r-mmappr2/PKGBUILD new file mode 100644 index 0000000000..840e1b3903 --- /dev/null +++ b/prepare/r-mmappr2/PKGBUILD @@ -0,0 +1,53 @@ +# system requirements: Ensembl VEP, Samtools +# Maintainer: Guoyi Zhang + +_pkgname=MMAPPR2 +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mutation Mapping Analysis Pipeline for Pooled RNA-Seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-data.table + r-dplyr + r-ensemblvep + r-genomeinfodb + r-genomicranges + r-gmapr + r-iranges + r-magrittr + r-rsamtools + r-s4vectors + r-stringr + r-tidyr + r-variantannotation + r-varianttools +) +optdepends=( + r-biocstyle + r-knitr + r-mmappr2data + r-mockery + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mmappr2/lilac.py b/prepare/r-mmappr2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mmappr2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mmappr2/lilac.yaml b/prepare/r-mmappr2/lilac.yaml new file mode 100644 index 0000000000..e49bd40e9f --- /dev/null +++ b/prepare/r-mmappr2/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-data.table +- r-dplyr +- r-ensemblvep +- r-genomeinfodb +- r-genomicranges +- r-gmapr +- r-iranges +- r-magrittr +- r-rsamtools +- r-s4vectors +- r-stringr +- r-tidyr +- r-variantannotation +- r-varianttools +update_on: +- regex: MMAPPR2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MMAPPR2 diff --git a/prepare/r-mmdiff2/PKGBUILD b/prepare/r-mmdiff2/PKGBUILD new file mode 100644 index 0000000000..1aebf9d7fc --- /dev/null +++ b/prepare/r-mmdiff2/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MMDiff2 +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Testing for ChIP-Seq data sets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biostrings + r-bsgenome + r-genomicranges + r-ggplot2 + r-locfit + r-rcolorbrewer + r-rsamtools + r-s4vectors + r-shiny +) +optdepends=( + r-biocstyle + r-bsgenome.mmusculus.ucsc.mm9 + r-knitr + r-mmdiffbamsubset + r-motifdb +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mmdiff2/lilac.py b/prepare/r-mmdiff2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mmdiff2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mmdiff2/lilac.yaml b/prepare/r-mmdiff2/lilac.yaml new file mode 100644 index 0000000000..da322a323d --- /dev/null +++ b/prepare/r-mmdiff2/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biostrings +- r-bsgenome +- r-genomicranges +- r-ggplot2 +- r-locfit +- r-rcolorbrewer +- r-rsamtools +- r-s4vectors +- r-shiny +update_on: +- regex: MMDiff2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MMDiff2 diff --git a/prepare/r-mmuphin/PKGBUILD b/prepare/r-mmuphin/PKGBUILD new file mode 100644 index 0000000000..cf321c8186 --- /dev/null +++ b/prepare/r-mmuphin/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MMUPHin +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-cowplot + r-dplyr + r-fpc + r-ggplot2 + r-igraph + r-maaslin2 + r-metafor + r-tidyr +) +optdepends=( + r-biocstyle + r-curatedmetagenomicdata + r-genefilter + r-knitr + r-magrittr + r-phyloseq + r-rmarkdown + r-testthat + r-vegan +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mmuphin/lilac.py b/prepare/r-mmuphin/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mmuphin/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mmuphin/lilac.yaml b/prepare/r-mmuphin/lilac.yaml new file mode 100644 index 0000000000..7ed5338e87 --- /dev/null +++ b/prepare/r-mmuphin/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cowplot +- r-dplyr +- r-fpc +- r-ggplot2 +- r-igraph +- r-maaslin2 +- r-metafor +- r-tidyr +update_on: +- regex: MMUPHin_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MMUPHin diff --git a/prepare/r-mnem/PKGBUILD b/prepare/r-mnem/PKGBUILD new file mode 100644 index 0000000000..7507922f19 --- /dev/null +++ b/prepare/r-mnem/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mnem +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mixture Nested Effects Models' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-e1071 + r-flexclust + r-ggplot2 + r-graph + r-linnorm + r-matrixstats + r-naturalsort + r-rcpp + r-rcppeigen + r-rgraphviz + r-snowfall + r-tsne + r-wesanderson +) +optdepends=( + r-biocgenerics + r-devtools + r-epinem + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mnem/lilac.py b/prepare/r-mnem/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mnem/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mnem/lilac.yaml b/prepare/r-mnem/lilac.yaml new file mode 100644 index 0000000000..90f4b1a86b --- /dev/null +++ b/prepare/r-mnem/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-e1071 +- r-flexclust +- r-ggplot2 +- r-graph +- r-linnorm +- r-matrixstats +- r-naturalsort +- r-rcpp +- r-rcppeigen +- r-rgraphviz +- r-snowfall +- r-tsne +- r-wesanderson +update_on: +- regex: mnem_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mnem diff --git a/prepare/r-mnormt/PKGBUILD b/prepare/r-mnormt/PKGBUILD new file mode 100644 index 0000000000..9c743f3855 --- /dev/null +++ b/prepare/r-mnormt/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mnormt +_pkgver=2.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The Multivariate Normal and t Distributions, and Their Truncated Versions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-tmvnsim +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mnormt/lilac.py b/prepare/r-mnormt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mnormt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mnormt/lilac.yaml b/prepare/r-mnormt/lilac.yaml new file mode 100644 index 0000000000..4bc475df41 --- /dev/null +++ b/prepare/r-mnormt/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-tmvnsim +update_on: +- regex: mnormt_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mnormt diff --git a/prepare/r-moanin/PKGBUILD b/prepare/r-moanin/PKGBUILD new file mode 100644 index 0000000000..d9f63461a1 --- /dev/null +++ b/prepare/r-moanin/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=moanin +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R Package for Time Course RNASeq Data Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-clusterr + r-edger + r-limma + r-matrixstats + r-nmi + r-reshape2 + r-s4vectors + r-summarizedexperiment + r-topgo + r-viridis + r-zoo +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-markdown + r-rmarkdown + r-testthat + r-timecoursedata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-moanin/lilac.py b/prepare/r-moanin/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-moanin/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-moanin/lilac.yaml b/prepare/r-moanin/lilac.yaml new file mode 100644 index 0000000000..62d41956de --- /dev/null +++ b/prepare/r-moanin/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clusterr +- r-edger +- r-limma +- r-matrixstats +- r-nmi +- r-reshape2 +- r-s4vectors +- r-summarizedexperiment +- r-topgo +- r-viridis +- r-zoo +update_on: +- regex: moanin_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/moanin diff --git a/prepare/r-moda/PKGBUILD b/prepare/r-moda/PKGBUILD new file mode 100644 index 0000000000..71212f67c0 --- /dev/null +++ b/prepare/r-moda/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MODA +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MODA: MOdule Differential Analysis for weighted gene co-expression network' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-amountain + r-dynamictreecut + r-igraph + r-rcolorbrewer + r-wgcna +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-moda/lilac.py b/prepare/r-moda/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-moda/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-moda/lilac.yaml b/prepare/r-moda/lilac.yaml new file mode 100644 index 0000000000..4c816cfd75 --- /dev/null +++ b/prepare/r-moda/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-amountain +- r-dynamictreecut +- r-igraph +- r-rcolorbrewer +- r-wgcna +update_on: +- regex: MODA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MODA diff --git a/prepare/r-modcon/PKGBUILD b/prepare/r-modcon/PKGBUILD new file mode 100644 index 0000000000..64a4add00e --- /dev/null +++ b/prepare/r-modcon/PKGBUILD @@ -0,0 +1,39 @@ +# system requirements: Perl +# Maintainer: Guoyi Zhang + +_pkgname=ModCon +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Modifying splice site usage by changing the mRNP code, while maintaining the genetic code' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table +) +optdepends=( + r-dplyr + r-knitr + r-rmarkdown + r-shiny + r-shinycssloaders + r-shinydashboard + r-shinyfiles + r-shinyjs + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-modcon/lilac.py b/prepare/r-modcon/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-modcon/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-modcon/lilac.yaml b/prepare/r-modcon/lilac.yaml new file mode 100644 index 0000000000..dd10c89759 --- /dev/null +++ b/prepare/r-modcon/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +update_on: +- regex: ModCon_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ModCon diff --git a/prepare/r-modeest/PKGBUILD b/prepare/r-modeest/PKGBUILD new file mode 100644 index 0000000000..de34f20414 --- /dev/null +++ b/prepare/r-modeest/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=modeest +_pkgver=2.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mode Estimation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-fbasics + r-stable + r-stabledist + r-statip +) +optdepends=( + r-evd + r-knitr + r-mvtnorm + r-testthat + r-vgam +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-modeest/lilac.py b/prepare/r-modeest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-modeest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-modeest/lilac.yaml b/prepare/r-modeest/lilac.yaml new file mode 100644 index 0000000000..c683d3adfe --- /dev/null +++ b/prepare/r-modeest/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fbasics +- r-stable +- r-stabledist +- r-statip +update_on: +- regex: modeest_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=modeest diff --git a/prepare/r-modelmetrics/PKGBUILD b/prepare/r-modelmetrics/PKGBUILD new file mode 100644 index 0000000000..91452b9e57 --- /dev/null +++ b/prepare/r-modelmetrics/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ModelMetrics +_pkgver=1.2.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Rapid Calculation of Model Metrics' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-rcpp +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-modelmetrics/lilac.py b/prepare/r-modelmetrics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-modelmetrics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-modelmetrics/lilac.yaml b/prepare/r-modelmetrics/lilac.yaml new file mode 100644 index 0000000000..23aa45cea1 --- /dev/null +++ b/prepare/r-modelmetrics/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-rcpp +update_on: +- regex: ModelMetrics_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ModelMetrics diff --git a/prepare/r-modelr/PKGBUILD b/prepare/r-modelr/PKGBUILD new file mode 100644 index 0000000000..e133874bde --- /dev/null +++ b/prepare/r-modelr/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=modelr +_pkgver=0.1.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Modelling Functions that Work with the Pipe' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-broom + r-magrittr + r-purrr + r-rlang + r-tibble + r-tidyr + r-tidyselect + r-vctrs +) +optdepends=( + r-compiler + r-covr + r-ggplot2 + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-modelr/lilac.py b/prepare/r-modelr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-modelr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-modelr/lilac.yaml b/prepare/r-modelr/lilac.yaml new file mode 100644 index 0000000000..028f9a056f --- /dev/null +++ b/prepare/r-modelr/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-broom +- r-magrittr +- r-purrr +- r-rlang +- r-tibble +- r-tidyr +- r-tidyselect +- r-vctrs +update_on: +- regex: modelr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=modelr diff --git a/prepare/r-modeltools/PKGBUILD b/prepare/r-modeltools/PKGBUILD new file mode 100644 index 0000000000..bdea0d3d51 --- /dev/null +++ b/prepare/r-modeltools/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=modeltools +_pkgver=0.2-23 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools and Classes for Statistical Models' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-modeltools/lilac.py b/prepare/r-modeltools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-modeltools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-modeltools/lilac.yaml b/prepare/r-modeltools/lilac.yaml new file mode 100644 index 0000000000..1936de5b60 --- /dev/null +++ b/prepare/r-modeltools/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: modeltools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=modeltools diff --git a/prepare/r-modstrings/PKGBUILD b/prepare/r-modstrings/PKGBUILD new file mode 100644 index 0000000000..02c070f609 --- /dev/null +++ b/prepare/r-modstrings/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Modstrings +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Working with modified nucleotide sequences' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biostrings + r-crayon + r-genomicranges + r-iranges + r-s4vectors + r-stringi + r-stringr + r-xvector +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat + r-usethis +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-modstrings/lilac.py b/prepare/r-modstrings/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-modstrings/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-modstrings/lilac.yaml b/prepare/r-modstrings/lilac.yaml new file mode 100644 index 0000000000..180b442e62 --- /dev/null +++ b/prepare/r-modstrings/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-crayon +- r-genomicranges +- r-iranges +- r-s4vectors +- r-stringi +- r-stringr +- r-xvector +update_on: +- regex: Modstrings_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Modstrings diff --git a/prepare/r-mofa2/PKGBUILD b/prepare/r-mofa2/PKGBUILD new file mode 100644 index 0000000000..3da38cf23d --- /dev/null +++ b/prepare/r-mofa2/PKGBUILD @@ -0,0 +1,65 @@ +# system requirements: Python (>=3), numpy, pandas, h5py, scipy, argparse,sklearn, mofapy2 +# Maintainer: Guoyi Zhang + +_pkgname=MOFA2 +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multi-Omics Factor Analysis v2' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-basilisk + r-corrplot + r-cowplot + r-delayedarray + r-dplyr + r-forcats + r-ggplot2 + r-ggrepel + r-hdf5array + r-magrittr + r-pheatmap + r-rcolorbrewer + r-reshape2 + r-reticulate + r-rhdf5 + r-rtsne + r-stringi + r-tidyr + r-uwot +) +optdepends=( + r-biocstyle + r-data.table + r-foreach + r-ggally + r-ggpubr + r-ggrastr + r-knitr + r-matrix + r-multiassayexperiment + r-mvtnorm + r-psych + r-rmarkdown + r-seurat + r-singlecellexperiment + r-summarizedexperiment + r-testthat + r-tidyverse +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mofa2/lilac.py b/prepare/r-mofa2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mofa2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mofa2/lilac.yaml b/prepare/r-mofa2/lilac.yaml new file mode 100644 index 0000000000..12c9630d41 --- /dev/null +++ b/prepare/r-mofa2/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-basilisk +- r-corrplot +- r-cowplot +- r-delayedarray +- r-dplyr +- r-forcats +- r-ggplot2 +- r-ggrepel +- r-hdf5array +- r-magrittr +- r-pheatmap +- r-rcolorbrewer +- r-reshape2 +- r-reticulate +- r-rhdf5 +- r-rtsne +- r-stringi +- r-tidyr +- r-uwot +update_on: +- regex: MOFA2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MOFA2 diff --git a/prepare/r-mogamun/PKGBUILD b/prepare/r-mogamun/PKGBUILD new file mode 100644 index 0000000000..d3b613dbf0 --- /dev/null +++ b/prepare/r-mogamun/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MOGAMUN +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-igraph + r-rcy3 + r-runit + r-stringr +) +optdepends=( + r-knitr + r-markdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mogamun/lilac.py b/prepare/r-mogamun/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mogamun/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mogamun/lilac.yaml b/prepare/r-mogamun/lilac.yaml new file mode 100644 index 0000000000..0a84e64974 --- /dev/null +++ b/prepare/r-mogamun/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-igraph +- r-rcy3 +- r-runit +- r-stringr +update_on: +- regex: MOGAMUN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MOGAMUN diff --git a/prepare/r-mogsa/PKGBUILD b/prepare/r-mogsa/PKGBUILD new file mode 100644 index 0000000000..e4657f3e35 --- /dev/null +++ b/prepare/r-mogsa/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mogsa +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multiple omics data integrative clustering and gene set analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-corpcor + r-genefilter + r-gplots + r-graphite + r-gseabase + r-svd +) +optdepends=( + r-biocstyle + r-knitr + r-org.hs.eg.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mogsa/lilac.py b/prepare/r-mogsa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mogsa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mogsa/lilac.yaml b/prepare/r-mogsa/lilac.yaml new file mode 100644 index 0000000000..1aa86b9dda --- /dev/null +++ b/prepare/r-mogsa/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-corpcor +- r-genefilter +- r-gplots +- r-graphite +- r-gseabase +- r-svd +update_on: +- regex: mogsa_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mogsa diff --git a/prepare/r-moma/PKGBUILD b/prepare/r-moma/PKGBUILD new file mode 100644 index 0000000000..ed2a74ca14 --- /dev/null +++ b/prepare/r-moma/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MOMA +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multi Omic Master Regulator Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-circlize + r-complexheatmap + r-dplyr + r-ggplot2 + r-magrittr + r-mkmisc + r-multiassayexperiment + r-qvalue + r-rcolorbrewer + r-readr + r-reshape2 + r-rlang + r-stringr + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat + r-viper +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-moma/lilac.py b/prepare/r-moma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-moma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-moma/lilac.yaml b/prepare/r-moma/lilac.yaml new file mode 100644 index 0000000000..d31ded84e4 --- /dev/null +++ b/prepare/r-moma/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circlize +- r-complexheatmap +- r-dplyr +- r-ggplot2 +- r-magrittr +- r-mkmisc +- r-multiassayexperiment +- r-qvalue +- r-rcolorbrewer +- r-readr +- r-reshape2 +- r-rlang +- r-stringr +- r-tibble +- r-tidyr +update_on: +- regex: MOMA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MOMA diff --git a/prepare/r-moments/PKGBUILD b/prepare/r-moments/PKGBUILD new file mode 100644 index 0000000000..aacd9f1c74 --- /dev/null +++ b/prepare/r-moments/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=moments +_pkgver=0.14 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Moments, cumulants, skewness, kurtosis and related tests' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-moments/lilac.py b/prepare/r-moments/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-moments/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-moments/lilac.yaml b/prepare/r-moments/lilac.yaml new file mode 100644 index 0000000000..e3454c1d1b --- /dev/null +++ b/prepare/r-moments/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: moments_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=moments diff --git a/prepare/r-monalisa/PKGBUILD b/prepare/r-monalisa/PKGBUILD new file mode 100644 index 0000000000..a28b55dd15 --- /dev/null +++ b/prepare/r-monalisa/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=monaLisa +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Binned Motif Enrichment Analysis and Visualization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-circlize + r-complexheatmap + r-genomeinfodb + r-genomicranges + r-glmnet + r-iranges + r-s4vectors + r-stabs + r-summarizedexperiment + r-tfbstools + r-vioplot + r-xvector +) +optdepends=( + r-biocstyle + r-bsgenome.mmusculus.ucsc.mm10 + r-gridextra + r-jaspar2020 + r-knitr + r-rmarkdown + r-testthat + r-txdb.mmusculus.ucsc.mm10.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-monalisa/lilac.py b/prepare/r-monalisa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-monalisa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-monalisa/lilac.yaml b/prepare/r-monalisa/lilac.yaml new file mode 100644 index 0000000000..f5153aa6ef --- /dev/null +++ b/prepare/r-monalisa/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-circlize +- r-complexheatmap +- r-genomeinfodb +- r-genomicranges +- r-glmnet +- r-iranges +- r-s4vectors +- r-stabs +- r-summarizedexperiment +- r-tfbstools +- r-vioplot +- r-xvector +update_on: +- regex: monaLisa_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/monaLisa diff --git a/prepare/r-monocle/PKGBUILD b/prepare/r-monocle/PKGBUILD new file mode 100644 index 0000000000..2ca1248d36 --- /dev/null +++ b/prepare/r-monocle/PKGBUILD @@ -0,0 +1,61 @@ +# Maintainer: Guoyi Zhang + +_pkgname=monocle +_pkgver=2.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-biocviews + r-combinat + r-ddrtree + r-densityclust + r-dplyr + r-fastica + r-ggplot2 + r-hsmmsinglecell + r-igraph + r-irlba + r-limma + r-matrixstats + r-pheatmap + r-plyr + r-proxy + r-qlcmatrix + r-rann + r-rcpp + r-reshape2 + r-rtsne + r-slam + r-stringr + r-tibble + r-vgam + r-viridis +) +optdepends=( + r-destiny + r-hmisc + r-knitr + r-scater + r-seurat + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-monocle/lilac.py b/prepare/r-monocle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-monocle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-monocle/lilac.yaml b/prepare/r-monocle/lilac.yaml new file mode 100644 index 0000000000..67c06c25ad --- /dev/null +++ b/prepare/r-monocle/lilac.yaml @@ -0,0 +1,36 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocviews +- r-combinat +- r-ddrtree +- r-densityclust +- r-dplyr +- r-fastica +- r-ggplot2 +- r-hsmmsinglecell +- r-igraph +- r-irlba +- r-limma +- r-matrixstats +- r-pheatmap +- r-plyr +- r-proxy +- r-qlcmatrix +- r-rann +- r-rcpp +- r-reshape2 +- r-rtsne +- r-slam +- r-stringr +- r-tibble +- r-vgam +- r-viridis +update_on: +- regex: monocle_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/monocle diff --git a/prepare/r-moonlightr/PKGBUILD b/prepare/r-moonlightr/PKGBUILD new file mode 100644 index 0000000000..cae8d3b3da --- /dev/null +++ b/prepare/r-moonlightr/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MoonlightR +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identify oncogenes and tumor suppressor genes from omics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-circlize + r-clusterprofiler + r-doparallel + r-dose + r-foreach + r-geoquery + r-gplots + r-hiver + r-limma + r-parmigene + r-randomforest + r-rcolorbrewer + r-rismed + r-summarizedexperiment + r-tcgabiolinks +) +optdepends=( + r-biocstyle + r-devtools + r-knitr + r-png + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-moonlightr/lilac.py b/prepare/r-moonlightr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-moonlightr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-moonlightr/lilac.yaml b/prepare/r-moonlightr/lilac.yaml new file mode 100644 index 0000000000..64e74d2733 --- /dev/null +++ b/prepare/r-moonlightr/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-circlize +- r-clusterprofiler +- r-doparallel +- r-dose +- r-foreach +- r-geoquery +- r-gplots +- r-hiver +- r-limma +- r-parmigene +- r-randomforest +- r-rcolorbrewer +- r-rismed +- r-summarizedexperiment +- r-tcgabiolinks +update_on: +- regex: MoonlightR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MoonlightR diff --git a/prepare/r-mosaiccore/PKGBUILD b/prepare/r-mosaiccore/PKGBUILD new file mode 100644 index 0000000000..3fe428e0db --- /dev/null +++ b/prepare/r-mosaiccore/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mosaicCore +_pkgver=0.9.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Common Utilities for Other MOSAIC-Family Packages' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-rlang + r-tidyr +) +optdepends=( + r-ggformula + r-mosaic + r-mosaicdata + r-nhanes + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mosaiccore/lilac.py b/prepare/r-mosaiccore/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mosaiccore/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mosaiccore/lilac.yaml b/prepare/r-mosaiccore/lilac.yaml new file mode 100644 index 0000000000..2ff67efc78 --- /dev/null +++ b/prepare/r-mosaiccore/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-rlang +- r-tidyr +update_on: +- regex: mosaicCore_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mosaicCore diff --git a/prepare/r-mosaics/PKGBUILD b/prepare/r-mosaics/PKGBUILD new file mode 100644 index 0000000000..805bf7ea4c --- /dev/null +++ b/prepare/r-mosaics/PKGBUILD @@ -0,0 +1,38 @@ +# system requirements: Perl +# Maintainer: Guoyi Zhang + +_pkgname=mosaics +_pkgver=2.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-rcpp + r-rsamtools + r-s4vectors +) +optdepends=( + r-mosaicsexample + r-parallel +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mosaics/lilac.py b/prepare/r-mosaics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mosaics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mosaics/lilac.yaml b/prepare/r-mosaics/lilac.yaml new file mode 100644 index 0000000000..9fb69e374c --- /dev/null +++ b/prepare/r-mosaics/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-rcpp +- r-rsamtools +- r-s4vectors +update_on: +- regex: mosaics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mosaics diff --git a/prepare/r-mosbi/PKGBUILD b/prepare/r-mosbi/PKGBUILD new file mode 100644 index 0000000000..60fef62669 --- /dev/null +++ b/prepare/r-mosbi/PKGBUILD @@ -0,0 +1,46 @@ +# system requirements: C++17, GNU make +# Maintainer: Guoyi Zhang + +_pkgname=mosbi +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Molecular Signature identification using Biclustering' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-akmbiclust + r-bh + r-biclust + r-fabia + r-igraph + r-isa2 + r-qubic + r-rcolorbrewer + r-rcpp + r-rcppparallel + r-xml2 +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runibic + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mosbi/lilac.py b/prepare/r-mosbi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mosbi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mosbi/lilac.yaml b/prepare/r-mosbi/lilac.yaml new file mode 100644 index 0000000000..537a413b26 --- /dev/null +++ b/prepare/r-mosbi/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-akmbiclust +- r-bh +- r-biclust +- r-fabia +- r-igraph +- r-isa2 +- r-qubic +- r-rcolorbrewer +- r-rcpp +- r-rcppparallel +- r-xml2 +update_on: +- regex: mosbi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mosbi diff --git a/prepare/r-mosim/PKGBUILD b/prepare/r-mosim/PKGBUILD new file mode 100644 index 0000000000..c9df685e3d --- /dev/null +++ b/prepare/r-mosim/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MOSim +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multi-Omics Simulation (MOSim)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-dplyr + r-ggplot2 + r-hiddenmarkov + r-iranges + r-lazyeval + r-matrixstats + r-purrr + r-rlang + r-s4vectors + r-scales + r-stringi + r-stringr + r-tibble + r-tidyr + r-zoo +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mosim/lilac.py b/prepare/r-mosim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mosim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mosim/lilac.yaml b/prepare/r-mosim/lilac.yaml new file mode 100644 index 0000000000..afd4d85a5c --- /dev/null +++ b/prepare/r-mosim/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-dplyr +- r-ggplot2 +- r-hiddenmarkov +- r-iranges +- r-lazyeval +- r-matrixstats +- r-purrr +- r-rlang +- r-s4vectors +- r-scales +- r-stringi +- r-stringr +- r-tibble +- r-tidyr +- r-zoo +update_on: +- regex: MOSim_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MOSim diff --git a/prepare/r-motifbreakr/PKGBUILD b/prepare/r-motifbreakr/PKGBUILD new file mode 100644 index 0000000000..662536fd9a --- /dev/null +++ b/prepare/r-motifbreakr/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=motifbreakR +_pkgver=2.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-grimport + r-gviz + r-iranges + r-matrixstats + r-motifdb + r-motifstack + r-rtracklayer + r-s4vectors + r-stringr + r-summarizedexperiment + r-tfmpvalue + r-variantannotation +) +optdepends=( + r-biocstyle + r-bsgenome.drerio.ucsc.danrer7 + r-bsgenome.hsapiens.ucsc.hg19 + r-knitr + r-rmarkdown + r-snplocs.hsapiens.dbsnp.20120608 + r-snplocs.hsapiens.dbsnp142.grch37 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-motifbreakr/lilac.py b/prepare/r-motifbreakr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-motifbreakr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-motifbreakr/lilac.yaml b/prepare/r-motifbreakr/lilac.yaml new file mode 100644 index 0000000000..10675ce500 --- /dev/null +++ b/prepare/r-motifbreakr/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-genomeinfodb +- r-genomicranges +- r-grimport +- r-gviz +- r-iranges +- r-matrixstats +- r-motifdb +- r-motifstack +- r-rtracklayer +- r-s4vectors +- r-stringr +- r-summarizedexperiment +- r-tfmpvalue +- r-variantannotation +update_on: +- regex: motifbreakR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/motifbreakR diff --git a/prepare/r-motifcounter/PKGBUILD b/prepare/r-motifcounter/PKGBUILD new file mode 100644 index 0000000000..59e6cd58f7 --- /dev/null +++ b/prepare/r-motifcounter/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=motifcounter +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R package for analysing TFBSs in DNA sequences' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings +) +optdepends=( + r-knitr + r-motifdb + r-prettydoc + r-rmarkdown + r-seqlogo + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-motifcounter/lilac.py b/prepare/r-motifcounter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-motifcounter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-motifcounter/lilac.yaml b/prepare/r-motifcounter/lilac.yaml new file mode 100644 index 0000000000..1c647099cd --- /dev/null +++ b/prepare/r-motifcounter/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +update_on: +- regex: motifcounter_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/motifcounter diff --git a/prepare/r-motifdb/PKGBUILD b/prepare/r-motifdb/PKGBUILD new file mode 100644 index 0000000000..928f493e58 --- /dev/null +++ b/prepare/r-motifdb/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MotifDb +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Annotated Collection of Protein-DNA Binding Sequence Motifs' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biostrings + r-genomicranges + r-iranges + r-rtracklayer + r-s4vectors + r-splitstackshape +) +optdepends=( + r-biocstyle + r-formatr + r-knitr + r-markdown + r-rmarkdown + r-runit + r-seqlogo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-motifdb/lilac.py b/prepare/r-motifdb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-motifdb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-motifdb/lilac.yaml b/prepare/r-motifdb/lilac.yaml new file mode 100644 index 0000000000..5cadb7d65c --- /dev/null +++ b/prepare/r-motifdb/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-genomicranges +- r-iranges +- r-rtracklayer +- r-s4vectors +- r-splitstackshape +update_on: +- regex: MotifDb_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MotifDb diff --git a/prepare/r-motifmatchr/PKGBUILD b/prepare/r-motifmatchr/PKGBUILD new file mode 100644 index 0000000000..37d5ad04bd --- /dev/null +++ b/prepare/r-motifmatchr/PKGBUILD @@ -0,0 +1,44 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=motifmatchr +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast Motif Matching in R' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-iranges + r-rcpp + r-rcpparmadillo + r-rsamtools + r-s4vectors + r-summarizedexperiment + r-tfbstools +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg19 + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-motifmatchr/lilac.py b/prepare/r-motifmatchr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-motifmatchr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-motifmatchr/lilac.yaml b/prepare/r-motifmatchr/lilac.yaml new file mode 100644 index 0000000000..a3ee5a3bed --- /dev/null +++ b/prepare/r-motifmatchr/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rcpp +- r-rcpparmadillo +- r-rsamtools +- r-s4vectors +- r-summarizedexperiment +- r-tfbstools +update_on: +- regex: motifmatchr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/motifmatchr diff --git a/prepare/r-motifstack/PKGBUILD b/prepare/r-motifstack/PKGBUILD new file mode 100644 index 0000000000..cccf802a3f --- /dev/null +++ b/prepare/r-motifstack/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=motifStack +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Plot stacked logos for single or multiple DNA, RNA and amino acid sequence' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ade4 + r-biostrings + r-ggplot2 + r-htmlwidgets + r-xml +) +optdepends=( + r-biocgenerics + r-biocstyle + r-grimport + r-grimport2 + r-knitr + r-motifdb + r-rcolorbrewer + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-motifstack/lilac.py b/prepare/r-motifstack/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-motifstack/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-motifstack/lilac.yaml b/prepare/r-motifstack/lilac.yaml new file mode 100644 index 0000000000..5ae0cbf9e5 --- /dev/null +++ b/prepare/r-motifstack/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ade4 +- r-biostrings +- r-ggplot2 +- r-htmlwidgets +- r-xml +update_on: +- regex: motifStack_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/motifStack diff --git a/prepare/r-mousefm/PKGBUILD b/prepare/r-mousefm/PKGBUILD new file mode 100644 index 0000000000..f0cb33aa38 --- /dev/null +++ b/prepare/r-mousefm/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MouseFM +_pkgver=1.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='In-silico methods for genetic finemapping in inbred mice' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-curl + r-data.table + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gtools + r-httr + r-iranges + r-jsonlite + r-reshape2 + r-rlist + r-scales + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mousefm/lilac.py b/prepare/r-mousefm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mousefm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mousefm/lilac.yaml b/prepare/r-mousefm/lilac.yaml new file mode 100644 index 0000000000..1f62a6ea62 --- /dev/null +++ b/prepare/r-mousefm/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-curl +- r-data.table +- r-dplyr +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-gtools +- r-httr +- r-iranges +- r-jsonlite +- r-reshape2 +- r-rlist +- r-scales +- r-tidyr +update_on: +- regex: MouseFM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MouseFM diff --git a/prepare/r-mpfe/PKGBUILD b/prepare/r-mpfe/PKGBUILD new file mode 100644 index 0000000000..e57bde9a8e --- /dev/null +++ b/prepare/r-mpfe/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MPFE +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mpfe/lilac.py b/prepare/r-mpfe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mpfe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mpfe/lilac.yaml b/prepare/r-mpfe/lilac.yaml new file mode 100644 index 0000000000..204c2b5d75 --- /dev/null +++ b/prepare/r-mpfe/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: MPFE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MPFE diff --git a/prepare/r-mpinet/PKGBUILD b/prepare/r-mpinet/PKGBUILD new file mode 100644 index 0000000000..81248f529d --- /dev/null +++ b/prepare/r-mpinet/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MPINet +_pkgver=1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The package can implement the network-based metabolite pathway identification of pathways.' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-biasedurn +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mpinet/lilac.py b/prepare/r-mpinet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mpinet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mpinet/lilac.yaml b/prepare/r-mpinet/lilac.yaml new file mode 100644 index 0000000000..2732b9623c --- /dev/null +++ b/prepare/r-mpinet/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biasedurn +update_on: +- regex: MPINet_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MPINet diff --git a/prepare/r-mpm/PKGBUILD b/prepare/r-mpm/PKGBUILD new file mode 100644 index 0000000000..e9c1cca28a --- /dev/null +++ b/prepare/r-mpm/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mpm +_pkgver=1.0-22 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multivariate Projection Methods' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mpm/lilac.py b/prepare/r-mpm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mpm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mpm/lilac.yaml b/prepare/r-mpm/lilac.yaml new file mode 100644 index 0000000000..d308b51d84 --- /dev/null +++ b/prepare/r-mpm/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: mpm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mpm diff --git a/prepare/r-mpmi/PKGBUILD b/prepare/r-mpmi/PKGBUILD new file mode 100644 index 0000000000..4c09a4f1a7 --- /dev/null +++ b/prepare/r-mpmi/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mpmi +_pkgver=0.43.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mixed-Pair Mutual Information Estimators' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mpmi/lilac.py b/prepare/r-mpmi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mpmi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mpmi/lilac.yaml b/prepare/r-mpmi/lilac.yaml new file mode 100644 index 0000000000..f167dd3d23 --- /dev/null +++ b/prepare/r-mpmi/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: mpmi_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mpmi diff --git a/prepare/r-mppa/PKGBUILD b/prepare/r-mppa/PKGBUILD new file mode 100644 index 0000000000..818389f8a7 --- /dev/null +++ b/prepare/r-mppa/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mppa +_pkgver=1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistics for analysing multiple simultaneous point processes on the real line' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mppa/lilac.py b/prepare/r-mppa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mppa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mppa/lilac.yaml b/prepare/r-mppa/lilac.yaml new file mode 100644 index 0000000000..80b5c20a22 --- /dev/null +++ b/prepare/r-mppa/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: mppa_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mppa diff --git a/prepare/r-mpra/PKGBUILD b/prepare/r-mpra/PKGBUILD new file mode 100644 index 0000000000..f5799d4005 --- /dev/null +++ b/prepare/r-mpra/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mpra +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analyze massively parallel reporter assays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-limma + r-s4vectors + r-scales + r-statmod + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mpra/lilac.py b/prepare/r-mpra/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mpra/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mpra/lilac.yaml b/prepare/r-mpra/lilac.yaml new file mode 100644 index 0000000000..a5728f4413 --- /dev/null +++ b/prepare/r-mpra/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-limma +- r-s4vectors +- r-scales +- r-statmod +- r-summarizedexperiment +update_on: +- regex: mpra_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mpra diff --git a/prepare/r-mpranalyze/PKGBUILD b/prepare/r-mpranalyze/PKGBUILD new file mode 100644 index 0000000000..1fd7621293 --- /dev/null +++ b/prepare/r-mpranalyze/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MPRAnalyze +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Analysis of MPRA data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-progress + r-summarizedexperiment +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mpranalyze/lilac.py b/prepare/r-mpranalyze/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mpranalyze/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mpranalyze/lilac.yaml b/prepare/r-mpranalyze/lilac.yaml new file mode 100644 index 0000000000..9a604ca54c --- /dev/null +++ b/prepare/r-mpranalyze/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-progress +- r-summarizedexperiment +update_on: +- regex: MPRAnalyze_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MPRAnalyze diff --git a/prepare/r-mqmetrics/PKGBUILD b/prepare/r-mqmetrics/PKGBUILD new file mode 100644 index 0000000000..88b0ca06bb --- /dev/null +++ b/prepare/r-mqmetrics/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MQmetrics +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quality Control of Protemics Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cowplot + r-dplyr + r-ggforce + r-gghalves + r-ggplot2 + r-ggpubr + r-ggrepel + r-ggridges + r-gridextra + r-gtable + r-knitr + r-magrittr + r-plyr + r-purrr + r-rcolorbrewer + r-readr + r-reshape2 + r-rlang + r-rmarkdown + r-scales + r-stringr + r-tidyr +) +optdepends=( + r-biocstyle + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mqmetrics/lilac.py b/prepare/r-mqmetrics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mqmetrics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mqmetrics/lilac.yaml b/prepare/r-mqmetrics/lilac.yaml new file mode 100644 index 0000000000..fb89de22ea --- /dev/null +++ b/prepare/r-mqmetrics/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cowplot +- r-dplyr +- r-ggforce +- r-gghalves +- r-ggplot2 +- r-ggpubr +- r-ggrepel +- r-ggridges +- r-gridextra +- r-gtable +- r-knitr +- r-magrittr +- r-plyr +- r-purrr +- r-rcolorbrewer +- r-readr +- r-reshape2 +- r-rlang +- r-rmarkdown +- r-scales +- r-stringr +- r-tidyr +update_on: +- regex: MQmetrics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MQmetrics diff --git a/prepare/r-mqtl/PKGBUILD b/prepare/r-mqtl/PKGBUILD new file mode 100644 index 0000000000..c9eb2e8cc5 --- /dev/null +++ b/prepare/r-mqtl/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mQTL +_pkgver=1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Metabolomic Quantitative Trait Locus Mapping' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-outliers + r-qtl +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mqtl/lilac.py b/prepare/r-mqtl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mqtl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mqtl/lilac.yaml b/prepare/r-mqtl/lilac.yaml new file mode 100644 index 0000000000..822b9a7ced --- /dev/null +++ b/prepare/r-mqtl/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-outliers +- r-qtl +update_on: +- regex: mQTL_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mQTL diff --git a/prepare/r-mrfdepth/PKGBUILD b/prepare/r-mrfdepth/PKGBUILD new file mode 100644 index 0000000000..4bf0002b00 --- /dev/null +++ b/prepare/r-mrfdepth/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mrfDepth +_pkgver=1.0.13 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Depth Measures in Multivariate, Regression and Functional Settings' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-geometry + r-ggplot2 + r-matrixstats + r-rcpp + r-rcpparmadillo + r-rcppeigen + r-reshape2 +) +optdepends=( + r-robustbase +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mrfdepth/lilac.py b/prepare/r-mrfdepth/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mrfdepth/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mrfdepth/lilac.yaml b/prepare/r-mrfdepth/lilac.yaml new file mode 100644 index 0000000000..c34e65139a --- /dev/null +++ b/prepare/r-mrfdepth/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-geometry +- r-ggplot2 +- r-matrixstats +- r-rcpp +- r-rcpparmadillo +- r-rcppeigen +- r-reshape2 +update_on: +- regex: mrfDepth_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mrfDepth diff --git a/prepare/r-mrmre/PKGBUILD b/prepare/r-mrmre/PKGBUILD new file mode 100644 index 0000000000..f78bb5f1a2 --- /dev/null +++ b/prepare/r-mrmre/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mRMRe +_pkgver=2.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Parallelized Minimum Redundancy, Maximum Relevance (mRMR)' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-igraph +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mrmre/lilac.py b/prepare/r-mrmre/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mrmre/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mrmre/lilac.yaml b/prepare/r-mrmre/lilac.yaml new file mode 100644 index 0000000000..3fdcca1d57 --- /dev/null +++ b/prepare/r-mrmre/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +update_on: +- regex: mRMRe_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mRMRe diff --git a/prepare/r-msa/PKGBUILD b/prepare/r-msa/PKGBUILD new file mode 100644 index 0000000000..c60a31a4dd --- /dev/null +++ b/prepare/r-msa/PKGBUILD @@ -0,0 +1,39 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=msa +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multiple Sequence Alignment' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-iranges + r-rcpp + r-s4vectors +) +optdepends=( + r-ape + r-biobase + r-knitr + r-phangorn + r-seqinr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msa/lilac.py b/prepare/r-msa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msa/lilac.yaml b/prepare/r-msa/lilac.yaml new file mode 100644 index 0000000000..1216d1a83f --- /dev/null +++ b/prepare/r-msa/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-iranges +- r-rcpp +- r-s4vectors +update_on: +- regex: msa_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/msa diff --git a/prepare/r-msbackendmassbank/PKGBUILD b/prepare/r-msbackendmassbank/PKGBUILD new file mode 100644 index 0000000000..15c229f4fe --- /dev/null +++ b/prepare/r-msbackendmassbank/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MsBackendMassbank +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mass Spectrometry Data Backend for MassBank record Files' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-dbi + r-iranges + r-mscoreutils + r-protgenerics + r-s4vectors + r-spectra +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-roxygen2 + r-rsqlite + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msbackendmassbank/lilac.py b/prepare/r-msbackendmassbank/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msbackendmassbank/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msbackendmassbank/lilac.yaml b/prepare/r-msbackendmassbank/lilac.yaml new file mode 100644 index 0000000000..a61f6b32be --- /dev/null +++ b/prepare/r-msbackendmassbank/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-dbi +- r-iranges +- r-mscoreutils +- r-protgenerics +- r-s4vectors +- r-spectra +update_on: +- regex: MsBackendMassbank_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MsBackendMassbank diff --git a/prepare/r-msbackendmgf/PKGBUILD b/prepare/r-msbackendmgf/PKGBUILD new file mode 100644 index 0000000000..fb3ab26461 --- /dev/null +++ b/prepare/r-msbackendmgf/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MsBackendMgf +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-iranges + r-mscoreutils + r-s4vectors + r-spectra +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msbackendmgf/lilac.py b/prepare/r-msbackendmgf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msbackendmgf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msbackendmgf/lilac.yaml b/prepare/r-msbackendmgf/lilac.yaml new file mode 100644 index 0000000000..8a2b43c5a0 --- /dev/null +++ b/prepare/r-msbackendmgf/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-iranges +- r-mscoreutils +- r-s4vectors +- r-spectra +update_on: +- regex: MsBackendMgf_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MsBackendMgf diff --git a/prepare/r-msbackendrawfilereader/PKGBUILD b/prepare/r-msbackendrawfilereader/PKGBUILD new file mode 100644 index 0000000000..b2443210a7 --- /dev/null +++ b/prepare/r-msbackendrawfilereader/PKGBUILD @@ -0,0 +1,44 @@ +# system requirements: mono-runtime 4.x or higher (including System.Datalibrary) on Linux/macOS, .Net Framework (>= 4.5.1) on MicrosoftWindows. +# Maintainer: Guoyi Zhang + +_pkgname=MsBackendRawFileReader +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-iranges + r-mscoreutils + r-rawrr + r-s4vectors + r-spectra +) +optdepends=( + r-biocstyle + r-experimenthub + r-knitr + r-lattice + r-mzr + r-protviz + r-rmarkdown + r-tartare + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msbackendrawfilereader/lilac.py b/prepare/r-msbackendrawfilereader/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msbackendrawfilereader/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msbackendrawfilereader/lilac.yaml b/prepare/r-msbackendrawfilereader/lilac.yaml new file mode 100644 index 0000000000..12d9623a71 --- /dev/null +++ b/prepare/r-msbackendrawfilereader/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-iranges +- r-mscoreutils +- r-rawrr +- r-s4vectors +- r-spectra +update_on: +- regex: MsBackendRawFileReader_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MsBackendRawFileReader diff --git a/prepare/r-mscoreutils/PKGBUILD b/prepare/r-mscoreutils/PKGBUILD new file mode 100644 index 0000000000..76c4333ad8 --- /dev/null +++ b/prepare/r-mscoreutils/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MsCoreUtils +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Core Utils for Mass Spectrometry Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-clue + r-rcpp + r-s4vectors +) +optdepends=( + r-biocstyle + r-impute + r-imputelcmd + r-knitr + r-norm + r-pcamethods + r-preprocesscore + r-rmarkdown + r-roxygen2 + r-testthat + r-vsn +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mscoreutils/lilac.py b/prepare/r-mscoreutils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mscoreutils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mscoreutils/lilac.yaml b/prepare/r-mscoreutils/lilac.yaml new file mode 100644 index 0000000000..3c208e0d47 --- /dev/null +++ b/prepare/r-mscoreutils/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clue +- r-rcpp +- r-s4vectors +update_on: +- regex: MsCoreUtils_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MsCoreUtils diff --git a/prepare/r-msfeatures/PKGBUILD b/prepare/r-msfeatures/PKGBUILD new file mode 100644 index 0000000000..fc2b2e6f4a --- /dev/null +++ b/prepare/r-msfeatures/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MsFeatures +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functionality for Mass Spectrometry Features' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-mscoreutils + r-protgenerics + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-pheatmap + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msfeatures/lilac.py b/prepare/r-msfeatures/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msfeatures/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msfeatures/lilac.yaml b/prepare/r-msfeatures/lilac.yaml new file mode 100644 index 0000000000..de462dc32c --- /dev/null +++ b/prepare/r-msfeatures/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mscoreutils +- r-protgenerics +- r-summarizedexperiment +update_on: +- regex: MsFeatures_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MsFeatures diff --git a/prepare/r-msgbsr/PKGBUILD b/prepare/r-msgbsr/PKGBUILD new file mode 100644 index 0000000000..799f5ccf9b --- /dev/null +++ b/prepare/r-msgbsr/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=msgbsR +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bsgenome + r-easyrnaseq + r-edger + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggbio + r-ggplot2 + r-iranges + r-plyr + r-r.utils + r-rsamtools + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-bsgenome.rnorvegicus.ucsc.rn6 + r-roxygen2 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msgbsr/lilac.py b/prepare/r-msgbsr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msgbsr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msgbsr/lilac.yaml b/prepare/r-msgbsr/lilac.yaml new file mode 100644 index 0000000000..ea4de65881 --- /dev/null +++ b/prepare/r-msgbsr/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +- r-easyrnaseq +- r-edger +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggbio +- r-ggplot2 +- r-iranges +- r-plyr +- r-r.utils +- r-rsamtools +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: msgbsR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/msgbsR diff --git a/prepare/r-msgfgui/PKGBUILD b/prepare/r-msgfgui/PKGBUILD new file mode 100644 index 0000000000..36f83d7c40 --- /dev/null +++ b/prepare/r-msgfgui/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MSGFgui +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A shiny GUI for MSGFplus' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-msgfplus + r-mzid + r-mzr + r-shiny + r-shinyfiles + r-xlsx +) +optdepends=( + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msgfgui/lilac.py b/prepare/r-msgfgui/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msgfgui/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msgfgui/lilac.yaml b/prepare/r-msgfgui/lilac.yaml new file mode 100644 index 0000000000..e32d5c8385 --- /dev/null +++ b/prepare/r-msgfgui/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-msgfplus +- r-mzid +- r-mzr +- r-shiny +- r-shinyfiles +- r-xlsx +update_on: +- regex: MSGFgui_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MSGFgui diff --git a/prepare/r-msgfplus/PKGBUILD b/prepare/r-msgfplus/PKGBUILD new file mode 100644 index 0000000000..0e7ac86f38 --- /dev/null +++ b/prepare/r-msgfplus/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: Java (>= 1.7) +# Maintainer: Guoyi Zhang + +_pkgname=MSGFplus +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An interface between R and MS-GF+' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-mzid + r-protgenerics +) +optdepends=( + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msgfplus/lilac.py b/prepare/r-msgfplus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msgfplus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msgfplus/lilac.yaml b/prepare/r-msgfplus/lilac.yaml new file mode 100644 index 0000000000..8ec6521041 --- /dev/null +++ b/prepare/r-msgfplus/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mzid +- r-protgenerics +update_on: +- regex: MSGFplus_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MSGFplus diff --git a/prepare/r-msgps/PKGBUILD b/prepare/r-msgps/PKGBUILD new file mode 100644 index 0000000000..05ffa4f163 --- /dev/null +++ b/prepare/r-msgps/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=msgps +_pkgver=1.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Degrees of Freedom of Elastic Net, Adaptive Lasso and Generalized Elastic Net' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msgps/lilac.py b/prepare/r-msgps/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msgps/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msgps/lilac.yaml b/prepare/r-msgps/lilac.yaml new file mode 100644 index 0000000000..a45fbc2b7d --- /dev/null +++ b/prepare/r-msgps/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: msgps_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=msgps diff --git a/prepare/r-msigdb/PKGBUILD b/prepare/r-msigdb/PKGBUILD new file mode 100644 index 0000000000..e257394ecd --- /dev/null +++ b/prepare/r-msigdb/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=msigdb +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An ExperimentHub Package for the Molecular Signatures Database (MSigDB)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CCPL:by-nc-sa') +depends=( + r + r-annotationdbi + r-annotationhub + r-experimenthub + r-gseabase + r-org.hs.eg.db + r-org.mm.eg.db +) +optdepends=( + r-biocfilecache + r-biocstyle + r-go.db + r-knitr + r-limma + r-prettydoc + r-rmarkdown + r-singscore + r-stringr + r-testthat + r-visse +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msigdb/lilac.py b/prepare/r-msigdb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msigdb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msigdb/lilac.yaml b/prepare/r-msigdb/lilac.yaml new file mode 100644 index 0000000000..4023f9c183 --- /dev/null +++ b/prepare/r-msigdb/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-experimenthub +- r-gseabase +- r-org.hs.eg.db +- r-org.mm.eg.db +update_on: +- regex: msigdb_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/msigdb diff --git a/prepare/r-msigdbr/PKGBUILD b/prepare/r-msigdbr/PKGBUILD new file mode 100644 index 0000000000..0859296bdc --- /dev/null +++ b/prepare/r-msigdbr/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=msigdbr +_pkgver=7.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-babelgene + r-dplyr + r-magrittr + r-rlang + r-tibble + r-tidyselect +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msigdbr/lilac.py b/prepare/r-msigdbr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msigdbr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msigdbr/lilac.yaml b/prepare/r-msigdbr/lilac.yaml new file mode 100644 index 0000000000..39a30b76f7 --- /dev/null +++ b/prepare/r-msigdbr/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-babelgene +- r-dplyr +- r-magrittr +- r-rlang +- r-tibble +- r-tidyselect +update_on: +- regex: msigdbr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=msigdbr diff --git a/prepare/r-msimpute/PKGBUILD b/prepare/r-msimpute/PKGBUILD new file mode 100644 index 0000000000..a8a8f91331 --- /dev/null +++ b/prepare/r-msimpute/PKGBUILD @@ -0,0 +1,45 @@ +# system requirements: python +# Maintainer: Guoyi Zhang + +_pkgname=msImpute +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Imputation of label-free mass spectrometry peptides' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-dplyr + r-fnn + r-limma + r-matrixstats + r-mvtnorm + r-pdist + r-reticulate + r-scran + r-softimpute + r-tidyr +) +optdepends=( + r-biocstyle + r-complexheatmap + r-imputelcmd + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msimpute/lilac.py b/prepare/r-msimpute/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msimpute/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msimpute/lilac.yaml b/prepare/r-msimpute/lilac.yaml new file mode 100644 index 0000000000..c579999239 --- /dev/null +++ b/prepare/r-msimpute/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-dplyr +- r-fnn +- r-limma +- r-matrixstats +- r-mvtnorm +- r-pdist +- r-reticulate +- r-scran +- r-softimpute +- r-tidyr +update_on: +- regex: msImpute_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/msImpute diff --git a/prepare/r-msm/PKGBUILD b/prepare/r-msm/PKGBUILD new file mode 100644 index 0000000000..d538d170dc --- /dev/null +++ b/prepare/r-msm/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=msm +_pkgver=1.6.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multi-State Markov and Hidden Markov Models in Continuous Time' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-expm + r-mvtnorm +) +optdepends=( + r-doparallel + r-flexsurv + r-foreach + r-minqa + r-mstate + r-numderiv + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msm/lilac.py b/prepare/r-msm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msm/lilac.yaml b/prepare/r-msm/lilac.yaml new file mode 100644 index 0000000000..c12e5f8482 --- /dev/null +++ b/prepare/r-msm/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-expm +- r-mvtnorm +update_on: +- regex: msm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=msm diff --git a/prepare/r-msmseda/PKGBUILD b/prepare/r-msmseda/PKGBUILD new file mode 100644 index 0000000000..203597616d --- /dev/null +++ b/prepare/r-msmseda/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=msmsEDA +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Exploratory Data Analysis of LC-MS/MS data by spectral counts' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-gplots + r-msnbase + r-rcolorbrewer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msmseda/lilac.py b/prepare/r-msmseda/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msmseda/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msmseda/lilac.yaml b/prepare/r-msmseda/lilac.yaml new file mode 100644 index 0000000000..c3adc43f62 --- /dev/null +++ b/prepare/r-msmseda/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gplots +- r-msnbase +- r-rcolorbrewer +update_on: +- regex: msmsEDA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/msmsEDA diff --git a/prepare/r-msmstests/PKGBUILD b/prepare/r-msmstests/PKGBUILD new file mode 100644 index 0000000000..15f26c14b0 --- /dev/null +++ b/prepare/r-msmstests/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=msmsTests +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='LC-MS/MS Differential Expression Tests' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-edger + r-msmseda + r-msnbase + r-qvalue +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msmstests/lilac.py b/prepare/r-msmstests/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msmstests/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msmstests/lilac.yaml b/prepare/r-msmstests/lilac.yaml new file mode 100644 index 0000000000..71c7dd549a --- /dev/null +++ b/prepare/r-msmstests/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-edger +- r-msmseda +- r-msnbase +- r-qvalue +update_on: +- regex: msmsTests_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/msmsTests diff --git a/prepare/r-msnbase/PKGBUILD b/prepare/r-msnbase/PKGBUILD new file mode 100644 index 0000000000..989fe17bdd --- /dev/null +++ b/prepare/r-msnbase/PKGBUILD @@ -0,0 +1,71 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MSnbase +_pkgver=2.20.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Base Functions and Classes for Mass Spectrometry and Proteomics' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-affy + r-biobase + r-biocgenerics + r-biocparallel + r-digest + r-ggplot2 + r-impute + r-iranges + r-maldiquant + r-mscoreutils + r-mzid + r-mzr + r-pcamethods + r-plyr + r-protgenerics + r-rcpp + r-s4vectors + r-scales + r-vsn + r-xml +) +optdepends=( + r-annotationhub + r-biocstyle + r-gplots + r-gridextra + r-imputelcmd + r-knitr + r-magrittr + r-microbenchmark + r-msdata + r-norm + r-proloc + r-prolocdata + r-pryr + r-rdisop + r-rgl + r-rmarkdown + r-rols + r-roxygen2 + r-rpx + r-shiny + r-summarizedexperiment + r-testthat + r-zoo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msnbase/lilac.py b/prepare/r-msnbase/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msnbase/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msnbase/lilac.yaml b/prepare/r-msnbase/lilac.yaml new file mode 100644 index 0000000000..a4727ce0e0 --- /dev/null +++ b/prepare/r-msnbase/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-digest +- r-ggplot2 +- r-impute +- r-iranges +- r-maldiquant +- r-mscoreutils +- r-mzid +- r-mzr +- r-pcamethods +- r-plyr +- r-protgenerics +- r-rcpp +- r-s4vectors +- r-scales +- r-vsn +- r-xml +update_on: +- regex: MSnbase_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MSnbase diff --git a/prepare/r-msnid/PKGBUILD b/prepare/r-msnid/PKGBUILD new file mode 100644 index 0000000000..608a429ff2 --- /dev/null +++ b/prepare/r-msnid/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MSnID +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-annotationhub + r-biobase + r-biocgenerics + r-biocstyle + r-biostrings + r-data.table + r-doparallel + r-dplyr + r-foreach + r-ggplot2 + r-iterators + r-msmstests + r-msnbase + r-mzid + r-mzr + r-protgenerics + r-purrr + r-r.cache + r-rcpp + r-reshape2 + r-rlang + r-runit + r-stringr + r-tibble + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msnid/lilac.py b/prepare/r-msnid/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msnid/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msnid/lilac.yaml b/prepare/r-msnid/lilac.yaml new file mode 100644 index 0000000000..73ffbfc091 --- /dev/null +++ b/prepare/r-msnid/lilac.yaml @@ -0,0 +1,35 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-biobase +- r-biocgenerics +- r-biocstyle +- r-biostrings +- r-data.table +- r-doparallel +- r-dplyr +- r-foreach +- r-ggplot2 +- r-iterators +- r-msmstests +- r-msnbase +- r-mzid +- r-mzr +- r-protgenerics +- r-purrr +- r-r.cache +- r-rcpp +- r-reshape2 +- r-rlang +- r-runit +- r-stringr +- r-tibble +- r-xtable +update_on: +- regex: MSnID_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MSnID diff --git a/prepare/r-msprep/PKGBUILD b/prepare/r-msprep/PKGBUILD new file mode 100644 index 0000000000..54380a6a61 --- /dev/null +++ b/prepare/r-msprep/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MSPrep +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-crmn + r-ddpcr + r-dplyr + r-magrittr + r-missforest + r-pcamethods + r-preprocesscore + r-rlang + r-s4vectors + r-stringr + r-summarizedexperiment + r-sva + r-tibble + r-tidyr + r-vim +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msprep/lilac.py b/prepare/r-msprep/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msprep/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msprep/lilac.yaml b/prepare/r-msprep/lilac.yaml new file mode 100644 index 0000000000..12adab8bad --- /dev/null +++ b/prepare/r-msprep/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-crmn +- r-ddpcr +- r-dplyr +- r-magrittr +- r-missforest +- r-pcamethods +- r-preprocesscore +- r-rlang +- r-s4vectors +- r-stringr +- r-summarizedexperiment +- r-sva +- r-tibble +- r-tidyr +- r-vim +update_on: +- regex: MSPrep_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MSPrep diff --git a/prepare/r-mspurity/PKGBUILD b/prepare/r-mspurity/PKGBUILD new file mode 100644 index 0000000000..2432a6d7d6 --- /dev/null +++ b/prepare/r-mspurity/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=msPurity +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dbi + r-dbplyr + r-dosnow + r-dplyr + r-fastcluster + r-foreach + r-ggplot2 + r-jsonlite + r-magrittr + r-mzr + r-plyr + r-rcpp + r-reshape2 + r-rsqlite + r-stringr + r-uuid +) +optdepends=( + r-biocstyle + r-camera + r-knitr + r-msnbase + r-mspuritydata + r-rmarkdown + r-rmysql + r-rpostgres + r-testthat + r-xcms +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mspurity/lilac.py b/prepare/r-mspurity/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mspurity/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mspurity/lilac.yaml b/prepare/r-mspurity/lilac.yaml new file mode 100644 index 0000000000..b7157dd07f --- /dev/null +++ b/prepare/r-mspurity/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dbi +- r-dbplyr +- r-dosnow +- r-dplyr +- r-fastcluster +- r-foreach +- r-ggplot2 +- r-jsonlite +- r-magrittr +- r-mzr +- r-plyr +- r-rcpp +- r-reshape2 +- r-rsqlite +- r-stringr +- r-uuid +update_on: +- regex: msPurity_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/msPurity diff --git a/prepare/r-msqc/PKGBUILD b/prepare/r-msqc/PKGBUILD new file mode 100644 index 0000000000..d18ab0f009 --- /dev/null +++ b/prepare/r-msqc/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MSQC +_pkgver=1.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multivariate Statistical Quality Control' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rgl +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msqc/lilac.py b/prepare/r-msqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msqc/lilac.yaml b/prepare/r-msqc/lilac.yaml new file mode 100644 index 0000000000..a1013055ad --- /dev/null +++ b/prepare/r-msqc/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rgl +update_on: +- regex: MSQC_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MSQC diff --git a/prepare/r-msqrob2/PKGBUILD b/prepare/r-msqrob2/PKGBUILD new file mode 100644 index 0000000000..7fdfcba1cc --- /dev/null +++ b/prepare/r-msqrob2/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=msqrob2 +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Robust statistical inference for quantitative LC-MS proteomics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-limma + r-lme4 + r-purrr + r-qfeatures + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-gridextra + r-knitr + r-matrixstats + r-mscoreutils + r-msdata + r-msnbase + r-multcomp + r-plotly + r-refmanager + r-rmarkdown + r-sessioninfo + r-testthat + r-tidyverse +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msqrob2/lilac.py b/prepare/r-msqrob2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msqrob2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msqrob2/lilac.yaml b/prepare/r-msqrob2/lilac.yaml new file mode 100644 index 0000000000..8793925e65 --- /dev/null +++ b/prepare/r-msqrob2/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-limma +- r-lme4 +- r-purrr +- r-qfeatures +- r-summarizedexperiment +update_on: +- regex: msqrob2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/msqrob2 diff --git a/prepare/r-msstats/PKGBUILD b/prepare/r-msstats/PKGBUILD new file mode 100644 index 0000000000..434904c299 --- /dev/null +++ b/prepare/r-msstats/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MSstats +_pkgver=4.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-checkmate + r-data.table + r-ggplot2 + r-ggrepel + r-gplots + r-limma + r-lme4 + r-marray + r-msstatsconvert + r-preprocesscore + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-markdown + r-msstatsbiodata + r-rmarkdown + r-tinytest +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msstats/lilac.py b/prepare/r-msstats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msstats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msstats/lilac.yaml b/prepare/r-msstats/lilac.yaml new file mode 100644 index 0000000000..fbb2c0a5ff --- /dev/null +++ b/prepare/r-msstats/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-checkmate +- r-data.table +- r-ggplot2 +- r-ggrepel +- r-gplots +- r-limma +- r-lme4 +- r-marray +- r-msstatsconvert +- r-preprocesscore +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: MSstats_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MSstats diff --git a/prepare/r-msstatsconvert/PKGBUILD b/prepare/r-msstatsconvert/PKGBUILD new file mode 100644 index 0000000000..10f8a197ed --- /dev/null +++ b/prepare/r-msstatsconvert/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MSstatsConvert +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-checkmate + r-data.table + r-log4r + r-stringi +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-tinytest +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msstatsconvert/lilac.py b/prepare/r-msstatsconvert/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msstatsconvert/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msstatsconvert/lilac.yaml b/prepare/r-msstatsconvert/lilac.yaml new file mode 100644 index 0000000000..9c84257929 --- /dev/null +++ b/prepare/r-msstatsconvert/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-checkmate +- r-data.table +- r-log4r +- r-stringi +update_on: +- regex: MSstatsConvert_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MSstatsConvert diff --git a/prepare/r-msstatslip/PKGBUILD b/prepare/r-msstatslip/PKGBUILD new file mode 100644 index 0000000000..bfde08ef0c --- /dev/null +++ b/prepare/r-msstatslip/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MSstatsLiP +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-checkmate + r-data.table + r-dplyr + r-factoextra + r-ggplot2 + r-ggpubr + r-gridextra + r-msstats + r-msstatsconvert + r-msstatsptm + r-purrr + r-rcpp + r-scales + r-stringr + r-tibble + r-tidyr + r-tidyverse +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-rmarkdown + r-tinytest +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msstatslip/lilac.py b/prepare/r-msstatslip/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msstatslip/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msstatslip/lilac.yaml b/prepare/r-msstatslip/lilac.yaml new file mode 100644 index 0000000000..ed06e5e273 --- /dev/null +++ b/prepare/r-msstatslip/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-checkmate +- r-data.table +- r-dplyr +- r-factoextra +- r-ggplot2 +- r-ggpubr +- r-gridextra +- r-msstats +- r-msstatsconvert +- r-msstatsptm +- r-purrr +- r-rcpp +- r-scales +- r-stringr +- r-tibble +- r-tidyr +- r-tidyverse +update_on: +- regex: MSstatsLiP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MSstatsLiP diff --git a/prepare/r-msstatslobd/PKGBUILD b/prepare/r-msstatslobd/PKGBUILD new file mode 100644 index 0000000000..ba8316f6ae --- /dev/null +++ b/prepare/r-msstatslobd/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MSstatsLOBD +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ggplot2 + r-minpack.lm + r-rcpp +) +optdepends=( + r-biocstyle + r-covr + r-dplyr + r-knitr + r-rmarkdown + r-tinytest +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msstatslobd/lilac.py b/prepare/r-msstatslobd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msstatslobd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msstatslobd/lilac.yaml b/prepare/r-msstatslobd/lilac.yaml new file mode 100644 index 0000000000..631b43c5cd --- /dev/null +++ b/prepare/r-msstatslobd/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-minpack.lm +- r-rcpp +update_on: +- regex: MSstatsLOBD_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MSstatsLOBD diff --git a/prepare/r-msstatsptm/PKGBUILD b/prepare/r-msstatsptm/PKGBUILD new file mode 100644 index 0000000000..4d06fae1b1 --- /dev/null +++ b/prepare/r-msstatsptm/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MSstatsPTM +_pkgver=1.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Characterization of Post-translational Modifications' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-checkmate + r-data.table + r-dplyr + r-ggplot2 + r-ggrepel + r-gridextra + r-msstats + r-msstatsconvert + r-msstatstmt + r-rcpp + r-stringr +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-rmarkdown + r-tinytest +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msstatsptm/lilac.py b/prepare/r-msstatsptm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msstatsptm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msstatsptm/lilac.yaml b/prepare/r-msstatsptm/lilac.yaml new file mode 100644 index 0000000000..0818da3358 --- /dev/null +++ b/prepare/r-msstatsptm/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-checkmate +- r-data.table +- r-dplyr +- r-ggplot2 +- r-ggrepel +- r-gridextra +- r-msstats +- r-msstatsconvert +- r-msstatstmt +- r-rcpp +- r-stringr +update_on: +- regex: MSstatsPTM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MSstatsPTM diff --git a/prepare/r-msstatsqc/PKGBUILD b/prepare/r-msstatsqc/PKGBUILD new file mode 100644 index 0000000000..b6370cc532 --- /dev/null +++ b/prepare/r-msstatsqc/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MSstatsQC +_pkgver=2.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Longitudinal system suitability monitoring and quality control for proteomic experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-dplyr + r-ggextra + r-ggplot2 + r-msnbase + r-plotly + r-qcmetrics +) +optdepends=( + r-knitr + r-rforproteomics + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msstatsqc/lilac.py b/prepare/r-msstatsqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msstatsqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msstatsqc/lilac.yaml b/prepare/r-msstatsqc/lilac.yaml new file mode 100644 index 0000000000..92c2ff433f --- /dev/null +++ b/prepare/r-msstatsqc/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggextra +- r-ggplot2 +- r-msnbase +- r-plotly +- r-qcmetrics +update_on: +- regex: MSstatsQC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MSstatsQC diff --git a/prepare/r-msstatsqcgui/PKGBUILD b/prepare/r-msstatsqcgui/PKGBUILD new file mode 100644 index 0000000000..c4da189350 --- /dev/null +++ b/prepare/r-msstatsqcgui/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MSstatsQCgui +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A graphical user interface for MSstatsQC package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-dplyr + r-ggextra + r-gridextra + r-msstatsqc + r-plotly + r-shiny +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msstatsqcgui/lilac.py b/prepare/r-msstatsqcgui/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msstatsqcgui/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msstatsqcgui/lilac.yaml b/prepare/r-msstatsqcgui/lilac.yaml new file mode 100644 index 0000000000..0facaba95e --- /dev/null +++ b/prepare/r-msstatsqcgui/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggextra +- r-gridextra +- r-msstatsqc +- r-plotly +- r-shiny +update_on: +- regex: MSstatsQCgui_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MSstatsQCgui diff --git a/prepare/r-msstatssamplesize/PKGBUILD b/prepare/r-msstatssamplesize/PKGBUILD new file mode 100644 index 0000000000..186dfd2174 --- /dev/null +++ b/prepare/r-msstatssamplesize/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MSstatsSampleSize +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Simulation tool for optimal design of high-dimensional MS-based proteomics experiment' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-caret + r-ggplot2 + r-gridextra + r-msstats + r-reshape2 +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msstatssamplesize/lilac.py b/prepare/r-msstatssamplesize/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msstatssamplesize/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msstatssamplesize/lilac.yaml b/prepare/r-msstatssamplesize/lilac.yaml new file mode 100644 index 0000000000..0802a17d3f --- /dev/null +++ b/prepare/r-msstatssamplesize/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-caret +- r-ggplot2 +- r-gridextra +- r-msstats +- r-reshape2 +update_on: +- regex: MSstatsSampleSize_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MSstatsSampleSize diff --git a/prepare/r-msstatstmt/PKGBUILD b/prepare/r-msstatstmt/PKGBUILD new file mode 100644 index 0000000000..9a7b99a297 --- /dev/null +++ b/prepare/r-msstatstmt/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MSstatsTMT +_pkgver=2.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-checkmate + r-data.table + r-ggplot2 + r-limma + r-lme4 + r-lmertest + r-msstats + r-msstatsconvert +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msstatstmt/lilac.py b/prepare/r-msstatstmt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msstatstmt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msstatstmt/lilac.yaml b/prepare/r-msstatstmt/lilac.yaml new file mode 100644 index 0000000000..33f0a6587b --- /dev/null +++ b/prepare/r-msstatstmt/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-checkmate +- r-data.table +- r-ggplot2 +- r-limma +- r-lme4 +- r-lmertest +- r-msstats +- r-msstatsconvert +update_on: +- regex: MSstatsTMT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MSstatsTMT diff --git a/prepare/r-msstatstmtptm/PKGBUILD b/prepare/r-msstatstmtptm/PKGBUILD new file mode 100644 index 0000000000..c10f120180 --- /dev/null +++ b/prepare/r-msstatstmtptm/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MSstatsTMTPTM +_pkgver=1.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-dplyr + r-ggplot2 + r-gridextra + r-msstatstmt + r-rcpp + r-reshape2 + r-stringr +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-msstats + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-msstatstmtptm/lilac.py b/prepare/r-msstatstmtptm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-msstatstmtptm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-msstatstmtptm/lilac.yaml b/prepare/r-msstatstmtptm/lilac.yaml new file mode 100644 index 0000000000..d5d6548988 --- /dev/null +++ b/prepare/r-msstatstmtptm/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-gridextra +- r-msstatstmt +- r-rcpp +- r-reshape2 +- r-stringr +update_on: +- regex: MSstatsTMTPTM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MSstatsTMTPTM diff --git a/prepare/r-mulcom/PKGBUILD b/prepare/r-mulcom/PKGBUILD new file mode 100644 index 0000000000..482fa4aeb8 --- /dev/null +++ b/prepare/r-mulcom/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Mulcom +_pkgver=1.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Calculates Mulcom test' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-fields +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mulcom/lilac.py b/prepare/r-mulcom/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mulcom/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mulcom/lilac.yaml b/prepare/r-mulcom/lilac.yaml new file mode 100644 index 0000000000..b5a720d708 --- /dev/null +++ b/prepare/r-mulcom/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-fields +update_on: +- regex: Mulcom_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Mulcom diff --git a/prepare/r-multcomp/PKGBUILD b/prepare/r-multcomp/PKGBUILD new file mode 100644 index 0000000000..4cad2b70db --- /dev/null +++ b/prepare/r-multcomp/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=multcomp +_pkgver=1.4-18 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Simultaneous Inference in General Parametric Models' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mvtnorm + r-sandwich + r-th.data +) +optdepends=( + r-coin + r-coxme + r-fixest + r-foreign + r-iswr + r-lme4 + r-lmtest + r-mass + r-nlme + r-robustbase + r-simcomp + r-tram + r-xtable +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multcomp/lilac.py b/prepare/r-multcomp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-multcomp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-multcomp/lilac.yaml b/prepare/r-multcomp/lilac.yaml new file mode 100644 index 0000000000..3a67c64aa1 --- /dev/null +++ b/prepare/r-multcomp/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mvtnorm +- r-sandwich +- r-th.data +update_on: +- regex: multcomp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=multcomp diff --git a/prepare/r-multcompview/PKGBUILD b/prepare/r-multcompview/PKGBUILD new file mode 100644 index 0000000000..b1def0e013 --- /dev/null +++ b/prepare/r-multcompview/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=multcompView +_pkgver=0.1-8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualizations of Paired Comparisons' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-mass + r-multcomp + r-pgirmess +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multcompview/lilac.py b/prepare/r-multcompview/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-multcompview/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-multcompview/lilac.yaml b/prepare/r-multcompview/lilac.yaml new file mode 100644 index 0000000000..afb2406dbf --- /dev/null +++ b/prepare/r-multcompview/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: multcompView_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=multcompView diff --git a/prepare/r-multiassayexperiment/PKGBUILD b/prepare/r-multiassayexperiment/PKGBUILD new file mode 100644 index 0000000000..67ad0dc397 --- /dev/null +++ b/prepare/r-multiassayexperiment/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MultiAssayExperiment +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Software for the integration of multi-omics experiments in Bioconductor' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-genomicranges + r-iranges + r-s4vectors + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-biocstyle + r-hdf5array + r-knitr + r-maftools + r-r.rsp + r-raggedexperiment + r-rmarkdown + r-survival + r-survminer + r-testthat + r-upsetr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multiassayexperiment/lilac.py b/prepare/r-multiassayexperiment/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-multiassayexperiment/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-multiassayexperiment/lilac.yaml b/prepare/r-multiassayexperiment/lilac.yaml new file mode 100644 index 0000000000..f01c40b337 --- /dev/null +++ b/prepare/r-multiassayexperiment/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-genomicranges +- r-iranges +- r-s4vectors +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: MultiAssayExperiment_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MultiAssayExperiment diff --git a/prepare/r-multibac/PKGBUILD b/prepare/r-multibac/PKGBUILD new file mode 100644 index 0000000000..8cf96bf22b --- /dev/null +++ b/prepare/r-multibac/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MultiBaC +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multiomic Batch effect Correction' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-multiassayexperiment + r-plotrix + r-ropls +) +optdepends=( + r-biocstyle + r-devtools + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multibac/lilac.py b/prepare/r-multibac/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-multibac/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-multibac/lilac.yaml b/prepare/r-multibac/lilac.yaml new file mode 100644 index 0000000000..92537dea87 --- /dev/null +++ b/prepare/r-multibac/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-multiassayexperiment +- r-plotrix +- r-ropls +update_on: +- regex: MultiBaC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MultiBaC diff --git a/prepare/r-multiclust/PKGBUILD b/prepare/r-multiclust/PKGBUILD new file mode 100644 index 0000000000..f12c7fef7f --- /dev/null +++ b/prepare/r-multiclust/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=multiClust +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-amap + r-ctc + r-dendextend + r-mclust +) +optdepends=( + r-biobase + r-biocgenerics + r-geoquery + r-gplots + r-knitr + r-preprocesscore + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multiclust/lilac.py b/prepare/r-multiclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-multiclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-multiclust/lilac.yaml b/prepare/r-multiclust/lilac.yaml new file mode 100644 index 0000000000..4b1f4683fc --- /dev/null +++ b/prepare/r-multiclust/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-amap +- r-ctc +- r-dendextend +- r-mclust +update_on: +- regex: multiClust_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/multiClust diff --git a/prepare/r-multicool/PKGBUILD b/prepare/r-multicool/PKGBUILD new file mode 100644 index 0000000000..f3379d00d2 --- /dev/null +++ b/prepare/r-multicool/PKGBUILD @@ -0,0 +1,28 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=multicool +_pkgver=0.1-12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Permutations of Multisets in Cool-Lex Order' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multicool/lilac.py b/prepare/r-multicool/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-multicool/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-multicool/lilac.yaml b/prepare/r-multicool/lilac.yaml new file mode 100644 index 0000000000..230cb23b1a --- /dev/null +++ b/prepare/r-multicool/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: multicool_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=multicool diff --git a/prepare/r-multicrispr/PKGBUILD b/prepare/r-multicrispr/PKGBUILD new file mode 100644 index 0000000000..9630e20fba --- /dev/null +++ b/prepare/r-multicrispr/PKGBUILD @@ -0,0 +1,59 @@ +# Maintainer: Guoyi Zhang + +_pkgname=multicrispr +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multi-locus multi-purpose Crispr/Cas design' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertive + r-biocgenerics + r-biostrings + r-bsgenome + r-crisprseek + r-data.table + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-karyoploter + r-magrittr + r-plyranges + r-rbowtie + r-reticulate + r-rtracklayer + r-stringi + r-tidyr + r-tidyselect +) +optdepends=( + r-annotationhub + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg38 + r-bsgenome.mmusculus.ucsc.mm10 + r-bsgenome.scerevisiae.ucsc.saccer1 + r-ensembldb + r-iranges + r-knitr + r-magick + r-rmarkdown + r-testthat + r-txdb.mmusculus.ucsc.mm10.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multicrispr/lilac.py b/prepare/r-multicrispr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-multicrispr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-multicrispr/lilac.yaml b/prepare/r-multicrispr/lilac.yaml new file mode 100644 index 0000000000..85fe743713 --- /dev/null +++ b/prepare/r-multicrispr/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertive +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-crisprseek +- r-data.table +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-karyoploter +- r-magrittr +- r-plyranges +- r-rbowtie +- r-reticulate +- r-rtracklayer +- r-stringi +- r-tidyr +- r-tidyselect +update_on: +- regex: multicrispr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/multicrispr diff --git a/prepare/r-multidataset/PKGBUILD b/prepare/r-multidataset/PKGBUILD new file mode 100644 index 0000000000..560b52e970 --- /dev/null +++ b/prepare/r-multidataset/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MultiDataSet +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Implementation of MultiDataSet and ResultSet' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-biobase + r-biocgenerics + r-genomicranges + r-ggplot2 + r-ggrepel + r-iranges + r-limma + r-qqman + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-brgedata + r-geoquery + r-iclusterplus + r-knitr + r-minfi + r-minfidata + r-multiassayexperiment + r-omicade4 + r-raggedexperiment + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multidataset/lilac.py b/prepare/r-multidataset/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-multidataset/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-multidataset/lilac.yaml b/prepare/r-multidataset/lilac.yaml new file mode 100644 index 0000000000..71fc2046aa --- /dev/null +++ b/prepare/r-multidataset/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-genomicranges +- r-ggplot2 +- r-ggrepel +- r-iranges +- r-limma +- r-qqman +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: MultiDataSet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MultiDataSet diff --git a/prepare/r-multigsea/PKGBUILD b/prepare/r-multigsea/PKGBUILD new file mode 100644 index 0000000000..e9a265acc3 --- /dev/null +++ b/prepare/r-multigsea/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=multiGSEA +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Combining GSEA-based pathway enrichment with multi omics data integration' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-dplyr + r-fgsea + r-graphite + r-magrittr + r-metap + r-rappdirs + r-rlang +) +optdepends=( + r-biocstyle + r-knitr + r-metaboliteidmapping + r-org.bt.eg.db + r-org.ce.eg.db + r-org.cf.eg.db + r-org.dm.eg.db + r-org.dr.eg.db + r-org.gg.eg.db + r-org.hs.eg.db + r-org.mm.eg.db + r-org.rn.eg.db + r-org.ss.eg.db + r-org.xl.eg.db + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multigsea/lilac.py b/prepare/r-multigsea/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-multigsea/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-multigsea/lilac.yaml b/prepare/r-multigsea/lilac.yaml new file mode 100644 index 0000000000..b0f1ba2f35 --- /dev/null +++ b/prepare/r-multigsea/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-dplyr +- r-fgsea +- r-graphite +- r-magrittr +- r-metap +- r-rappdirs +- r-rlang +update_on: +- regex: multiGSEA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/multiGSEA diff --git a/prepare/r-multihiccompare/PKGBUILD b/prepare/r-multihiccompare/PKGBUILD new file mode 100644 index 0000000000..02db5c2603 --- /dev/null +++ b/prepare/r-multihiccompare/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=multiHiCcompare +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-aggregation + r-biocparallel + r-data.table + r-dplyr + r-edger + r-genomeinfodb + r-genomeinfodbdata + r-genomicranges + r-hiccompare + r-pbapply + r-pheatmap + r-qqman +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multihiccompare/lilac.py b/prepare/r-multihiccompare/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-multihiccompare/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-multihiccompare/lilac.yaml b/prepare/r-multihiccompare/lilac.yaml new file mode 100644 index 0000000000..acd1224f1a --- /dev/null +++ b/prepare/r-multihiccompare/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aggregation +- r-biocparallel +- r-data.table +- r-dplyr +- r-edger +- r-genomeinfodb +- r-genomeinfodbdata +- r-genomicranges +- r-hiccompare +- r-pbapply +- r-pheatmap +- r-qqman +update_on: +- regex: multiHiCcompare_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/multiHiCcompare diff --git a/prepare/r-multimed/PKGBUILD b/prepare/r-multimed/PKGBUILD new file mode 100644 index 0000000000..586ce3b436 --- /dev/null +++ b/prepare/r-multimed/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MultiMed +_pkgver=2.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Testing multiple biological mediators simultaneously' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multimed/lilac.py b/prepare/r-multimed/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-multimed/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-multimed/lilac.yaml b/prepare/r-multimed/lilac.yaml new file mode 100644 index 0000000000..3e983cc23a --- /dev/null +++ b/prepare/r-multimed/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: MultiMed_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MultiMed diff --git a/prepare/r-multimir/PKGBUILD b/prepare/r-multimir/PKGBUILD new file mode 100644 index 0000000000..9e5eb5caf9 --- /dev/null +++ b/prepare/r-multimir/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=multiMiR +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integration of multiple microRNA-target databases with their disease and drug associations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-biocgenerics + r-dplyr + r-purrr + r-rcurl + r-tibble + r-xml +) +optdepends=( + r-biocstyle + r-edger + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multimir/lilac.py b/prepare/r-multimir/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-multimir/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-multimir/lilac.yaml b/prepare/r-multimir/lilac.yaml new file mode 100644 index 0000000000..16dd5ba95a --- /dev/null +++ b/prepare/r-multimir/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-dplyr +- r-purrr +- r-rcurl +- r-tibble +- r-xml +update_on: +- regex: multiMiR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/multiMiR diff --git a/prepare/r-multiomicsviz/PKGBUILD b/prepare/r-multiomicsviz/PKGBUILD new file mode 100644 index 0000000000..02eb8b8608 --- /dev/null +++ b/prepare/r-multiomicsviz/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=multiOmicsViz +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Plot the effect of one omics data on other omics data along the chromosome' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-doparallel + r-foreach + r-summarizedexperiment +) +optdepends=( + r-biocgenerics +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multiomicsviz/lilac.py b/prepare/r-multiomicsviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-multiomicsviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-multiomicsviz/lilac.yaml b/prepare/r-multiomicsviz/lilac.yaml new file mode 100644 index 0000000000..309da24d8b --- /dev/null +++ b/prepare/r-multiomicsviz/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-foreach +- r-summarizedexperiment +update_on: +- regex: multiOmicsViz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/multiOmicsViz diff --git a/prepare/r-multipanelfigure/PKGBUILD b/prepare/r-multipanelfigure/PKGBUILD new file mode 100644 index 0000000000..c2c94ddf6d --- /dev/null +++ b/prepare/r-multipanelfigure/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=multipanelfigure +_pkgver=2.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Infrastructure to Assemble Multi-Panel Figures (from Grobs)' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertive.base + r-assertive.files + r-assertive.numbers + r-assertive.properties + r-assertive.types + r-ggplot2 + r-gridgraphics + r-gtable + r-magick + r-magrittr + r-stringi +) +optdepends=( + r-complexheatmap + r-grdevices + r-knitr + r-lattice + r-markdown + r-rmarkdown + r-roxygen2 + r-venndiagram +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multipanelfigure/lilac.py b/prepare/r-multipanelfigure/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-multipanelfigure/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-multipanelfigure/lilac.yaml b/prepare/r-multipanelfigure/lilac.yaml new file mode 100644 index 0000000000..e5c5b4cf69 --- /dev/null +++ b/prepare/r-multipanelfigure/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertive.base +- r-assertive.files +- r-assertive.numbers +- r-assertive.properties +- r-assertive.types +- r-ggplot2 +- r-gridgraphics +- r-gtable +- r-magick +- r-magrittr +- r-stringi +update_on: +- regex: multipanelfigure_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=multipanelfigure diff --git a/prepare/r-multiscan/PKGBUILD b/prepare/r-multiscan/PKGBUILD new file mode 100644 index 0000000000..60cdcd634c --- /dev/null +++ b/prepare/r-multiscan/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=multiscan +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R package for combining multiple scans' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multiscan/lilac.py b/prepare/r-multiscan/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-multiscan/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-multiscan/lilac.yaml b/prepare/r-multiscan/lilac.yaml new file mode 100644 index 0000000000..0266ff1509 --- /dev/null +++ b/prepare/r-multiscan/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: multiscan_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/multiscan diff --git a/prepare/r-multisight/PKGBUILD b/prepare/r-multisight/PKGBUILD new file mode 100644 index 0000000000..8849428e9d --- /dev/null +++ b/prepare/r-multisight/PKGBUILD @@ -0,0 +1,62 @@ +# Maintainer: Guoyi Zhang + +_pkgname=multiSight +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multi-omics Classification, Functional Enrichment and Network Inference analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CeCILL') +depends=( + r + r-anylib + r-biosigner + r-caret + r-clusterprofiler + r-config + r-deseq2 + r-dplyr + r-dt + r-easypubmed + r-enrichplot + r-golem + r-htmltools + r-igraph + r-infotheo + r-metap + r-mixomics + r-networkd3 + r-ppcor + r-r6 + r-reactomepa + r-rmarkdown + r-rwikipathways + r-shiny + r-shinydashboard + r-stringr +) +optdepends=( + r-attempt + r-biocstyle + r-knitr + r-markdown + r-org.mm.eg.db + r-processx + r-rlang + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multisight/lilac.py b/prepare/r-multisight/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-multisight/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-multisight/lilac.yaml b/prepare/r-multisight/lilac.yaml new file mode 100644 index 0000000000..18a9baff17 --- /dev/null +++ b/prepare/r-multisight/lilac.yaml @@ -0,0 +1,34 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-anylib +- r-biosigner +- r-caret +- r-clusterprofiler +- r-config +- r-deseq2 +- r-dplyr +- r-dt +- r-easypubmed +- r-enrichplot +- r-golem +- r-htmltools +- r-igraph +- r-infotheo +- r-metap +- r-mixomics +- r-networkd3 +- r-ppcor +- r-r6 +- r-reactomepa +- r-rmarkdown +- r-rwikipathways +- r-shiny +- r-shinydashboard +- r-stringr +update_on: +- regex: multiSight_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/multiSight diff --git a/prepare/r-multtest/PKGBUILD b/prepare/r-multtest/PKGBUILD new file mode 100644 index 0000000000..251065aec7 --- /dev/null +++ b/prepare/r-multtest/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=multtest +_pkgver=2.50.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Resampling-based multiple hypothesis testing' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-biocgenerics +) +optdepends=( + r-snow +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-multtest/lilac.py b/prepare/r-multtest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-multtest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-multtest/lilac.yaml b/prepare/r-multtest/lilac.yaml new file mode 100644 index 0000000000..a1478e6a64 --- /dev/null +++ b/prepare/r-multtest/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +update_on: +- regex: multtest_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/multtest diff --git a/prepare/r-mumin/PKGBUILD b/prepare/r-mumin/PKGBUILD new file mode 100644 index 0000000000..a9e1a6c132 --- /dev/null +++ b/prepare/r-mumin/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MuMIn +_pkgver=1.43.17 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multi-Model Inference' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-aod + r-aods3 + r-betareg + r-caper + r-coxme + r-cplm + r-gamlss + r-gamm4 + r-gee + r-geem + r-geepack + r-glmmml + r-lme4 + r-logistf + r-mass + r-mcmcglmm + r-mgcv + r-nnet + r-ordinal + r-pscl + r-spatialreg + r-spdep + r-splm + r-survival + r-unmarked +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mumin/lilac.py b/prepare/r-mumin/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mumin/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mumin/lilac.yaml b/prepare/r-mumin/lilac.yaml new file mode 100644 index 0000000000..bb1477a67a --- /dev/null +++ b/prepare/r-mumin/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: MuMIn_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=MuMIn diff --git a/prepare/r-mumosa/PKGBUILD b/prepare/r-mumosa/PKGBUILD new file mode 100644 index 0000000000..e021a5ac17 --- /dev/null +++ b/prepare/r-mumosa/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mumosa +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multi-Modal Single-Cell Analysis Methods' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-batchelor + r-beachmat + r-biocgenerics + r-biocneighbors + r-biocparallel + r-biocsingular + r-delayedarray + r-delayedmatrixstats + r-igraph + r-iranges + r-metapod + r-s4vectors + r-scaledmatrix + r-scran + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-uwot +) +optdepends=( + r-biocstyle + r-bluster + r-dropletutils + r-knitr + r-rmarkdown + r-scater + r-scrnaseq + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mumosa/lilac.py b/prepare/r-mumosa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mumosa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mumosa/lilac.yaml b/prepare/r-mumosa/lilac.yaml new file mode 100644 index 0000000000..3645920a6a --- /dev/null +++ b/prepare/r-mumosa/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-batchelor +- r-beachmat +- r-biocgenerics +- r-biocneighbors +- r-biocparallel +- r-biocsingular +- r-delayedarray +- r-delayedmatrixstats +- r-igraph +- r-iranges +- r-metapod +- r-s4vectors +- r-scaledmatrix +- r-scran +- r-scuttle +- r-singlecellexperiment +- r-summarizedexperiment +- r-uwot +update_on: +- regex: mumosa_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mumosa diff --git a/prepare/r-mungesumstats/PKGBUILD b/prepare/r-mungesumstats/PKGBUILD new file mode 100644 index 0000000000..a662b25e54 --- /dev/null +++ b/prepare/r-mungesumstats/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MungeSumstats +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Standardise summary statistics from GWAS' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-bsgenome + r-data.table + r-dplyr + r-genomeinfodb + r-genomicranges + r-googleauthr + r-httr + r-jsonlite + r-magrittr + r-r.utils + r-rcurl + r-rtracklayer + r-stringr + r-variantannotation +) +optdepends=( + r-biocgenerics + r-biocstyle + r-bsgenome.hsapiens.1000genomes.hs37d5 + r-bsgenome.hsapiens.ncbi.grch38 + r-covr + r-iranges + r-knitr + r-markdown + r-matrixgenerics + r-rmarkdown + r-rsamtools + r-s4vectors + r-seqminer + r-snplocs.hsapiens.dbsnp144.grch37 + r-snplocs.hsapiens.dbsnp144.grch38 + r-testthat + r-upsetr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mungesumstats/lilac.py b/prepare/r-mungesumstats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mungesumstats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mungesumstats/lilac.yaml b/prepare/r-mungesumstats/lilac.yaml new file mode 100644 index 0000000000..5b4c53f9cc --- /dev/null +++ b/prepare/r-mungesumstats/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome +- r-data.table +- r-dplyr +- r-genomeinfodb +- r-genomicranges +- r-googleauthr +- r-httr +- r-jsonlite +- r-magrittr +- r-r.utils +- r-rcurl +- r-rtracklayer +- r-stringr +- r-variantannotation +update_on: +- regex: MungeSumstats_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MungeSumstats diff --git a/prepare/r-munsell/PKGBUILD b/prepare/r-munsell/PKGBUILD new file mode 100644 index 0000000000..f4acd72aa7 --- /dev/null +++ b/prepare/r-munsell/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=munsell +_pkgver=0.5.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities for Using Munsell Colours' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-colorspace +) +optdepends=( + r-ggplot2 + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-munsell/lilac.py b/prepare/r-munsell/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-munsell/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-munsell/lilac.yaml b/prepare/r-munsell/lilac.yaml new file mode 100644 index 0000000000..421eb22e80 --- /dev/null +++ b/prepare/r-munsell/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colorspace +update_on: +- regex: munsell_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=munsell diff --git a/prepare/r-mus.musculus/PKGBUILD b/prepare/r-mus.musculus/PKGBUILD new file mode 100644 index 0000000000..1ec656985c --- /dev/null +++ b/prepare/r-mus.musculus/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Mus.musculus +_pkgver=1.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation package for the Mus.musculus object' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-genomicfeatures + r-go.db + r-org.mm.eg.db + r-organismdbi + r-txdb.mmusculus.ucsc.mm10.knowngene +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mus.musculus/lilac.py b/prepare/r-mus.musculus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mus.musculus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mus.musculus/lilac.yaml b/prepare/r-mus.musculus/lilac.yaml new file mode 100644 index 0000000000..93aa071a32 --- /dev/null +++ b/prepare/r-mus.musculus/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-genomicfeatures +- r-go.db +- r-org.mm.eg.db +- r-organismdbi +- r-txdb.mmusculus.ucsc.mm10.knowngene +update_on: +- regex: Mus.musculus_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Mus.musculus diff --git a/prepare/r-muscat/PKGBUILD b/prepare/r-muscat/PKGBUILD new file mode 100644 index 0000000000..af9dc53407 --- /dev/null +++ b/prepare/r-muscat/PKGBUILD @@ -0,0 +1,65 @@ +# Maintainer: Guoyi Zhang + +_pkgname=muscat +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multi-sample multi-group scRNA-seq data analysis tools' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-blme + r-complexheatmap + r-data.table + r-deseq2 + r-dplyr + r-edger + r-ggplot2 + r-glmmtmb + r-limma + r-lme4 + r-lmertest + r-matrixstats + r-progress + r-purrr + r-s4vectors + r-scales + r-scater + r-sctransform + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-variancepartition + r-viridis +) +optdepends=( + r-biocstyle + r-countsimqc + r-cowplot + r-experimenthub + r-icobra + r-knitr + r-phylogram + r-rcolorbrewer + r-reshape2 + r-rmarkdown + r-statmod + r-testthat + r-upsetr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-muscat/lilac.py b/prepare/r-muscat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-muscat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-muscat/lilac.yaml b/prepare/r-muscat/lilac.yaml new file mode 100644 index 0000000000..d1eb0457b7 --- /dev/null +++ b/prepare/r-muscat/lilac.yaml @@ -0,0 +1,33 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-blme +- r-complexheatmap +- r-data.table +- r-deseq2 +- r-dplyr +- r-edger +- r-ggplot2 +- r-glmmtmb +- r-limma +- r-lme4 +- r-lmertest +- r-matrixstats +- r-progress +- r-purrr +- r-s4vectors +- r-scales +- r-scater +- r-sctransform +- r-scuttle +- r-singlecellexperiment +- r-summarizedexperiment +- r-variancepartition +- r-viridis +update_on: +- regex: muscat_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/muscat diff --git a/prepare/r-muscle/PKGBUILD b/prepare/r-muscle/PKGBUILD new file mode 100644 index 0000000000..82c7f38d15 --- /dev/null +++ b/prepare/r-muscle/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=muscle +_pkgver=3.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multiple Sequence Alignment with MUSCLE' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Unlimited') +depends=( + r + r-biostrings +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-muscle/lilac.py b/prepare/r-muscle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-muscle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-muscle/lilac.yaml b/prepare/r-muscle/lilac.yaml new file mode 100644 index 0000000000..283133f7f2 --- /dev/null +++ b/prepare/r-muscle/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +update_on: +- regex: muscle_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/muscle diff --git a/prepare/r-musicatk/PKGBUILD b/prepare/r-musicatk/PKGBUILD new file mode 100644 index 0000000000..187c607cdb --- /dev/null +++ b/prepare/r-musicatk/PKGBUILD @@ -0,0 +1,86 @@ +# Maintainer: Guoyi Zhang + +_pkgname=musicatk +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mutational Signature Comprehensive Analysis Toolkit' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biostrings + r-bsgenome + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.hsapiens.ucsc.hg38 + r-bsgenome.mmusculus.ucsc.mm10 + r-bsgenome.mmusculus.ucsc.mm9 + r-complexheatmap + r-cowplot + r-data.table + r-decomptumor2sig + r-deconstructsigs + r-dplyr + r-factoextra + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggrepel + r-gridextra + r-gtools + r-iranges + r-maftools + r-magrittr + r-matrixtests + r-mcmcprecision + r-nmf + r-philentropy + r-plotly + r-rlang + r-s4vectors + r-shiny + r-shinyalert + r-shinybs + r-shinybusy + r-shinydashboard + r-shinyjqui + r-shinyjs + r-sortable + r-stringi + r-stringr + r-summarizedexperiment + r-tcgabiolinks + r-tibble + r-tidyr + r-topicmodels + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.hsapiens.ucsc.hg38.knowngene + r-uwot + r-variantannotation + r-withr +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-qpdf + r-rmarkdown + r-survival + r-testthat + r-xvector +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-musicatk/lilac.py b/prepare/r-musicatk/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-musicatk/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-musicatk/lilac.yaml b/prepare/r-musicatk/lilac.yaml new file mode 100644 index 0000000000..53d8b14e15 --- /dev/null +++ b/prepare/r-musicatk/lilac.yaml @@ -0,0 +1,59 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome +- r-bsgenome.hsapiens.ucsc.hg19 +- r-bsgenome.hsapiens.ucsc.hg38 +- r-bsgenome.mmusculus.ucsc.mm10 +- r-bsgenome.mmusculus.ucsc.mm9 +- r-complexheatmap +- r-cowplot +- r-data.table +- r-decomptumor2sig +- r-deconstructsigs +- r-dplyr +- r-factoextra +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-ggrepel +- r-gridextra +- r-gtools +- r-iranges +- r-maftools +- r-magrittr +- r-matrixtests +- r-mcmcprecision +- r-nmf +- r-philentropy +- r-plotly +- r-rlang +- r-s4vectors +- r-shiny +- r-shinyalert +- r-shinybs +- r-shinybusy +- r-shinydashboard +- r-shinyjqui +- r-shinyjs +- r-sortable +- r-stringi +- r-stringr +- r-summarizedexperiment +- r-tcgabiolinks +- r-tibble +- r-tidyr +- r-topicmodels +- r-txdb.hsapiens.ucsc.hg19.knowngene +- r-txdb.hsapiens.ucsc.hg38.knowngene +- r-uwot +- r-variantannotation +- r-withr +update_on: +- regex: musicatk_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/musicatk diff --git a/prepare/r-mustat/PKGBUILD b/prepare/r-mustat/PKGBUILD new file mode 100644 index 0000000000..bb42bd4cc8 --- /dev/null +++ b/prepare/r-mustat/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=muStat +_pkgver=1.7.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Prentice Rank Sum Test and McNemar Test' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mustat/lilac.py b/prepare/r-mustat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mustat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mustat/lilac.yaml b/prepare/r-mustat/lilac.yaml new file mode 100644 index 0000000000..036d07a7d7 --- /dev/null +++ b/prepare/r-mustat/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: muStat_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=muStat diff --git a/prepare/r-mutationalpatterns/PKGBUILD b/prepare/r-mutationalpatterns/PKGBUILD new file mode 100644 index 0000000000..66c2d6249c --- /dev/null +++ b/prepare/r-mutationalpatterns/PKGBUILD @@ -0,0 +1,62 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MutationalPatterns +_pkgver=3.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Comprehensive genome-wide analysis of mutational processes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-biostrings + r-bsgenome + r-cowplot + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggalluvial + r-ggdendro + r-ggplot2 + r-iranges + r-magrittr + r-nmf + r-pracma + r-purrr + r-rcolorbrewer + r-s4vectors + r-stringr + r-tibble + r-tidyr + r-variantannotation +) +optdepends=( + r-annotationdbi + r-biocstyle + r-biomart + r-bsgenome.hsapiens.ucsc.hg19 + r-ccfindr + r-genomicfeatures + r-gridextra + r-knitr + r-rmarkdown + r-rtracklayer + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mutationalpatterns/lilac.py b/prepare/r-mutationalpatterns/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mutationalpatterns/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mutationalpatterns/lilac.yaml b/prepare/r-mutationalpatterns/lilac.yaml new file mode 100644 index 0000000000..77a2b22ab2 --- /dev/null +++ b/prepare/r-mutationalpatterns/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-cowplot +- r-dplyr +- r-genomeinfodb +- r-genomicranges +- r-ggalluvial +- r-ggdendro +- r-ggplot2 +- r-iranges +- r-magrittr +- r-nmf +- r-pracma +- r-purrr +- r-rcolorbrewer +- r-s4vectors +- r-stringr +- r-tibble +- r-tidyr +- r-variantannotation +update_on: +- regex: MutationalPatterns_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MutationalPatterns diff --git a/prepare/r-mutoss/PKGBUILD b/prepare/r-mutoss/PKGBUILD new file mode 100644 index 0000000000..cafc8075a2 --- /dev/null +++ b/prepare/r-mutoss/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mutoss +_pkgver=0.1-12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Unified Multiple Testing Procedures' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-multcomp + r-multtest + r-mvtnorm + r-plotrix +) +optdepends=( + r-fdrtool + r-lattice + r-qvalue + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mutoss/lilac.py b/prepare/r-mutoss/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mutoss/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mutoss/lilac.yaml b/prepare/r-mutoss/lilac.yaml new file mode 100644 index 0000000000..a76d14baa5 --- /dev/null +++ b/prepare/r-mutoss/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-multcomp +- r-multtest +- r-mvtnorm +- r-plotrix +update_on: +- regex: mutoss_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mutoss diff --git a/prepare/r-mvcclass/PKGBUILD b/prepare/r-mvcclass/PKGBUILD new file mode 100644 index 0000000000..60bdfd28ea --- /dev/null +++ b/prepare/r-mvcclass/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MVCClass +_pkgver=1.68.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Model-View-Controller (MVC) Classes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mvcclass/lilac.py b/prepare/r-mvcclass/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mvcclass/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mvcclass/lilac.yaml b/prepare/r-mvcclass/lilac.yaml new file mode 100644 index 0000000000..1c0e37673e --- /dev/null +++ b/prepare/r-mvcclass/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: MVCClass_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MVCClass diff --git a/prepare/r-mvoutlier/PKGBUILD b/prepare/r-mvoutlier/PKGBUILD new file mode 100644 index 0000000000..a71f8db607 --- /dev/null +++ b/prepare/r-mvoutlier/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mvoutlier +_pkgver=2.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multivariate Outlier Detection Based on Robust Methods' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-robustbase + r-sgeostat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mvoutlier/lilac.py b/prepare/r-mvoutlier/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mvoutlier/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mvoutlier/lilac.yaml b/prepare/r-mvoutlier/lilac.yaml new file mode 100644 index 0000000000..4ecbc0776a --- /dev/null +++ b/prepare/r-mvoutlier/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-robustbase +- r-sgeostat +update_on: +- regex: mvoutlier_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mvoutlier diff --git a/prepare/r-mvtnorm/PKGBUILD b/prepare/r-mvtnorm/PKGBUILD new file mode 100644 index 0000000000..00aa2f8613 --- /dev/null +++ b/prepare/r-mvtnorm/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mvtnorm +_pkgver=1.1-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multivariate Normal and t Distributions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mvtnorm/lilac.py b/prepare/r-mvtnorm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mvtnorm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mvtnorm/lilac.yaml b/prepare/r-mvtnorm/lilac.yaml new file mode 100644 index 0000000000..15e4d5efcc --- /dev/null +++ b/prepare/r-mvtnorm/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: mvtnorm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=mvtnorm diff --git a/prepare/r-mwastools/PKGBUILD b/prepare/r-mwastools/PKGBUILD new file mode 100644 index 0000000000..f0d418ef45 --- /dev/null +++ b/prepare/r-mwastools/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=MWASTools +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MWASTools: an integrated pipeline to perform metabolome-wide association studies' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CCPL:by-nc-sa') +depends=( + r + r-car + r-complexheatmap + r-ggplot2 + r-glm2 + r-gridextra + r-igraph + r-kegggraph + r-keggrest + r-ppcor + r-qvalue + r-rcurl + r-summarizedexperiment +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mwastools/lilac.py b/prepare/r-mwastools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mwastools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mwastools/lilac.yaml b/prepare/r-mwastools/lilac.yaml new file mode 100644 index 0000000000..ac7a402467 --- /dev/null +++ b/prepare/r-mwastools/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-car +- r-complexheatmap +- r-ggplot2 +- r-glm2 +- r-gridextra +- r-igraph +- r-kegggraph +- r-keggrest +- r-ppcor +- r-qvalue +- r-rcurl +- r-summarizedexperiment +update_on: +- regex: MWASTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/MWASTools diff --git a/prepare/r-mygene/PKGBUILD b/prepare/r-mygene/PKGBUILD new file mode 100644 index 0000000000..54ce81b98a --- /dev/null +++ b/prepare/r-mygene/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mygene +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Access MyGene.Info_ services' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-genomicfeatures + r-hmisc + r-httr + r-jsonlite + r-plyr + r-s4vectors + r-sqldf +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mygene/lilac.py b/prepare/r-mygene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mygene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mygene/lilac.yaml b/prepare/r-mygene/lilac.yaml new file mode 100644 index 0000000000..4fa12b6c66 --- /dev/null +++ b/prepare/r-mygene/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicfeatures +- r-hmisc +- r-httr +- r-jsonlite +- r-plyr +- r-s4vectors +- r-sqldf +update_on: +- regex: mygene_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mygene diff --git a/prepare/r-myvariant/PKGBUILD b/prepare/r-myvariant/PKGBUILD new file mode 100644 index 0000000000..7e2080e200 --- /dev/null +++ b/prepare/r-myvariant/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=myvariant +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Accesses MyVariant.info variant query and annotation services' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-genomeinfodb + r-hmisc + r-httr + r-jsonlite + r-magrittr + r-plyr + r-s4vectors + r-variantannotation +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-myvariant/lilac.py b/prepare/r-myvariant/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-myvariant/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-myvariant/lilac.yaml b/prepare/r-myvariant/lilac.yaml new file mode 100644 index 0000000000..198cfcd875 --- /dev/null +++ b/prepare/r-myvariant/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomeinfodb +- r-hmisc +- r-httr +- r-jsonlite +- r-magrittr +- r-plyr +- r-s4vectors +- r-variantannotation +update_on: +- regex: myvariant_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/myvariant diff --git a/prepare/r-mzid/PKGBUILD b/prepare/r-mzid/PKGBUILD new file mode 100644 index 0000000000..4c3337ce57 --- /dev/null +++ b/prepare/r-mzid/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=mzID +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An mzIdentML parser for R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-doparallel + r-foreach + r-iterators + r-plyr + r-protgenerics + r-xml +) +optdepends=( + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mzid/lilac.py b/prepare/r-mzid/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mzid/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mzid/lilac.yaml b/prepare/r-mzid/lilac.yaml new file mode 100644 index 0000000000..65fe13d7c0 --- /dev/null +++ b/prepare/r-mzid/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-foreach +- r-iterators +- r-plyr +- r-protgenerics +- r-xml +update_on: +- regex: mzID_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mzID diff --git a/prepare/r-mzr/PKGBUILD b/prepare/r-mzr/PKGBUILD new file mode 100644 index 0000000000..ce4fbface0 --- /dev/null +++ b/prepare/r-mzr/PKGBUILD @@ -0,0 +1,43 @@ +# system requirements: C++11, GNU make +# Maintainer: Guoyi Zhang + +_pkgname=mzR +_pkgver=2.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-ncdf4 + r-protgenerics + r-rcpp + r-rhdf5lib + r-zlibbioc +) +optdepends=( + r-biocstyle + r-knitr + r-msdata + r-mzid + r-rmarkdown + r-runit + r-xml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-mzr/lilac.py b/prepare/r-mzr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-mzr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-mzr/lilac.yaml b/prepare/r-mzr/lilac.yaml new file mode 100644 index 0000000000..cb03c0e835 --- /dev/null +++ b/prepare/r-mzr/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-ncdf4 +- r-protgenerics +- r-rcpp +- r-rhdf5lib +- r-zlibbioc +update_on: +- regex: mzR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/mzR diff --git a/prepare/r-nabor/PKGBUILD b/prepare/r-nabor/PKGBUILD new file mode 100644 index 0000000000..a80b9b02e6 --- /dev/null +++ b/prepare/r-nabor/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nabor +_pkgver=0.5.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Wraps 'libnabo', a Fast K Nearest Neighbour Library for Low Dimensions" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-bh + r-rcpp + r-rcppeigen +) +optdepends=( + r-rann + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nabor/lilac.py b/prepare/r-nabor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nabor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nabor/lilac.yaml b/prepare/r-nabor/lilac.yaml new file mode 100644 index 0000000000..9e7e705e5b --- /dev/null +++ b/prepare/r-nabor/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-rcpp +- r-rcppeigen +update_on: +- regex: nabor_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=nabor diff --git a/prepare/r-nada/PKGBUILD b/prepare/r-nada/PKGBUILD new file mode 100644 index 0000000000..394aaeb9a2 --- /dev/null +++ b/prepare/r-nada/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NADA +_pkgver=1.6-1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Nondetects and Data Analysis for Environmental Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nada/lilac.py b/prepare/r-nada/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nada/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nada/lilac.yaml b/prepare/r-nada/lilac.yaml new file mode 100644 index 0000000000..58239a8c1a --- /dev/null +++ b/prepare/r-nada/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: NADA_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=NADA diff --git a/prepare/r-nadfinder/PKGBUILD b/prepare/r-nadfinder/PKGBUILD new file mode 100644 index 0000000000..e5891b459d --- /dev/null +++ b/prepare/r-nadfinder/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NADfinder +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Call wide peaks for sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-atacseqqc + r-baseline + r-biocgenerics + r-corrplot + r-csaw + r-empiricalbrownsmethod + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-limma + r-metap + r-rsamtools + r-rtracklayer + r-s4vectors + r-signal + r-summarizedexperiment + r-trackviewer +) +optdepends=( + r-biocmanager + r-biocstyle + r-bsgenome.mmusculus.ucsc.mm10 + r-knitr + r-rmarkdown + r-runit + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nadfinder/lilac.py b/prepare/r-nadfinder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nadfinder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nadfinder/lilac.yaml b/prepare/r-nadfinder/lilac.yaml new file mode 100644 index 0000000000..e966d3cc19 --- /dev/null +++ b/prepare/r-nadfinder/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-atacseqqc +- r-baseline +- r-biocgenerics +- r-corrplot +- r-csaw +- r-empiricalbrownsmethod +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-limma +- r-metap +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-signal +- r-summarizedexperiment +- r-trackviewer +update_on: +- regex: NADfinder_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NADfinder diff --git a/prepare/r-naivebayes/PKGBUILD b/prepare/r-naivebayes/PKGBUILD new file mode 100644 index 0000000000..fa9d3b8403 --- /dev/null +++ b/prepare/r-naivebayes/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=naivebayes +_pkgver=0.9.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='High Performance Implementation of the Naive Bayes Algorithm' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-matrix +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-naivebayes/lilac.py b/prepare/r-naivebayes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-naivebayes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-naivebayes/lilac.yaml b/prepare/r-naivebayes/lilac.yaml new file mode 100644 index 0000000000..18cc166284 --- /dev/null +++ b/prepare/r-naivebayes/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: naivebayes_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=naivebayes diff --git a/prepare/r-nanomethviz/PKGBUILD b/prepare/r-nanomethviz/PKGBUILD new file mode 100644 index 0000000000..db2fbd1901 --- /dev/null +++ b/prepare/r-nanomethviz/PKGBUILD @@ -0,0 +1,67 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=NanoMethViz +_pkgver=2.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualise methlation data from Oxford Nanopore sequencing' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Apache') +depends=( + r + r-annotationdbi + r-assertthat + r-biocsingular + r-bsseq + r-cpp11 + r-data.table + r-dplyr + r-e1071 + r-forcats + r-fs + r-genomicranges + r-ggplot2 + r-ggthemes + r-glue + r-limma + r-patchwork + r-purrr + r-rcpp + r-readr + r-rlang + r-rsamtools + r-rsqlite + r-s4vectors + r-scales + r-scico + r-stringr + r-summarizedexperiment + r-tibble + r-tidyr + r-withr + r-zlibbioc +) +optdepends=( + r-covr + r-dss + r-homo.sapiens + r-knitr + r-mus.musculus + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nanomethviz/lilac.py b/prepare/r-nanomethviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nanomethviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nanomethviz/lilac.yaml b/prepare/r-nanomethviz/lilac.yaml new file mode 100644 index 0000000000..ebfd5fbf9e --- /dev/null +++ b/prepare/r-nanomethviz/lilac.yaml @@ -0,0 +1,40 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-assertthat +- r-biocsingular +- r-bsseq +- r-cpp11 +- r-data.table +- r-dplyr +- r-e1071 +- r-forcats +- r-fs +- r-genomicranges +- r-ggplot2 +- r-ggthemes +- r-glue +- r-limma +- r-patchwork +- r-purrr +- r-rcpp +- r-readr +- r-rlang +- r-rsamtools +- r-rsqlite +- r-s4vectors +- r-scales +- r-scico +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-tidyr +- r-withr +- r-zlibbioc +update_on: +- regex: NanoMethViz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NanoMethViz diff --git a/prepare/r-nanostringdiff/PKGBUILD b/prepare/r-nanostringdiff/PKGBUILD new file mode 100644 index 0000000000..e725870b81 --- /dev/null +++ b/prepare/r-nanostringdiff/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NanoStringDiff +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential Expression Analysis of NanoString nCounter Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-matrixstats + r-rcpp +) +optdepends=( + r-biocstyle + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nanostringdiff/lilac.py b/prepare/r-nanostringdiff/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nanostringdiff/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nanostringdiff/lilac.yaml b/prepare/r-nanostringdiff/lilac.yaml new file mode 100644 index 0000000000..c18a83c382 --- /dev/null +++ b/prepare/r-nanostringdiff/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-matrixstats +- r-rcpp +update_on: +- regex: NanoStringDiff_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NanoStringDiff diff --git a/prepare/r-nanostringnctools/PKGBUILD b/prepare/r-nanostringnctools/PKGBUILD new file mode 100644 index 0000000000..d520548ef0 --- /dev/null +++ b/prepare/r-nanostringnctools/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NanoStringNCTools +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='NanoString nCounter Tools' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-biocgenerics + r-biostrings + r-ggbeeswarm + r-ggiraph + r-ggplot2 + r-ggthemes + r-iranges + r-pheatmap + r-rcolorbrewer + r-s4vectors +) +optdepends=( + r-biovizbase + r-ggbio + r-knitr + r-qpdf + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nanostringnctools/lilac.py b/prepare/r-nanostringnctools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nanostringnctools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nanostringnctools/lilac.yaml b/prepare/r-nanostringnctools/lilac.yaml new file mode 100644 index 0000000000..65f34727ba --- /dev/null +++ b/prepare/r-nanostringnctools/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biostrings +- r-ggbeeswarm +- r-ggiraph +- r-ggplot2 +- r-ggthemes +- r-iranges +- r-pheatmap +- r-rcolorbrewer +- r-s4vectors +update_on: +- regex: NanoStringNCTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NanoStringNCTools diff --git a/prepare/r-nanostringqcpro/PKGBUILD b/prepare/r-nanostringqcpro/PKGBUILD new file mode 100644 index 0000000000..f2f52dfa0f --- /dev/null +++ b/prepare/r-nanostringqcpro/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NanoStringQCPro +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quality metrics and data processing methods for NanoString mRNA gene expression data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biobase + r-knitr + r-nmf + r-org.hs.eg.db + r-png + r-rcolorbrewer +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nanostringqcpro/lilac.py b/prepare/r-nanostringqcpro/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nanostringqcpro/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nanostringqcpro/lilac.yaml b/prepare/r-nanostringqcpro/lilac.yaml new file mode 100644 index 0000000000..4556e5beb8 --- /dev/null +++ b/prepare/r-nanostringqcpro/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-knitr +- r-nmf +- r-org.hs.eg.db +- r-png +- r-rcolorbrewer +update_on: +- regex: NanoStringQCPro_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NanoStringQCPro diff --git a/prepare/r-nanotator/PKGBUILD b/prepare/r-nanotator/PKGBUILD new file mode 100644 index 0000000000..691a3a6ac3 --- /dev/null +++ b/prepare/r-nanotator/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nanotatoR +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Next generation structural variant annotation and classification' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-annotationdbi + r-curl + r-dplyr + r-genomicranges + r-hash + r-httr + r-knitr + r-openxlsx + r-org.hs.eg.db + r-rentrez + r-rlang + r-stringr + r-testthat + r-tidyverse + r-varfrompdb + r-xml + r-xml2r +) +optdepends=( + r-rmarkdown + r-yaml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nanotator/lilac.py b/prepare/r-nanotator/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nanotator/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nanotator/lilac.yaml b/prepare/r-nanotator/lilac.yaml new file mode 100644 index 0000000000..dacdb4aef3 --- /dev/null +++ b/prepare/r-nanotator/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-curl +- r-dplyr +- r-genomicranges +- r-hash +- r-httr +- r-knitr +- r-openxlsx +- r-org.hs.eg.db +- r-rentrez +- r-rlang +- r-stringr +- r-testthat +- r-tidyverse +- r-varfrompdb +- r-xml +- r-xml2r +update_on: +- regex: nanotatoR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/nanotatoR diff --git a/prepare/r-nanotime/PKGBUILD b/prepare/r-nanotime/PKGBUILD new file mode 100644 index 0000000000..af06f1f0f4 --- /dev/null +++ b/prepare/r-nanotime/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nanotime +_pkgver=0.3.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Nanosecond-Resolution Time Support for R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bit64 + r-rcpp + r-rcppcctz + r-rcppdate + r-zoo +) +optdepends=( + r-data.table + r-tinytest + r-xts +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nanotime/lilac.py b/prepare/r-nanotime/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nanotime/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nanotime/lilac.yaml b/prepare/r-nanotime/lilac.yaml new file mode 100644 index 0000000000..3067f056b9 --- /dev/null +++ b/prepare/r-nanotime/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bit64 +- r-rcpp +- r-rcppcctz +- r-rcppdate +- r-zoo +update_on: +- regex: nanotime_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=nanotime diff --git a/prepare/r-nanotube/PKGBUILD b/prepare/r-nanotube/PKGBUILD new file mode 100644 index 0000000000..78f9b27fd5 --- /dev/null +++ b/prepare/r-nanotube/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NanoTube +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Easy Pipeline for NanoString nCounter Data Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-fgsea + r-ggplot2 + r-limma + r-reshape +) +optdepends=( + r-grid + r-kableextra + r-knitr + r-nanostringdiff + r-pheatmap + r-plotly + r-qusage + r-rlang + r-rmarkdown + r-ruv + r-shiny + r-testthat + r-xlsx +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nanotube/lilac.py b/prepare/r-nanotube/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nanotube/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nanotube/lilac.yaml b/prepare/r-nanotube/lilac.yaml new file mode 100644 index 0000000000..532dea794f --- /dev/null +++ b/prepare/r-nanotube/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-fgsea +- r-ggplot2 +- r-limma +- r-reshape +update_on: +- regex: NanoTube_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NanoTube diff --git a/prepare/r-naturalsort/PKGBUILD b/prepare/r-naturalsort/PKGBUILD new file mode 100644 index 0000000000..ea05ec4c06 --- /dev/null +++ b/prepare/r-naturalsort/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=naturalsort +_pkgver=0.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Natural Ordering' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-naturalsort/lilac.py b/prepare/r-naturalsort/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-naturalsort/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-naturalsort/lilac.yaml b/prepare/r-naturalsort/lilac.yaml new file mode 100644 index 0000000000..d0dca56e5b --- /dev/null +++ b/prepare/r-naturalsort/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: naturalsort_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=naturalsort diff --git a/prepare/r-nbamseq/PKGBUILD b/prepare/r-nbamseq/PKGBUILD new file mode 100644 index 0000000000..f63d562207 --- /dev/null +++ b/prepare/r-nbamseq/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NBAMSeq +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Negative Binomial Additive Model for RNA-Seq Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-deseq2 + r-genefilter + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-ggplot2 + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nbamseq/lilac.py b/prepare/r-nbamseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nbamseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nbamseq/lilac.yaml b/prepare/r-nbamseq/lilac.yaml new file mode 100644 index 0000000000..e560d0e695 --- /dev/null +++ b/prepare/r-nbamseq/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-deseq2 +- r-genefilter +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: NBAMSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NBAMSeq diff --git a/prepare/r-nbclust/PKGBUILD b/prepare/r-nbclust/PKGBUILD new file mode 100644 index 0000000000..d627722898 --- /dev/null +++ b/prepare/r-nbclust/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NbClust +_pkgver=3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Determining the Best Number of Clusters in a Data Set' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nbclust/lilac.py b/prepare/r-nbclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nbclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nbclust/lilac.yaml b/prepare/r-nbclust/lilac.yaml new file mode 100644 index 0000000000..45898c219c --- /dev/null +++ b/prepare/r-nbclust/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: NbClust_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=NbClust diff --git a/prepare/r-nbpseq/PKGBUILD b/prepare/r-nbpseq/PKGBUILD new file mode 100644 index 0000000000..4849d81bd2 --- /dev/null +++ b/prepare/r-nbpseq/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NBPSeq +_pkgver=0.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Negative Binomial Models for RNA-Sequencing Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-qvalue +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nbpseq/lilac.py b/prepare/r-nbpseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nbpseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nbpseq/lilac.yaml b/prepare/r-nbpseq/lilac.yaml new file mode 100644 index 0000000000..2d7ac7755c --- /dev/null +++ b/prepare/r-nbpseq/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-qvalue +update_on: +- regex: NBPSeq_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=NBPSeq diff --git a/prepare/r-nbsplice/PKGBUILD b/prepare/r-nbsplice/PKGBUILD new file mode 100644 index 0000000000..ea5aed43dc --- /dev/null +++ b/prepare/r-nbsplice/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NBSplice +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Negative Binomial Models to detect Differential Splicing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-car + r-edger + r-ggplot2 + r-mppa + r-reshape2 +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-markdown + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nbsplice/lilac.py b/prepare/r-nbsplice/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nbsplice/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nbsplice/lilac.yaml b/prepare/r-nbsplice/lilac.yaml new file mode 100644 index 0000000000..57dbaf6e47 --- /dev/null +++ b/prepare/r-nbsplice/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-car +- r-edger +- r-ggplot2 +- r-mppa +- r-reshape2 +update_on: +- regex: NBSplice_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NBSplice diff --git a/prepare/r-ncdf4/PKGBUILD b/prepare/r-ncdf4/PKGBUILD new file mode 100644 index 0000000000..c62da3c68c --- /dev/null +++ b/prepare/r-ncdf4/PKGBUILD @@ -0,0 +1,27 @@ +# system requirements: netcdf library version 4.1 or later +# Maintainer: Guoyi Zhang + +_pkgname=ncdf4 +_pkgver=1.19 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ncdf4/lilac.py b/prepare/r-ncdf4/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ncdf4/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ncdf4/lilac.yaml b/prepare/r-ncdf4/lilac.yaml new file mode 100644 index 0000000000..6bb5d7a95e --- /dev/null +++ b/prepare/r-ncdf4/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ncdf4_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ncdf4 diff --git a/prepare/r-ncdfflow/PKGBUILD b/prepare/r-ncdfflow/PKGBUILD new file mode 100644 index 0000000000..5ae156ca3b --- /dev/null +++ b/prepare/r-ncdfflow/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ncdfFlow +_pkgver=2.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-bh + r-biobase + r-biocgenerics + r-flowcore + r-rcpp + r-rcpparmadillo + r-rhdf5lib + r-zlibbioc +) +optdepends=( + r-flowstats + r-knitr + r-parallel + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ncdfflow/lilac.py b/prepare/r-ncdfflow/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ncdfflow/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ncdfflow/lilac.yaml b/prepare/r-ncdfflow/lilac.yaml new file mode 100644 index 0000000000..87282f9b43 --- /dev/null +++ b/prepare/r-ncdfflow/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-biobase +- r-biocgenerics +- r-flowcore +- r-rcpp +- r-rcpparmadillo +- r-rhdf5lib +- r-zlibbioc +update_on: +- regex: ncdfFlow_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ncdfFlow diff --git a/prepare/r-ncgtw/PKGBUILD b/prepare/r-ncgtw/PKGBUILD new file mode 100644 index 0000000000..8a47a9c500 --- /dev/null +++ b/prepare/r-ncgtw/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ncGTW +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-rcpp + r-xcms +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ncgtw/lilac.py b/prepare/r-ncgtw/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ncgtw/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ncgtw/lilac.yaml b/prepare/r-ncgtw/lilac.yaml new file mode 100644 index 0000000000..39cd2b76a7 --- /dev/null +++ b/prepare/r-ncgtw/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-rcpp +- r-xcms +update_on: +- regex: ncGTW_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ncGTW diff --git a/prepare/r-ncigraph/PKGBUILD b/prepare/r-ncigraph/PKGBUILD new file mode 100644 index 0000000000..54f3f59de3 --- /dev/null +++ b/prepare/r-ncigraph/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NCIgraph +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pathways from the NCI Pathways Database' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-graph + r-kegggraph + r-r.methodss3 + r-rbgl + r-rcy3 +) +optdepends=( + r-degraph + r-rgraphviz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ncigraph/lilac.py b/prepare/r-ncigraph/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ncigraph/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ncigraph/lilac.yaml b/prepare/r-ncigraph/lilac.yaml new file mode 100644 index 0000000000..2c0be3cb4a --- /dev/null +++ b/prepare/r-ncigraph/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +- r-kegggraph +- r-r.methodss3 +- r-rbgl +- r-rcy3 +update_on: +- regex: NCIgraph_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NCIgraph diff --git a/prepare/r-ncmisc/PKGBUILD b/prepare/r-ncmisc/PKGBUILD new file mode 100644 index 0000000000..e4ba292697 --- /dev/null +++ b/prepare/r-ncmisc/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NCmisc +_pkgver=1.1.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Miscellaneous Functions for Creating Adaptive Functions and Scripts' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-proftools +) +optdepends=( + r-kernsmooth + r-matrix +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ncmisc/lilac.py b/prepare/r-ncmisc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ncmisc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ncmisc/lilac.yaml b/prepare/r-ncmisc/lilac.yaml new file mode 100644 index 0000000000..3d494bfd2c --- /dev/null +++ b/prepare/r-ncmisc/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-proftools +update_on: +- regex: NCmisc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=NCmisc diff --git a/prepare/r-ncrnatools/PKGBUILD b/prepare/r-ncrnatools/PKGBUILD new file mode 100644 index 0000000000..f990b9d5bd --- /dev/null +++ b/prepare/r-ncrnatools/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ncRNAtools +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R toolkit for non-coding RNA' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicranges + r-ggplot2 + r-httr + r-iranges + r-s4vectors + r-xml2 +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ncrnatools/lilac.py b/prepare/r-ncrnatools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ncrnatools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ncrnatools/lilac.yaml b/prepare/r-ncrnatools/lilac.yaml new file mode 100644 index 0000000000..bfbd4f52d9 --- /dev/null +++ b/prepare/r-ncrnatools/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-ggplot2 +- r-httr +- r-iranges +- r-s4vectors +- r-xml2 +update_on: +- regex: ncRNAtools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ncRNAtools diff --git a/prepare/r-ndexr/PKGBUILD b/prepare/r-ndexr/PKGBUILD new file mode 100644 index 0000000000..9309744976 --- /dev/null +++ b/prepare/r-ndexr/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ndexr +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='NDEx R client library' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-httr + r-igraph + r-jsonlite + r-plyr + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ndexr/lilac.py b/prepare/r-ndexr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ndexr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ndexr/lilac.yaml b/prepare/r-ndexr/lilac.yaml new file mode 100644 index 0000000000..1b6ab8705b --- /dev/null +++ b/prepare/r-ndexr/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-httr +- r-igraph +- r-jsonlite +- r-plyr +- r-tidyr +update_on: +- regex: ndexr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ndexr diff --git a/prepare/r-nearbynding/PKGBUILD b/prepare/r-nearbynding/PKGBUILD new file mode 100644 index 0000000000..08d5f4ca69 --- /dev/null +++ b/prepare/r-nearbynding/PKGBUILD @@ -0,0 +1,48 @@ +# system requirements: bedtools (>= 2.28.0), Stereogene (>= v2.22), CapR(>= 1.1.1) +# Maintainer: Guoyi Zhang + +_pkgname=nearBynding +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Discern RNA structure proximal to protein binding' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gplots + r-magrittr + r-matrixstats + r-plyranges + r-r.utils + r-rlang + r-rsamtools + r-rtracklayer + r-s4vectors + r-transport + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.hsapiens.ucsc.hg38.knowngene +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nearbynding/lilac.py b/prepare/r-nearbynding/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nearbynding/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nearbynding/lilac.yaml b/prepare/r-nearbynding/lilac.yaml new file mode 100644 index 0000000000..3365ce4516 --- /dev/null +++ b/prepare/r-nearbynding/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-dplyr +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-gplots +- r-magrittr +- r-matrixstats +- r-plyranges +- r-r.utils +- r-rlang +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-transport +- r-txdb.hsapiens.ucsc.hg19.knowngene +- r-txdb.hsapiens.ucsc.hg38.knowngene +update_on: +- regex: nearBynding_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/nearBynding diff --git a/prepare/r-nebulosa/PKGBUILD b/prepare/r-nebulosa/PKGBUILD new file mode 100644 index 0000000000..6b7ad73b27 --- /dev/null +++ b/prepare/r-nebulosa/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Nebulosa +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-ks + r-patchwork + r-seurat + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocfilecache + r-biocstyle + r-covr + r-dropletutils + r-igraph + r-knitr + r-rmarkdown + r-scater + r-scran + r-seuratobject + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nebulosa/lilac.py b/prepare/r-nebulosa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nebulosa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nebulosa/lilac.yaml b/prepare/r-nebulosa/lilac.yaml new file mode 100644 index 0000000000..6ba366c9ca --- /dev/null +++ b/prepare/r-nebulosa/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-ks +- r-patchwork +- r-seurat +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: Nebulosa_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Nebulosa diff --git a/prepare/r-neighbornet/PKGBUILD b/prepare/r-neighbornet/PKGBUILD new file mode 100644 index 0000000000..35a7fbd39f --- /dev/null +++ b/prepare/r-neighbornet/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NeighborNet +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Neighbor_net analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CCPL:by-nc-sa') +depends=( + r + r-graph +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-neighbornet/lilac.py b/prepare/r-neighbornet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-neighbornet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-neighbornet/lilac.yaml b/prepare/r-neighbornet/lilac.yaml new file mode 100644 index 0000000000..f31ab3eca0 --- /dev/null +++ b/prepare/r-neighbornet/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +update_on: +- regex: NeighborNet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NeighborNet diff --git a/prepare/r-nempi/PKGBUILD b/prepare/r-nempi/PKGBUILD new file mode 100644 index 0000000000..2164187220 --- /dev/null +++ b/prepare/r-nempi/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nempi +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Inferring unobserved perturbations from gene expression data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-e1071 + r-epinem + r-matrixstats + r-mnem + r-naturalsort + r-randomforest +) +optdepends=( + r-biocgenerics + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nempi/lilac.py b/prepare/r-nempi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nempi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nempi/lilac.yaml b/prepare/r-nempi/lilac.yaml new file mode 100644 index 0000000000..341cff788a --- /dev/null +++ b/prepare/r-nempi/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-e1071 +- r-epinem +- r-matrixstats +- r-mnem +- r-naturalsort +- r-randomforest +update_on: +- regex: nempi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/nempi diff --git a/prepare/r-neo4r/PKGBUILD b/prepare/r-neo4r/PKGBUILD new file mode 100644 index 0000000000..cb1b86d329 --- /dev/null +++ b/prepare/r-neo4r/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=neo4r +_pkgver=0.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="A 'Neo4J' Driver" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-attempt + r-data.table + r-glue + r-httr + r-igraph + r-jsonlite + r-magrittr + r-purrr + r-r6 + r-rlang + r-rstudioapi + r-shiny + r-tibble + r-tidyr + r-tidyselect +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-neo4r/lilac.py b/prepare/r-neo4r/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-neo4r/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-neo4r/lilac.yaml b/prepare/r-neo4r/lilac.yaml new file mode 100644 index 0000000000..e1a787d79c --- /dev/null +++ b/prepare/r-neo4r/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-attempt +- r-data.table +- r-glue +- r-httr +- r-igraph +- r-jsonlite +- r-magrittr +- r-purrr +- r-r6 +- r-rlang +- r-rstudioapi +- r-shiny +- r-tibble +- r-tidyr +- r-tidyselect +update_on: +- regex: neo4r_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=neo4r diff --git a/prepare/r-netbiov/PKGBUILD b/prepare/r-netbiov/PKGBUILD new file mode 100644 index 0000000000..54b1444894 --- /dev/null +++ b/prepare/r-netbiov/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=netbiov +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A package for visualizing complex biological network' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-igraph +) +optdepends=( + r-biocgenerics + r-biocstyle + r-matrix + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-netbiov/lilac.py b/prepare/r-netbiov/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-netbiov/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-netbiov/lilac.yaml b/prepare/r-netbiov/lilac.yaml new file mode 100644 index 0000000000..95865e5ad6 --- /dev/null +++ b/prepare/r-netbiov/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +update_on: +- regex: netbiov_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/netbiov diff --git a/prepare/r-netboost/PKGBUILD b/prepare/r-netboost/PKGBUILD new file mode 100644 index 0000000000..34d35814cf --- /dev/null +++ b/prepare/r-netboost/PKGBUILD @@ -0,0 +1,39 @@ +# system requirements: GNU make, Bash, Perl, Gzip +# Maintainer: Guoyi Zhang + +_pkgname=netboost +_pkgver=2.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Network Analysis Supported by Boosting' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-colorspace + r-dynamictreecut + r-impute + r-r.utils + r-rcpp + r-rcppparallel + r-wgcna +) +optdepends=( + r-knitr + r-markdown + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-netboost/lilac.py b/prepare/r-netboost/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-netboost/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-netboost/lilac.yaml b/prepare/r-netboost/lilac.yaml new file mode 100644 index 0000000000..6a344df2df --- /dev/null +++ b/prepare/r-netboost/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colorspace +- r-dynamictreecut +- r-impute +- r-r.utils +- r-rcpp +- r-rcppparallel +- r-wgcna +update_on: +- regex: netboost_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/netboost diff --git a/prepare/r-netboxr/PKGBUILD b/prepare/r-netboxr/PKGBUILD new file mode 100644 index 0000000000..48dfae3d36 --- /dev/null +++ b/prepare/r-netboxr/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=netboxr +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='netboxr' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-clusterprofiler + r-data.table + r-dt + r-gplots + r-igraph + r-jsonlite + r-plyr + r-rcolorbrewer +) +optdepends=( + r-biocstyle + r-cgdsr + r-knitr + r-org.hs.eg.db + r-paxtoolsr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-netboxr/lilac.py b/prepare/r-netboxr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-netboxr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-netboxr/lilac.yaml b/prepare/r-netboxr/lilac.yaml new file mode 100644 index 0000000000..bc367c3a49 --- /dev/null +++ b/prepare/r-netboxr/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clusterprofiler +- r-data.table +- r-dt +- r-gplots +- r-igraph +- r-jsonlite +- r-plyr +- r-rcolorbrewer +update_on: +- regex: netboxr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/netboxr diff --git a/prepare/r-netdx/PKGBUILD b/prepare/r-netdx/PKGBUILD new file mode 100644 index 0000000000..9fecb257aa --- /dev/null +++ b/prepare/r-netdx/PKGBUILD @@ -0,0 +1,59 @@ +# Maintainer: Guoyi Zhang + +_pkgname=netDx +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Network-based patient classifier' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-bigmemory + r-biocfilecache + r-combinat + r-doparallel + r-foreach + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-glmnet + r-httr + r-igraph + r-iranges + r-multiassayexperiment + r-plotrix + r-pracma + r-rappdirs + r-rcolorbrewer + r-reshape2 + r-rocr + r-rtsne + r-s4vectors +) +optdepends=( + r-biocstyle + r-clusterexperiment + r-curatedtcgadata + r-knitr + r-netsmooth + r-rcy3 + r-rmarkdown + r-scater + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-netdx/lilac.py b/prepare/r-netdx/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-netdx/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-netdx/lilac.yaml b/prepare/r-netdx/lilac.yaml new file mode 100644 index 0000000000..c06d3c4047 --- /dev/null +++ b/prepare/r-netdx/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bigmemory +- r-biocfilecache +- r-combinat +- r-doparallel +- r-foreach +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-glmnet +- r-httr +- r-igraph +- r-iranges +- r-multiassayexperiment +- r-plotrix +- r-pracma +- r-rappdirs +- r-rcolorbrewer +- r-reshape2 +- r-rocr +- r-rtsne +- r-s4vectors +update_on: +- regex: netDx_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/netDx diff --git a/prepare/r-nethet/PKGBUILD b/prepare/r-nethet/PKGBUILD new file mode 100644 index 0000000000..1f2adcf826 --- /dev/null +++ b/prepare/r-nethet/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nethet +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A bioconductor package for high-dimensional exploration of biological network heterogeneity' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-compquadform + r-genenet + r-ggm + r-ggplot2 + r-glasso + r-glmnet + r-gsa + r-huge + r-icsnp + r-limma + r-mclust + r-multtest + r-mvtnorm + r-network +) +optdepends=( + r-biocstyle + r-knitr + r-testthat + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nethet/lilac.py b/prepare/r-nethet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nethet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nethet/lilac.yaml b/prepare/r-nethet/lilac.yaml new file mode 100644 index 0000000000..8f21c7a8b9 --- /dev/null +++ b/prepare/r-nethet/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-compquadform +- r-genenet +- r-ggm +- r-ggplot2 +- r-glasso +- r-glmnet +- r-gsa +- r-huge +- r-icsnp +- r-limma +- r-mclust +- r-multtest +- r-mvtnorm +- r-network +update_on: +- regex: nethet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/nethet diff --git a/prepare/r-netomics/PKGBUILD b/prepare/r-netomics/PKGBUILD new file mode 100644 index 0000000000..88a90b270d --- /dev/null +++ b/prepare/r-netomics/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=netOmics +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multi-Omics (time-course) network-based integration and interpretation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-dplyr + r-ggplot2 + r-go.db + r-gprofiler2 + r-igraph + r-magrittr + r-minet + r-purrr + r-randomwalkrestartmh + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-mixomics + r-rmarkdown + r-testthat + r-tidyverse + r-timeomics +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-netomics/lilac.py b/prepare/r-netomics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-netomics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-netomics/lilac.yaml b/prepare/r-netomics/lilac.yaml new file mode 100644 index 0000000000..c629ac1a37 --- /dev/null +++ b/prepare/r-netomics/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-dplyr +- r-ggplot2 +- r-go.db +- r-gprofiler2 +- r-igraph +- r-magrittr +- r-minet +- r-purrr +- r-randomwalkrestartmh +- r-tibble +- r-tidyr +update_on: +- regex: netOmics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/netOmics diff --git a/prepare/r-netpathminer/PKGBUILD b/prepare/r-netpathminer/PKGBUILD new file mode 100644 index 0000000000..bb7c4a1f86 --- /dev/null +++ b/prepare/r-netpathminer/PKGBUILD @@ -0,0 +1,36 @@ +# system requirements: libxml2, libSBML (>= 5.5) +# Maintainer: Guoyi Zhang + +_pkgname=NetPathMiner +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='NetPathMiner for Biological Network Construction, Path Mining and Visualization' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-igraph +) +optdepends=( + r-biocstyle + r-graph + r-knitr + r-rbiopaxparser + r-rcurl + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-netpathminer/lilac.py b/prepare/r-netpathminer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-netpathminer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-netpathminer/lilac.yaml b/prepare/r-netpathminer/lilac.yaml new file mode 100644 index 0000000000..4688df1069 --- /dev/null +++ b/prepare/r-netpathminer/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +update_on: +- regex: NetPathMiner_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NetPathMiner diff --git a/prepare/r-netprior/PKGBUILD b/prepare/r-netprior/PKGBUILD new file mode 100644 index 0000000000..1cafa89d85 --- /dev/null +++ b/prepare/r-netprior/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=netprioR +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A model for network-based prioritisation of genes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-doparallel + r-dplyr + r-foreach + r-ggplot2 + r-gridextra + r-proc + r-sparsemvn +) +optdepends=( + r-biocstyle + r-knitr + r-pander +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-netprior/lilac.py b/prepare/r-netprior/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-netprior/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-netprior/lilac.yaml b/prepare/r-netprior/lilac.yaml new file mode 100644 index 0000000000..6e94e5901e --- /dev/null +++ b/prepare/r-netprior/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-dplyr +- r-foreach +- r-ggplot2 +- r-gridextra +- r-proc +- r-sparsemvn +update_on: +- regex: netprioR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/netprioR diff --git a/prepare/r-netrep/PKGBUILD b/prepare/r-netrep/PKGBUILD new file mode 100644 index 0000000000..d8a7e9d580 --- /dev/null +++ b/prepare/r-netrep/PKGBUILD @@ -0,0 +1,41 @@ +# system requirements: A compiler with C++11 support for the threadlibrary, Requires Rtools >= 33 (i.e. R >= 3.3.0) to build onWindows. +# Maintainer: Guoyi Zhang + +_pkgname=NetRep +_pkgver=1.2.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Permutation Testing Network Module Preservation Across Datasets' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-bh + r-foreach + r-rcolorbrewer + r-rcpp + r-rcpparmadillo + r-rhpcblasctl + r-statmod +) +optdepends=( + r-bigmemory + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-netrep/lilac.py b/prepare/r-netrep/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-netrep/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-netrep/lilac.yaml b/prepare/r-netrep/lilac.yaml new file mode 100644 index 0000000000..86c35bbed8 --- /dev/null +++ b/prepare/r-netrep/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-bh +- r-foreach +- r-rcolorbrewer +- r-rcpp +- r-rcpparmadillo +- r-rhpcblasctl +- r-statmod +update_on: +- regex: NetRep_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=NetRep diff --git a/prepare/r-netresponse/PKGBUILD b/prepare/r-netresponse/PKGBUILD new file mode 100644 index 0000000000..1568c503ea --- /dev/null +++ b/prepare/r-netresponse/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=netresponse +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functional Network Analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocstyle + r-dmt + r-ggplot2 + r-graph + r-igraph + r-mclust + r-minet + r-plyr + r-qvalue + r-rcolorbrewer + r-reshape2 + r-rgraphviz + r-rmarkdown +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-netresponse/lilac.py b/prepare/r-netresponse/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-netresponse/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-netresponse/lilac.yaml b/prepare/r-netresponse/lilac.yaml new file mode 100644 index 0000000000..fcf82e124c --- /dev/null +++ b/prepare/r-netresponse/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocstyle +- r-dmt +- r-ggplot2 +- r-graph +- r-igraph +- r-mclust +- r-minet +- r-plyr +- r-qvalue +- r-rcolorbrewer +- r-reshape2 +- r-rgraphviz +- r-rmarkdown +update_on: +- regex: netresponse_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/netresponse diff --git a/prepare/r-netsam/PKGBUILD b/prepare/r-netsam/PKGBUILD new file mode 100644 index 0000000000..4572919d20 --- /dev/null +++ b/prepare/r-netsam/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NetSAM +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Network Seriation And Modularization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-annotationdbi + r-biomart + r-dbi + r-doparallel + r-foreach + r-go.db + r-igraph + r-r2html + r-seriation + r-wgcna +) +optdepends=( + r-biocgenerics + r-knitr + r-markdown + r-org.at.tair.db + r-org.ce.eg.db + r-org.cf.eg.db + r-org.dm.eg.db + r-org.dr.eg.db + r-org.hs.eg.db + r-org.mm.eg.db + r-org.rn.eg.db + r-org.sc.sgd.db + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-netsam/lilac.py b/prepare/r-netsam/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-netsam/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-netsam/lilac.yaml b/prepare/r-netsam/lilac.yaml new file mode 100644 index 0000000000..04d594241e --- /dev/null +++ b/prepare/r-netsam/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biomart +- r-dbi +- r-doparallel +- r-foreach +- r-go.db +- r-igraph +- r-r2html +- r-seriation +- r-wgcna +update_on: +- regex: NetSAM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NetSAM diff --git a/prepare/r-netsmooth/PKGBUILD b/prepare/r-netsmooth/PKGBUILD new file mode 100644 index 0000000000..a5b237f8c3 --- /dev/null +++ b/prepare/r-netsmooth/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=netSmooth +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Network smoothing for scRNAseq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-clusterexperiment + r-data.table + r-delayedarray + r-entropy + r-hdf5array + r-scater + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocparallel + r-biocstyle + r-biomart + r-ggplot2 + r-igraph + r-knitr + r-nmi + r-pheatmap + r-rmarkdown + r-rtsne + r-stringdb + r-testthat + r-uwot +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-netsmooth/lilac.py b/prepare/r-netsmooth/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-netsmooth/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-netsmooth/lilac.yaml b/prepare/r-netsmooth/lilac.yaml new file mode 100644 index 0000000000..8707cafd7c --- /dev/null +++ b/prepare/r-netsmooth/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clusterexperiment +- r-data.table +- r-delayedarray +- r-entropy +- r-hdf5array +- r-scater +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: netSmooth_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/netSmooth diff --git a/prepare/r-network/PKGBUILD b/prepare/r-network/PKGBUILD new file mode 100644 index 0000000000..e034db74e5 --- /dev/null +++ b/prepare/r-network/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=network +_pkgver=1.17.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Classes for Relational Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-magrittr + r-statnet.common + r-tibble +) +optdepends=( + r-covr + r-sna + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-network/lilac.py b/prepare/r-network/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-network/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-network/lilac.yaml b/prepare/r-network/lilac.yaml new file mode 100644 index 0000000000..1c985162cd --- /dev/null +++ b/prepare/r-network/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-magrittr +- r-statnet.common +- r-tibble +update_on: +- regex: network_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=network diff --git a/prepare/r-networkbma/PKGBUILD b/prepare/r-networkbma/PKGBUILD new file mode 100644 index 0000000000..6e8cfe2ff5 --- /dev/null +++ b/prepare/r-networkbma/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: liblapack-dev +# Maintainer: Guoyi Zhang + +_pkgname=networkBMA +_pkgver=2.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Regression-based network inference using Bayesian Model Averaging' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bh + r-bma + r-leaps + r-rcpp + r-rcpparmadillo + r-rcppeigen +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-networkbma/lilac.py b/prepare/r-networkbma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-networkbma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-networkbma/lilac.yaml b/prepare/r-networkbma/lilac.yaml new file mode 100644 index 0000000000..6df710a7f7 --- /dev/null +++ b/prepare/r-networkbma/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-bma +- r-leaps +- r-rcpp +- r-rcpparmadillo +- r-rcppeigen +update_on: +- regex: networkBMA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/networkBMA diff --git a/prepare/r-networkd3/PKGBUILD b/prepare/r-networkd3/PKGBUILD new file mode 100644 index 0000000000..a106539e01 --- /dev/null +++ b/prepare/r-networkd3/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=networkD3 +_pkgver=0.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='D3 JavaScript Network Graphs from R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-htmlwidgets + r-igraph + r-magrittr +) +optdepends=( + r-htmltools + r-jsonlite + r-knitr + r-shiny +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-networkd3/lilac.py b/prepare/r-networkd3/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-networkd3/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-networkd3/lilac.yaml b/prepare/r-networkd3/lilac.yaml new file mode 100644 index 0000000000..fe605c5474 --- /dev/null +++ b/prepare/r-networkd3/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmlwidgets +- r-igraph +- r-magrittr +update_on: +- regex: networkD3_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=networkD3 diff --git a/prepare/r-neuca/PKGBUILD b/prepare/r-neuca/PKGBUILD new file mode 100644 index 0000000000..c3dda8b76e --- /dev/null +++ b/prepare/r-neuca/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NeuCA +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='NEUral network-based single-Cell Annotation tool' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-e1071 + r-keras + r-limma + r-singlecellexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-networkd3 + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-neuca/lilac.py b/prepare/r-neuca/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-neuca/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-neuca/lilac.yaml b/prepare/r-neuca/lilac.yaml new file mode 100644 index 0000000000..b55c0fe050 --- /dev/null +++ b/prepare/r-neuca/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-e1071 +- r-keras +- r-limma +- r-singlecellexperiment +update_on: +- regex: NeuCA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NeuCA diff --git a/prepare/r-newwave/PKGBUILD b/prepare/r-newwave/PKGBUILD new file mode 100644 index 0000000000..db1b821bcf --- /dev/null +++ b/prepare/r-newwave/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NewWave +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Negative binomial model for scRNA-seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocsingular + r-delayedarray + r-irlba + r-sharedobject + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-ggplot2 + r-knitr + r-mclust + r-rcpp + r-rmarkdown + r-rtsne + r-splatter + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-newwave/lilac.py b/prepare/r-newwave/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-newwave/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-newwave/lilac.yaml b/prepare/r-newwave/lilac.yaml new file mode 100644 index 0000000000..6846ee7d8c --- /dev/null +++ b/prepare/r-newwave/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocsingular +- r-delayedarray +- r-irlba +- r-sharedobject +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: NewWave_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NewWave diff --git a/prepare/r-ngsreports/PKGBUILD b/prepare/r-ngsreports/PKGBUILD new file mode 100644 index 0000000000..ebb5e833f2 --- /dev/null +++ b/prepare/r-ngsreports/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ngsReports +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Load FastqQC reports and other NGS related files' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-biocgenerics + r-biostrings + r-checkmate + r-dplyr + r-dt + r-forcats + r-ggdendro + r-ggplot2 + r-lifecycle + r-lubridate + r-pander + r-plotly + r-readr + r-reshape2 + r-rmarkdown + r-scales + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-zoo +) +optdepends=( + r-biocstyle + r-cairo + r-knitr + r-testthat + r-truncnorm +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ngsreports/lilac.py b/prepare/r-ngsreports/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ngsreports/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ngsreports/lilac.yaml b/prepare/r-ngsreports/lilac.yaml new file mode 100644 index 0000000000..58ba68a4d1 --- /dev/null +++ b/prepare/r-ngsreports/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-checkmate +- r-dplyr +- r-dt +- r-forcats +- r-ggdendro +- r-ggplot2 +- r-lifecycle +- r-lubridate +- r-pander +- r-plotly +- r-readr +- r-reshape2 +- r-rmarkdown +- r-scales +- r-stringr +- r-tibble +- r-tidyr +- r-tidyselect +- r-zoo +update_on: +- regex: ngsReports_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ngsReports diff --git a/prepare/r-nhpoisson/PKGBUILD b/prepare/r-nhpoisson/PKGBUILD new file mode 100644 index 0000000000..e5a9b0824e --- /dev/null +++ b/prepare/r-nhpoisson/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NHPoisson +_pkgver=3.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Modelling and Validation of Non Homogeneous Poisson Processes' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-car +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nhpoisson/lilac.py b/prepare/r-nhpoisson/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nhpoisson/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nhpoisson/lilac.yaml b/prepare/r-nhpoisson/lilac.yaml new file mode 100644 index 0000000000..5f864561d1 --- /dev/null +++ b/prepare/r-nhpoisson/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-car +update_on: +- regex: NHPoisson_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=NHPoisson diff --git a/prepare/r-nistunits/PKGBUILD b/prepare/r-nistunits/PKGBUILD new file mode 100644 index 0000000000..8fa48a350a --- /dev/null +++ b/prepare/r-nistunits/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NISTunits +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fundamental Physical Constants and Unit Conversions from NIST' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nistunits/lilac.py b/prepare/r-nistunits/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nistunits/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nistunits/lilac.yaml b/prepare/r-nistunits/lilac.yaml new file mode 100644 index 0000000000..5481e2931c --- /dev/null +++ b/prepare/r-nistunits/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: NISTunits_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=NISTunits diff --git a/prepare/r-nleqslv/PKGBUILD b/prepare/r-nleqslv/PKGBUILD new file mode 100644 index 0000000000..b07b978fbb --- /dev/null +++ b/prepare/r-nleqslv/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nleqslv +_pkgver=3.3.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Solve Systems of Nonlinear Equations' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nleqslv/lilac.py b/prepare/r-nleqslv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nleqslv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nleqslv/lilac.yaml b/prepare/r-nleqslv/lilac.yaml new file mode 100644 index 0000000000..4fb342db0c --- /dev/null +++ b/prepare/r-nleqslv/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: nleqslv_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=nleqslv diff --git a/prepare/r-nloptr/PKGBUILD b/prepare/r-nloptr/PKGBUILD new file mode 100644 index 0000000000..87eff145e3 --- /dev/null +++ b/prepare/r-nloptr/PKGBUILD @@ -0,0 +1,36 @@ +# system requirements: A system installation of NLopt >= 2.4.0 (withheaders) will be used if available. +# Maintainer: Guoyi Zhang + +_pkgname=nloptr +_pkgver=1.2.2.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Interface to NLopt' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +optdepends=( + r-inline + r-knitr + r-rmarkdown + r-testthat +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nloptr/lilac.py b/prepare/r-nloptr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nloptr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nloptr/lilac.yaml b/prepare/r-nloptr/lilac.yaml new file mode 100644 index 0000000000..e39d0813c6 --- /dev/null +++ b/prepare/r-nloptr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: nloptr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=nloptr diff --git a/prepare/r-nlp/PKGBUILD b/prepare/r-nlp/PKGBUILD new file mode 100644 index 0000000000..0fee61d2ab --- /dev/null +++ b/prepare/r-nlp/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NLP +_pkgver=0.2-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Natural Language Processing Infrastructure' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-cleannlp + r-spacyr + r-udpipe +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nlp/lilac.py b/prepare/r-nlp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nlp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nlp/lilac.yaml b/prepare/r-nlp/lilac.yaml new file mode 100644 index 0000000000..3555516c60 --- /dev/null +++ b/prepare/r-nlp/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: NLP_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=NLP diff --git a/prepare/r-nls2/PKGBUILD b/prepare/r-nls2/PKGBUILD new file mode 100644 index 0000000000..9a2f34f3e5 --- /dev/null +++ b/prepare/r-nls2/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nls2 +_pkgver=0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Non-linear regression with brute force' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-proto +) +optdepends=( + r-nlstools +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nls2/lilac.py b/prepare/r-nls2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nls2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nls2/lilac.yaml b/prepare/r-nls2/lilac.yaml new file mode 100644 index 0000000000..7308adeadb --- /dev/null +++ b/prepare/r-nls2/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-proto +update_on: +- regex: nls2_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=nls2 diff --git a/prepare/r-nmf/PKGBUILD b/prepare/r-nmf/PKGBUILD new file mode 100644 index 0000000000..5d7b0167a3 --- /dev/null +++ b/prepare/r-nmf/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NMF +_pkgver=0.23.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Algorithms and Framework for Nonnegative Matrix Factorization (NMF)' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocmanager + r-colorspace + r-digest + r-doparallel + r-foreach + r-ggplot2 + r-gridbase + r-pkgmaker + r-rcolorbrewer + r-registry + r-reshape2 + r-rngtools + r-stringr +) +optdepends=( + r-bibtex + r-bigmemory + r-corpcor + r-devtools + r-dompi + r-fastica + r-knitr + r-mail + r-runit + r-synchronicity + r-xtable +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nmf/lilac.py b/prepare/r-nmf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nmf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nmf/lilac.yaml b/prepare/r-nmf/lilac.yaml new file mode 100644 index 0000000000..e8d9eacc8d --- /dev/null +++ b/prepare/r-nmf/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocmanager +- r-colorspace +- r-digest +- r-doparallel +- r-foreach +- r-ggplot2 +- r-gridbase +- r-pkgmaker +- r-rcolorbrewer +- r-registry +- r-reshape2 +- r-rngtools +- r-stringr +update_on: +- regex: NMF_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=NMF diff --git a/prepare/r-nmi/PKGBUILD b/prepare/r-nmi/PKGBUILD new file mode 100644 index 0000000000..3cf85fd5cf --- /dev/null +++ b/prepare/r-nmi/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NMI +_pkgver=2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Normalized Mutual Information of Community Structure in Network' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nmi/lilac.py b/prepare/r-nmi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nmi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nmi/lilac.yaml b/prepare/r-nmi/lilac.yaml new file mode 100644 index 0000000000..927f03ec28 --- /dev/null +++ b/prepare/r-nmi/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: NMI_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=NMI diff --git a/prepare/r-nnlasso/PKGBUILD b/prepare/r-nnlasso/PKGBUILD new file mode 100644 index 0000000000..bd015f1b3e --- /dev/null +++ b/prepare/r-nnlasso/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nnlasso +_pkgver=0.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Non-Negative Lasso and Elastic Net Penalized Generalized Linear Models' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nnlasso/lilac.py b/prepare/r-nnlasso/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nnlasso/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nnlasso/lilac.yaml b/prepare/r-nnlasso/lilac.yaml new file mode 100644 index 0000000000..89d85e3458 --- /dev/null +++ b/prepare/r-nnlasso/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: nnlasso_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=nnlasso diff --git a/prepare/r-nnls/PKGBUILD b/prepare/r-nnls/PKGBUILD new file mode 100644 index 0000000000..2cb0a413e7 --- /dev/null +++ b/prepare/r-nnls/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nnls +_pkgver=1.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The Lawson-Hanson algorithm for non-negative least squares (NNLS)' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nnls/lilac.py b/prepare/r-nnls/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nnls/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nnls/lilac.yaml b/prepare/r-nnls/lilac.yaml new file mode 100644 index 0000000000..b339cef2ba --- /dev/null +++ b/prepare/r-nnls/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: nnls_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=nnls diff --git a/prepare/r-nnnorm/PKGBUILD b/prepare/r-nnnorm/PKGBUILD new file mode 100644 index 0000000000..936e16068a --- /dev/null +++ b/prepare/r-nnnorm/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nnNorm +_pkgver=2.58.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Spatial and intensity based normalization of cDNA microarray data based on robust neural nets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-marray +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nnnorm/lilac.py b/prepare/r-nnnorm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nnnorm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nnnorm/lilac.yaml b/prepare/r-nnnorm/lilac.yaml new file mode 100644 index 0000000000..8239ec328c --- /dev/null +++ b/prepare/r-nnnorm/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-marray +update_on: +- regex: nnNorm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/nnNorm diff --git a/prepare/r-nntensor/PKGBUILD b/prepare/r-nntensor/PKGBUILD new file mode 100644 index 0000000000..f327be3d65 --- /dev/null +++ b/prepare/r-nntensor/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nnTensor +_pkgver=1.1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Non-Negative Tensor Decomposition' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-fields + r-ggplot2 + r-plot3d + r-rtensor + r-tagcloud +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nntensor/lilac.py b/prepare/r-nntensor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nntensor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nntensor/lilac.yaml b/prepare/r-nntensor/lilac.yaml new file mode 100644 index 0000000000..8a43216e0b --- /dev/null +++ b/prepare/r-nntensor/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fields +- r-ggplot2 +- r-plot3d +- r-rtensor +- r-tagcloud +update_on: +- regex: nnTensor_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=nnTensor diff --git a/prepare/r-noiseq/PKGBUILD b/prepare/r-noiseq/PKGBUILD new file mode 100644 index 0000000000..e673380802 --- /dev/null +++ b/prepare/r-noiseq/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NOISeq +_pkgver=2.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Exploratory analysis and differential expression for RNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-noiseq/lilac.py b/prepare/r-noiseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-noiseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-noiseq/lilac.yaml b/prepare/r-noiseq/lilac.yaml new file mode 100644 index 0000000000..0be320962a --- /dev/null +++ b/prepare/r-noiseq/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: NOISeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NOISeq diff --git a/prepare/r-nondetects/PKGBUILD b/prepare/r-nondetects/PKGBUILD new file mode 100644 index 0000000000..81442492ad --- /dev/null +++ b/prepare/r-nondetects/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nondetects +_pkgver=2.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Non-detects in qPCR data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-arm + r-biobase + r-htqpcr + r-limma + r-mvtnorm +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nondetects/lilac.py b/prepare/r-nondetects/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nondetects/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nondetects/lilac.yaml b/prepare/r-nondetects/lilac.yaml new file mode 100644 index 0000000000..f1b3eb37ab --- /dev/null +++ b/prepare/r-nondetects/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-arm +- r-biobase +- r-htqpcr +- r-limma +- r-mvtnorm +update_on: +- regex: nondetects_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/nondetects diff --git a/prepare/r-nor1mix/PKGBUILD b/prepare/r-nor1mix/PKGBUILD new file mode 100644 index 0000000000..c32305c4d7 --- /dev/null +++ b/prepare/r-nor1mix/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nor1mix +_pkgver=1.3-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Normal aka Gaussian (1-d) Mixture Models (S3 Classes and Methods)' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-cluster +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nor1mix/lilac.py b/prepare/r-nor1mix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nor1mix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nor1mix/lilac.yaml b/prepare/r-nor1mix/lilac.yaml new file mode 100644 index 0000000000..fc1eb048f5 --- /dev/null +++ b/prepare/r-nor1mix/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: nor1mix_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=nor1mix diff --git a/prepare/r-norce/PKGBUILD b/prepare/r-norce/PKGBUILD new file mode 100644 index 0000000000..2287b14ced --- /dev/null +++ b/prepare/r-norce/PKGBUILD @@ -0,0 +1,73 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NoRCE +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-biomart + r-dbi + r-dbplyr + r-dplyr + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-go.db + r-igraph + r-iranges + r-keggrest + r-png + r-rcurl + r-reactome.db + r-readr + r-reshape2 + r-rsqlite + r-rtracklayer + r-rwikipathways + r-s4vectors + r-summarizedexperiment + r-tidyr + r-zlibbioc +) +optdepends=( + r-biocgenerics + r-knitr + r-markdown + r-methods + r-org.ce.eg.db + r-org.dm.eg.db + r-org.dr.eg.db + r-org.hs.eg.db + r-org.mm.eg.db + r-org.rn.eg.db + r-org.sc.sgd.db + r-rmarkdown + r-testthat + r-txdb.celegans.ucsc.ce11.refgene + r-txdb.dmelanogaster.ucsc.dm6.ensgene + r-txdb.drerio.ucsc.danrer10.refgene + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.hsapiens.ucsc.hg38.knowngene + r-txdb.mmusculus.ucsc.mm10.knowngene + r-txdb.rnorvegicus.ucsc.rn6.refgene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-norce/lilac.py b/prepare/r-norce/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-norce/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-norce/lilac.yaml b/prepare/r-norce/lilac.yaml new file mode 100644 index 0000000000..e023e33449 --- /dev/null +++ b/prepare/r-norce/lilac.yaml @@ -0,0 +1,33 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biomart +- r-dbi +- r-dbplyr +- r-dplyr +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-go.db +- r-igraph +- r-iranges +- r-keggrest +- r-png +- r-rcurl +- r-reactome.db +- r-readr +- r-reshape2 +- r-rsqlite +- r-rtracklayer +- r-rwikipathways +- r-s4vectors +- r-summarizedexperiment +- r-tidyr +- r-zlibbioc +update_on: +- regex: NoRCE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NoRCE diff --git a/prepare/r-norm/PKGBUILD b/prepare/r-norm/PKGBUILD new file mode 100644 index 0000000000..758db3b02e --- /dev/null +++ b/prepare/r-norm/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=norm +_pkgver=1.0-9.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of multivariate normal datasets with missing values' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('custom') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-norm/lilac.py b/prepare/r-norm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-norm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-norm/lilac.yaml b/prepare/r-norm/lilac.yaml new file mode 100644 index 0000000000..9f3f60d254 --- /dev/null +++ b/prepare/r-norm/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: norm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=norm diff --git a/prepare/r-normalize450k/PKGBUILD b/prepare/r-normalize450k/PKGBUILD new file mode 100644 index 0000000000..e8425e089f --- /dev/null +++ b/prepare/r-normalize450k/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=normalize450K +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Preprocessing of Illumina Infinium 450K data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-biobase + r-illuminaio + r-quadprog +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-normalize450k/lilac.py b/prepare/r-normalize450k/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-normalize450k/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-normalize450k/lilac.yaml b/prepare/r-normalize450k/lilac.yaml new file mode 100644 index 0000000000..0c1f84806c --- /dev/null +++ b/prepare/r-normalize450k/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-illuminaio +- r-quadprog +update_on: +- regex: normalize450K_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/normalize450K diff --git a/prepare/r-normalyzerde/PKGBUILD b/prepare/r-normalyzerde/PKGBUILD new file mode 100644 index 0000000000..9be545dcdf --- /dev/null +++ b/prepare/r-normalyzerde/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NormalyzerDE +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Evaluation of normalization methods and calculation of differential expression analysis statistics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ape + r-biobase + r-car + r-ggforce + r-ggplot2 + r-limma + r-matrixstats + r-preprocesscore + r-raster + r-rcmdrmisc + r-summarizedexperiment + r-vsn +) +optdepends=( + r-biocstyle + r-hexbin + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-normalyzerde/lilac.py b/prepare/r-normalyzerde/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-normalyzerde/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-normalyzerde/lilac.yaml b/prepare/r-normalyzerde/lilac.yaml new file mode 100644 index 0000000000..fc8d60557b --- /dev/null +++ b/prepare/r-normalyzerde/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-biobase +- r-car +- r-ggforce +- r-ggplot2 +- r-limma +- r-matrixstats +- r-preprocesscore +- r-raster +- r-rcmdrmisc +- r-summarizedexperiment +- r-vsn +update_on: +- regex: NormalyzerDE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NormalyzerDE diff --git a/prepare/r-normqpcr/PKGBUILD b/prepare/r-normqpcr/PKGBUILD new file mode 100644 index 0000000000..b06fa3d1b7 --- /dev/null +++ b/prepare/r-normqpcr/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NormqPCR +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for normalisation of RT-qPCR data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-qpcr + r-rcolorbrewer + r-readqpcr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-normqpcr/lilac.py b/prepare/r-normqpcr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-normqpcr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-normqpcr/lilac.yaml b/prepare/r-normqpcr/lilac.yaml new file mode 100644 index 0000000000..80c53e2a79 --- /dev/null +++ b/prepare/r-normqpcr/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-qpcr +- r-rcolorbrewer +- r-readqpcr +update_on: +- regex: NormqPCR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NormqPCR diff --git a/prepare/r-normr/PKGBUILD b/prepare/r-normr/PKGBUILD new file mode 100644 index 0000000000..3665c0bbbe --- /dev/null +++ b/prepare/r-normr/PKGBUILD @@ -0,0 +1,41 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=normr +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Normalization and difference calling in ChIP-seq data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bamsignals + r-genomeinfodb + r-genomicranges + r-iranges + r-qvalue + r-rcpp + r-rtracklayer +) +optdepends=( + r-biocparallel + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-normr/lilac.py b/prepare/r-normr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-normr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-normr/lilac.yaml b/prepare/r-normr/lilac.yaml new file mode 100644 index 0000000000..0198caa02a --- /dev/null +++ b/prepare/r-normr/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bamsignals +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-qvalue +- r-rcpp +- r-rtracklayer +update_on: +- regex: normr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/normr diff --git a/prepare/r-nortest/PKGBUILD b/prepare/r-nortest/PKGBUILD new file mode 100644 index 0000000000..8ce175adfe --- /dev/null +++ b/prepare/r-nortest/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nortest +_pkgver=1.0-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tests for Normality' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nortest/lilac.py b/prepare/r-nortest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nortest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nortest/lilac.yaml b/prepare/r-nortest/lilac.yaml new file mode 100644 index 0000000000..e4def23008 --- /dev/null +++ b/prepare/r-nortest/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: nortest_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=nortest diff --git a/prepare/r-nozzle.r1/PKGBUILD b/prepare/r-nozzle.r1/PKGBUILD new file mode 100644 index 0000000000..492c5c4c39 --- /dev/null +++ b/prepare/r-nozzle.r1/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Nozzle.R1 +_pkgver=1.1-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Nozzle Reports' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nozzle.r1/lilac.py b/prepare/r-nozzle.r1/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nozzle.r1/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nozzle.r1/lilac.yaml b/prepare/r-nozzle.r1/lilac.yaml new file mode 100644 index 0000000000..e6ef1b25bb --- /dev/null +++ b/prepare/r-nozzle.r1/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Nozzle.R1_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Nozzle.R1 diff --git a/prepare/r-np/PKGBUILD b/prepare/r-np/PKGBUILD new file mode 100644 index 0000000000..5bf4456f1b --- /dev/null +++ b/prepare/r-np/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=np +_pkgver=0.60-11 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Nonparametric Kernel Smoothing Methods for Mixed Data Types' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-cubature + r-quadprog + r-quantreg +) +optdepends=( + r-mass +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-np/lilac.py b/prepare/r-np/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-np/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-np/lilac.yaml b/prepare/r-np/lilac.yaml new file mode 100644 index 0000000000..92858e9ffa --- /dev/null +++ b/prepare/r-np/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cubature +- r-quadprog +- r-quantreg +update_on: +- regex: np_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=np diff --git a/prepare/r-nparc/PKGBUILD b/prepare/r-nparc/PKGBUILD new file mode 100644 index 0000000000..337e234b6b --- /dev/null +++ b/prepare/r-nparc/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NPARC +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Non-parametric analysis of response curves for thermal proteome profiling experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-broom + r-dplyr + r-magrittr + r-rlang + r-tidyr +) +optdepends=( + r-biocstyle + r-devtools + r-ggplot2 + r-knitr + r-rmarkdown + r-rprojroot + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nparc/lilac.py b/prepare/r-nparc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nparc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nparc/lilac.yaml b/prepare/r-nparc/lilac.yaml new file mode 100644 index 0000000000..d7648a272c --- /dev/null +++ b/prepare/r-nparc/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-broom +- r-dplyr +- r-magrittr +- r-rlang +- r-tidyr +update_on: +- regex: NPARC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NPARC diff --git a/prepare/r-npgsea/PKGBUILD b/prepare/r-npgsea/PKGBUILD new file mode 100644 index 0000000000..8e4c7c50f2 --- /dev/null +++ b/prepare/r-npgsea/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=npGSEA +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-gseabase +) +optdepends=( + r-all + r-biocstyle + r-genefilter + r-hgu95av2.db + r-limma + r-reportingtools +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-npgsea/lilac.py b/prepare/r-npgsea/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-npgsea/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-npgsea/lilac.yaml b/prepare/r-npgsea/lilac.yaml new file mode 100644 index 0000000000..979e329d49 --- /dev/null +++ b/prepare/r-npgsea/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-gseabase +update_on: +- regex: npGSEA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/npGSEA diff --git a/prepare/r-nsga2r/PKGBUILD b/prepare/r-nsga2r/PKGBUILD new file mode 100644 index 0000000000..730bc211bb --- /dev/null +++ b/prepare/r-nsga2r/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nsga2R +_pkgver=1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Elitist Non-dominated Sorting Genetic Algorithm based on R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-mco +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nsga2r/lilac.py b/prepare/r-nsga2r/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nsga2r/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nsga2r/lilac.yaml b/prepare/r-nsga2r/lilac.yaml new file mode 100644 index 0000000000..1f438ea49d --- /dev/null +++ b/prepare/r-nsga2r/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mco +update_on: +- regex: nsga2R_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=nsga2R diff --git a/prepare/r-nsprcomp/PKGBUILD b/prepare/r-nsprcomp/PKGBUILD new file mode 100644 index 0000000000..67a1033e67 --- /dev/null +++ b/prepare/r-nsprcomp/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nsprcomp +_pkgver=0.5.1-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Non-Negative and Sparse PCA' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-mass + r-roxygen2 + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nsprcomp/lilac.py b/prepare/r-nsprcomp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nsprcomp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nsprcomp/lilac.yaml b/prepare/r-nsprcomp/lilac.yaml new file mode 100644 index 0000000000..2118883b87 --- /dev/null +++ b/prepare/r-nsprcomp/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: nsprcomp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=nsprcomp diff --git a/prepare/r-ntw/PKGBUILD b/prepare/r-ntw/PKGBUILD new file mode 100644 index 0000000000..11c12906e2 --- /dev/null +++ b/prepare/r-ntw/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NTW +_pkgver=1.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Predict gene network using an Ordinary Differential Equation (ODE) based method' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-mvtnorm +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ntw/lilac.py b/prepare/r-ntw/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ntw/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ntw/lilac.yaml b/prepare/r-ntw/lilac.yaml new file mode 100644 index 0000000000..22666a7511 --- /dev/null +++ b/prepare/r-ntw/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mvtnorm +update_on: +- regex: NTW_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NTW diff --git a/prepare/r-nucleosim/PKGBUILD b/prepare/r-nucleosim/PKGBUILD new file mode 100644 index 0000000000..7723ee04e7 --- /dev/null +++ b/prepare/r-nucleosim/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nucleoSim +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generate synthetic nucleosome maps' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-iranges + r-s4vectors +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nucleosim/lilac.py b/prepare/r-nucleosim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nucleosim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nucleosim/lilac.yaml b/prepare/r-nucleosim/lilac.yaml new file mode 100644 index 0000000000..b031da962a --- /dev/null +++ b/prepare/r-nucleosim/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-iranges +- r-s4vectors +update_on: +- regex: nucleoSim_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/nucleoSim diff --git a/prepare/r-nucler/PKGBUILD b/prepare/r-nucler/PKGBUILD new file mode 100644 index 0000000000..332b3f2fb6 --- /dev/null +++ b/prepare/r-nucler/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nucleR +_pkgver=2.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Nucleosome positioning package for R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-biocgenerics + r-biostrings + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-magrittr + r-rsamtools + r-s4vectors + r-shortread +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nucler/lilac.py b/prepare/r-nucler/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nucler/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nucler/lilac.yaml b/prepare/r-nucler/lilac.yaml new file mode 100644 index 0000000000..c000578817 --- /dev/null +++ b/prepare/r-nucler/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biostrings +- r-dplyr +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-magrittr +- r-rsamtools +- r-s4vectors +- r-shortread +update_on: +- regex: nucleR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/nucleR diff --git a/prepare/r-nucpos/PKGBUILD b/prepare/r-nucpos/PKGBUILD new file mode 100644 index 0000000000..b28f157f00 --- /dev/null +++ b/prepare/r-nucpos/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nuCpos +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package for prediction of nucleosome positions' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r +) +optdepends=( + r-biostrings + r-nupop + r-testthat +) +makedepends=( + gcc-fortran +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nucpos/lilac.py b/prepare/r-nucpos/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nucpos/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nucpos/lilac.yaml b/prepare/r-nucpos/lilac.yaml new file mode 100644 index 0000000000..330fbe0473 --- /dev/null +++ b/prepare/r-nucpos/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: nuCpos_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/nuCpos diff --git a/prepare/r-nullranges/PKGBUILD b/prepare/r-nullranges/PKGBUILD new file mode 100644 index 0000000000..b8f38d3bca --- /dev/null +++ b/prepare/r-nullranges/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=nullranges +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generation of null ranges via bootstrapping or covariate matching' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-ggridges + r-interactionset + r-iranges + r-ks + r-plyranges + r-progress + r-rlang + r-s4vectors + r-scales + r-speedglm +) +optdepends=( + r-annotationhub + r-cobalt + r-dnacopy + r-ensdb.hsapiens.v86 + r-excluderanges + r-knitr + r-magrittr + r-microbenchmark + r-nullrangesdata + r-patchwork + r-plotgardener + r-rcpphmm + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nullranges/lilac.py b/prepare/r-nullranges/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nullranges/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nullranges/lilac.yaml b/prepare/r-nullranges/lilac.yaml new file mode 100644 index 0000000000..5a74eff990 --- /dev/null +++ b/prepare/r-nullranges/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-ggridges +- r-interactionset +- r-iranges +- r-ks +- r-plyranges +- r-progress +- r-rlang +- r-s4vectors +- r-scales +- r-speedglm +update_on: +- regex: nullranges_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/nullranges diff --git a/prepare/r-numbers/PKGBUILD b/prepare/r-numbers/PKGBUILD new file mode 100644 index 0000000000..d899448798 --- /dev/null +++ b/prepare/r-numbers/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=numbers +_pkgver=0.8-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Number-Theoretic Functions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-gmp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-numbers/lilac.py b/prepare/r-numbers/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-numbers/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-numbers/lilac.yaml b/prepare/r-numbers/lilac.yaml new file mode 100644 index 0000000000..5e9443daa8 --- /dev/null +++ b/prepare/r-numbers/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: numbers_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=numbers diff --git a/prepare/r-numderiv/PKGBUILD b/prepare/r-numderiv/PKGBUILD new file mode 100644 index 0000000000..efc3049016 --- /dev/null +++ b/prepare/r-numderiv/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=numDeriv +_pkgver=2016.8-1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Accurate Numerical Derivatives' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-numderiv/lilac.py b/prepare/r-numderiv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-numderiv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-numderiv/lilac.yaml b/prepare/r-numderiv/lilac.yaml new file mode 100644 index 0000000000..9483372b59 --- /dev/null +++ b/prepare/r-numderiv/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: numDeriv_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=numDeriv diff --git a/prepare/r-nupop/PKGBUILD b/prepare/r-nupop/PKGBUILD new file mode 100644 index 0000000000..bd5c6c2705 --- /dev/null +++ b/prepare/r-nupop/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NuPoP +_pkgver=2.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package for nucleosome positioning prediction' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown +) +makedepends=( + gcc-fortran +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nupop/lilac.py b/prepare/r-nupop/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nupop/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nupop/lilac.yaml b/prepare/r-nupop/lilac.yaml new file mode 100644 index 0000000000..40cdf36581 --- /dev/null +++ b/prepare/r-nupop/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: NuPoP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NuPoP diff --git a/prepare/r-nxtirfcore/PKGBUILD b/prepare/r-nxtirfcore/PKGBUILD new file mode 100644 index 0000000000..29fa1529f0 --- /dev/null +++ b/prepare/r-nxtirfcore/PKGBUILD @@ -0,0 +1,69 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=NxtIRFcore +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationhub + r-biocfilecache + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-data.table + r-delayedarray + r-delayedmatrixstats + r-fst + r-genefilter + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-hdf5array + r-iranges + r-magrittr + r-nxtirfdata + r-plotly + r-r.utils + r-rcpp + r-rcppprogress + r-rhdf5 + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-zlibbioc +) +optdepends=( + r-crayon + r-deseq2 + r-doubleexpseq + r-egg + r-knitr + r-limma + r-openssl + r-pheatmap + r-rmarkdown + r-rsubread + r-shiny + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nxtirfcore/lilac.py b/prepare/r-nxtirfcore/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nxtirfcore/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nxtirfcore/lilac.yaml b/prepare/r-nxtirfcore/lilac.yaml new file mode 100644 index 0000000000..8c57a5768b --- /dev/null +++ b/prepare/r-nxtirfcore/lilac.yaml @@ -0,0 +1,36 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-biocfilecache +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-data.table +- r-delayedarray +- r-delayedmatrixstats +- r-fst +- r-genefilter +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-hdf5array +- r-iranges +- r-magrittr +- r-nxtirfdata +- r-plotly +- r-r.utils +- r-rcpp +- r-rcppprogress +- r-rhdf5 +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +- r-zlibbioc +update_on: +- regex: NxtIRFcore_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NxtIRFcore diff --git a/prepare/r-nxtirfdata/PKGBUILD b/prepare/r-nxtirfdata/PKGBUILD new file mode 100644 index 0000000000..86e5663b0e --- /dev/null +++ b/prepare/r-nxtirfdata/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=NxtIRFdata +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data for NxtIRF' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocfilecache + r-experimenthub + r-r.utils + r-rtracklayer +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-nxtirfdata/lilac.py b/prepare/r-nxtirfdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-nxtirfdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-nxtirfdata/lilac.yaml b/prepare/r-nxtirfdata/lilac.yaml new file mode 100644 index 0000000000..38ebaf38e1 --- /dev/null +++ b/prepare/r-nxtirfdata/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-experimenthub +- r-r.utils +- r-rtracklayer +update_on: +- regex: NxtIRFdata_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/NxtIRFdata diff --git a/prepare/r-objectproperties/PKGBUILD b/prepare/r-objectproperties/PKGBUILD new file mode 100644 index 0000000000..42813dd3b0 --- /dev/null +++ b/prepare/r-objectproperties/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=objectProperties +_pkgver=0.6.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Factory of Self-Describing Properties' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-objectsignals +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-objectproperties/lilac.py b/prepare/r-objectproperties/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-objectproperties/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-objectproperties/lilac.yaml b/prepare/r-objectproperties/lilac.yaml new file mode 100644 index 0000000000..fa88f55112 --- /dev/null +++ b/prepare/r-objectproperties/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-objectsignals +update_on: +- regex: objectProperties_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=objectProperties diff --git a/prepare/r-objectsignals/PKGBUILD b/prepare/r-objectsignals/PKGBUILD new file mode 100644 index 0000000000..455ce8b734 --- /dev/null +++ b/prepare/r-objectsignals/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=objectSignals +_pkgver=0.10.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='objectSignals' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-objectsignals/lilac.py b/prepare/r-objectsignals/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-objectsignals/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-objectsignals/lilac.yaml b/prepare/r-objectsignals/lilac.yaml new file mode 100644 index 0000000000..90dbf18dca --- /dev/null +++ b/prepare/r-objectsignals/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: objectSignals_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=objectSignals diff --git a/prepare/r-occugene/PKGBUILD b/prepare/r-occugene/PKGBUILD new file mode 100644 index 0000000000..9c10e35df8 --- /dev/null +++ b/prepare/r-occugene/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=occugene +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for Multinomial Occupancy Distribution' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-occugene/lilac.py b/prepare/r-occugene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-occugene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-occugene/lilac.yaml b/prepare/r-occugene/lilac.yaml new file mode 100644 index 0000000000..702fb62e8a --- /dev/null +++ b/prepare/r-occugene/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: occugene_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/occugene diff --git a/prepare/r-ocplus/PKGBUILD b/prepare/r-ocplus/PKGBUILD new file mode 100644 index 0000000000..15afa8a629 --- /dev/null +++ b/prepare/r-ocplus/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OCplus +_pkgver=1.68.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Operating characteristics plus sample size and local fdr for microarray experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-akima + r-multtest +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ocplus/lilac.py b/prepare/r-ocplus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ocplus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ocplus/lilac.yaml b/prepare/r-ocplus/lilac.yaml new file mode 100644 index 0000000000..59c2923471 --- /dev/null +++ b/prepare/r-ocplus/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-akima +- r-multtest +update_on: +- regex: OCplus_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OCplus diff --git a/prepare/r-oder/PKGBUILD b/prepare/r-oder/PKGBUILD new file mode 100644 index 0000000000..019c5fd128 --- /dev/null +++ b/prepare/r-oder/PKGBUILD @@ -0,0 +1,59 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ODER +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Optimising the Definition of Expressed Regions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocfilecache + r-biocgenerics + r-dasper + r-data.table + r-derfinder + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-ggpubr + r-ggrepel + r-iranges + r-magrittr + r-megadepth + r-plyr + r-purrr + r-rtracklayer + r-s4vectors + r-stringr + r-tibble +) +optdepends=( + r-biocstyle + r-covr + r-genomicfeatures + r-knitr + r-recount + r-refmanager + r-rmarkdown + r-sessioninfo + r-summarizedexperiment + r-testthat + r-xfun +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-oder/lilac.py b/prepare/r-oder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-oder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-oder/lilac.yaml b/prepare/r-oder/lilac.yaml new file mode 100644 index 0000000000..81aa4c1441 --- /dev/null +++ b/prepare/r-oder/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-biocgenerics +- r-dasper +- r-data.table +- r-derfinder +- r-dplyr +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-ggpubr +- r-ggrepel +- r-iranges +- r-magrittr +- r-megadepth +- r-plyr +- r-purrr +- r-rtracklayer +- r-s4vectors +- r-stringr +- r-tibble +update_on: +- regex: ODER_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ODER diff --git a/prepare/r-odseq/PKGBUILD b/prepare/r-odseq/PKGBUILD new file mode 100644 index 0000000000..004f0124ec --- /dev/null +++ b/prepare/r-odseq/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=odseq +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Outlier detection in multiple sequence alignments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-kebabs + r-mclust + r-msa +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-odseq/lilac.py b/prepare/r-odseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-odseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-odseq/lilac.yaml b/prepare/r-odseq/lilac.yaml new file mode 100644 index 0000000000..5bd75a2c3c --- /dev/null +++ b/prepare/r-odseq/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-kebabs +- r-mclust +- r-msa +update_on: +- regex: odseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/odseq diff --git a/prepare/r-officer/PKGBUILD b/prepare/r-officer/PKGBUILD new file mode 100644 index 0000000000..f0e088d1f8 --- /dev/null +++ b/prepare/r-officer/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=officer +_pkgver=0.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Manipulation of Microsoft Word and PowerPoint Documents' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-r6 + r-uuid + r-xml2 + r-zip +) +optdepends=( + r-base64enc + r-devemf + r-ggplot2 + r-knitr + r-rmarkdown + r-rsvg + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-officer/lilac.py b/prepare/r-officer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-officer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-officer/lilac.yaml b/prepare/r-officer/lilac.yaml new file mode 100644 index 0000000000..8d08c6f265 --- /dev/null +++ b/prepare/r-officer/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-r6 +- r-uuid +- r-xml2 +- r-zip +update_on: +- regex: officer_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=officer diff --git a/prepare/r-oligo/PKGBUILD b/prepare/r-oligo/PKGBUILD new file mode 100644 index 0000000000..f052e2f29a --- /dev/null +++ b/prepare/r-oligo/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Guoyi Zhang + +_pkgname=oligo +_pkgver=1.58.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Preprocessing tools for oligonucleotide arrays' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-affxparser + r-affyio + r-biobase + r-biocgenerics + r-biostrings + r-dbi + r-ff + r-oligoclasses + r-preprocesscore + r-rsqlite + r-zlibbioc +) +optdepends=( + r-acme + r-annotationdbi + r-biocstyle + r-biomart + r-bsgenome.hsapiens.ucsc.hg18 + r-domc + r-dompi + r-genefilter + r-hapmap100kxba + r-knitr + r-limma + r-maqcexpression4plex + r-oligodata + r-pd.hg.u95av2 + r-pd.hg18.60mer.expr + r-pd.huex.1.0.st.v2 + r-pd.hugene.1.0.st.v1 + r-pd.mapping50k.xba240 + r-rcolorbrewer + r-rcurl + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-oligo/lilac.py b/prepare/r-oligo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-oligo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-oligo/lilac.yaml b/prepare/r-oligo/lilac.yaml new file mode 100644 index 0000000000..b5bf61b513 --- /dev/null +++ b/prepare/r-oligo/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affxparser +- r-affyio +- r-biobase +- r-biocgenerics +- r-biostrings +- r-dbi +- r-ff +- r-oligoclasses +- r-preprocesscore +- r-rsqlite +- r-zlibbioc +update_on: +- regex: oligo_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/oligo diff --git a/prepare/r-oligoclasses/PKGBUILD b/prepare/r-oligoclasses/PKGBUILD new file mode 100644 index 0000000000..79da34cad5 --- /dev/null +++ b/prepare/r-oligoclasses/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Guoyi Zhang + +_pkgname=oligoClasses +_pkgver=1.56.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Classes for high-throughput arrays supported by oligo and crlmm' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affyio + r-biobase + r-biocgenerics + r-biocmanager + r-biostrings + r-dbi + r-ff + r-foreach + r-genomicranges + r-iranges + r-rsqlite + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-crlmm + r-domc + r-dompi + r-doparallel + r-doredis + r-dosnow + r-genomewidesnp5crlmm + r-genomewidesnp6crlmm + r-hapmapsnp5 + r-hapmapsnp6 + r-human370v1ccrlmm + r-pd.genomewidesnp.5 + r-pd.genomewidesnp.6 + r-pd.mapping250k.nsp + r-pd.mapping250k.sty + r-pd.mapping50k.hind240 + r-pd.mapping50k.xba240 + r-runit + r-vanillaice +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-oligoclasses/lilac.py b/prepare/r-oligoclasses/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-oligoclasses/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-oligoclasses/lilac.yaml b/prepare/r-oligoclasses/lilac.yaml new file mode 100644 index 0000000000..a9b282ca3a --- /dev/null +++ b/prepare/r-oligoclasses/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affyio +- r-biobase +- r-biocgenerics +- r-biocmanager +- r-biostrings +- r-dbi +- r-ff +- r-foreach +- r-genomicranges +- r-iranges +- r-rsqlite +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: oligoClasses_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/oligoClasses diff --git a/prepare/r-olin/PKGBUILD b/prepare/r-olin/PKGBUILD new file mode 100644 index 0000000000..a1b58cd02e --- /dev/null +++ b/prepare/r-olin/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OLIN +_pkgver=1.72.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Optimized local intensity-dependent normalisation of two-color microarrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-limma + r-locfit + r-marray +) +optdepends=( + r-convert +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-olin/lilac.py b/prepare/r-olin/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-olin/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-olin/lilac.yaml b/prepare/r-olin/lilac.yaml new file mode 100644 index 0000000000..14efe73c23 --- /dev/null +++ b/prepare/r-olin/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-limma +- r-locfit +- r-marray +update_on: +- regex: OLIN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OLIN diff --git a/prepare/r-olingui/PKGBUILD b/prepare/r-olingui/PKGBUILD new file mode 100644 index 0000000000..f469160c98 --- /dev/null +++ b/prepare/r-olingui/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OLINgui +_pkgver=1.68.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Graphical user interface for OLIN' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-marray + r-olin + r-tkwidgets + r-widgettools +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-olingui/lilac.py b/prepare/r-olingui/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-olingui/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-olingui/lilac.yaml b/prepare/r-olingui/lilac.yaml new file mode 100644 index 0000000000..db87e1c29b --- /dev/null +++ b/prepare/r-olingui/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-marray +- r-olin +- r-tkwidgets +- r-widgettools +update_on: +- regex: OLINgui_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OLINgui diff --git a/prepare/r-omadb/PKGBUILD b/prepare/r-omadb/PKGBUILD new file mode 100644 index 0000000000..66d47f4eb5 --- /dev/null +++ b/prepare/r-omadb/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OmaDB +_pkgver=2.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R wrapper for the OMA REST API' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-biostrings + r-genomicranges + r-httr + r-iranges + r-jsonlite + r-plyr + r-topgo +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-omadb/lilac.py b/prepare/r-omadb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-omadb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-omadb/lilac.yaml b/prepare/r-omadb/lilac.yaml new file mode 100644 index 0000000000..ca704f6e01 --- /dev/null +++ b/prepare/r-omadb/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-biostrings +- r-genomicranges +- r-httr +- r-iranges +- r-jsonlite +- r-plyr +- r-topgo +update_on: +- regex: OmaDB_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OmaDB diff --git a/prepare/r-omicade4/PKGBUILD b/prepare/r-omicade4/PKGBUILD new file mode 100644 index 0000000000..f85b42034d --- /dev/null +++ b/prepare/r-omicade4/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=omicade4 +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multiple co-inertia analysis of omics datasets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ade4 + r-biobase + r-made4 +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-omicade4/lilac.py b/prepare/r-omicade4/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-omicade4/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-omicade4/lilac.yaml b/prepare/r-omicade4/lilac.yaml new file mode 100644 index 0000000000..081ff75359 --- /dev/null +++ b/prepare/r-omicade4/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ade4 +- r-biobase +- r-made4 +update_on: +- regex: omicade4_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/omicade4 diff --git a/prepare/r-omiccircos/PKGBUILD b/prepare/r-omiccircos/PKGBUILD new file mode 100644 index 0000000000..c8aebc70ec --- /dev/null +++ b/prepare/r-omiccircos/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OmicCircos +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='High-quality circular visualization of omics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicranges +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-omiccircos/lilac.py b/prepare/r-omiccircos/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-omiccircos/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-omiccircos/lilac.yaml b/prepare/r-omiccircos/lilac.yaml new file mode 100644 index 0000000000..35d775b75c --- /dev/null +++ b/prepare/r-omiccircos/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +update_on: +- regex: OmicCircos_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OmicCircos diff --git a/prepare/r-omicplotr/PKGBUILD b/prepare/r-omicplotr/PKGBUILD new file mode 100644 index 0000000000..6a861f3092 --- /dev/null +++ b/prepare/r-omicplotr/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=omicplotR +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visual Exploration of Omic Datasets Using a Shiny App' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-aldex2 + r-compositions + r-dt + r-jsonlite + r-knitr + r-matrixstats + r-rmarkdown + r-shiny + r-vegan + r-zcompositions +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-omicplotr/lilac.py b/prepare/r-omicplotr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-omicplotr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-omicplotr/lilac.yaml b/prepare/r-omicplotr/lilac.yaml new file mode 100644 index 0000000000..b203c3ec7a --- /dev/null +++ b/prepare/r-omicplotr/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aldex2 +- r-compositions +- r-dt +- r-jsonlite +- r-knitr +- r-matrixstats +- r-rmarkdown +- r-shiny +- r-vegan +- r-zcompositions +update_on: +- regex: omicplotR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/omicplotR diff --git a/prepare/r-omicrexposome/PKGBUILD b/prepare/r-omicrexposome/PKGBUILD new file mode 100644 index 0000000000..d4d27e15a3 --- /dev/null +++ b/prepare/r-omicrexposome/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=omicRexposome +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Exposome and omic data associatin and integration analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-ggplot2 + r-ggrepel + r-gridextra + r-isva + r-limma + r-multidataset + r-omicade4 + r-pma + r-rexposome + r-smartsva + r-stringr + r-summarizedexperiment + r-sva +) +optdepends=( + r-biocstyle + r-brgedata + r-knitr + r-rmarkdown + r-snpstats +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-omicrexposome/lilac.py b/prepare/r-omicrexposome/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-omicrexposome/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-omicrexposome/lilac.yaml b/prepare/r-omicrexposome/lilac.yaml new file mode 100644 index 0000000000..ee7d76e5bb --- /dev/null +++ b/prepare/r-omicrexposome/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-ggplot2 +- r-ggrepel +- r-gridextra +- r-isva +- r-limma +- r-multidataset +- r-omicade4 +- r-pma +- r-rexposome +- r-smartsva +- r-stringr +- r-summarizedexperiment +- r-sva +update_on: +- regex: omicRexposome_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/omicRexposome diff --git a/prepare/r-omicslonda/PKGBUILD b/prepare/r-omicslonda/PKGBUILD new file mode 100644 index 0000000000..27b56b6542 --- /dev/null +++ b/prepare/r-omicslonda/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OmicsLonDA +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Omics Longitudinal Differential Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-biocparallel + r-ggplot2 + r-gss + r-plyr + r-pracma + r-summarizedexperiment + r-zoo +) +optdepends=( + r-biocmanager + r-devtools + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-omicslonda/lilac.py b/prepare/r-omicslonda/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-omicslonda/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-omicslonda/lilac.yaml b/prepare/r-omicslonda/lilac.yaml new file mode 100644 index 0000000000..29d41c0c24 --- /dev/null +++ b/prepare/r-omicslonda/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-ggplot2 +- r-gss +- r-plyr +- r-pracma +- r-summarizedexperiment +- r-zoo +update_on: +- regex: OmicsLonDA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OmicsLonDA diff --git a/prepare/r-omicspca/PKGBUILD b/prepare/r-omicspca/PKGBUILD new file mode 100644 index 0000000000..d1b5616d8f --- /dev/null +++ b/prepare/r-omicspca/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OMICsPCA +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-clvalid + r-corrplot + r-cowplot + r-data.table + r-factoextra + r-factominer + r-fpc + r-genomeinfodb + r-ggplot2 + r-helloranges + r-iranges + r-kableextra + r-magick + r-multiassayexperiment + r-nbclust + r-omicspcadata + r-pdftools + r-performanceanalytics + r-reshape2 + r-rgl + r-rmarkdown + r-rtracklayer + r-tidyr +) +optdepends=( + r-biocgenerics + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-omicspca/lilac.py b/prepare/r-omicspca/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-omicspca/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-omicspca/lilac.yaml b/prepare/r-omicspca/lilac.yaml new file mode 100644 index 0000000000..fbdf69bd8c --- /dev/null +++ b/prepare/r-omicspca/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clvalid +- r-corrplot +- r-cowplot +- r-data.table +- r-factoextra +- r-factominer +- r-fpc +- r-genomeinfodb +- r-ggplot2 +- r-helloranges +- r-iranges +- r-kableextra +- r-magick +- r-multiassayexperiment +- r-nbclust +- r-omicspcadata +- r-pdftools +- r-performanceanalytics +- r-reshape2 +- r-rgl +- r-rmarkdown +- r-rtracklayer +- r-tidyr +update_on: +- regex: OMICsPCA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OMICsPCA diff --git a/prepare/r-omicspcadata/PKGBUILD b/prepare/r-omicspcadata/PKGBUILD new file mode 100644 index 0000000000..35e368a63a --- /dev/null +++ b/prepare/r-omicspcadata/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OMICsPCAdata +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Supporting data for package OMICsPCA' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-multiassayexperiment +) +optdepends=( + r-kableextra + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-omicspcadata/lilac.py b/prepare/r-omicspcadata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-omicspcadata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-omicspcadata/lilac.yaml b/prepare/r-omicspcadata/lilac.yaml new file mode 100644 index 0000000000..0f40269e90 --- /dev/null +++ b/prepare/r-omicspcadata/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-multiassayexperiment +update_on: +- regex: OMICsPCAdata_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OMICsPCAdata diff --git a/prepare/r-omicsprint/PKGBUILD b/prepare/r-omicsprint/PKGBUILD new file mode 100644 index 0000000000..84aff75485 --- /dev/null +++ b/prepare/r-omicsprint/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=omicsPrint +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cross omic genetic fingerprinting' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-matrixstats + r-multiassayexperiment + r-raggedexperiment + r-summarizedexperiment +) +optdepends=( + r-biocparallel + r-biocstyle + r-fdb.infiniummethylation.hg19 + r-genomicranges + r-geoquery + r-knitr + r-rmarkdown + r-rsamtools + r-snpstats + r-testthat + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-omicsprint/lilac.py b/prepare/r-omicsprint/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-omicsprint/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-omicsprint/lilac.yaml b/prepare/r-omicsprint/lilac.yaml new file mode 100644 index 0000000000..1e1e24b33e --- /dev/null +++ b/prepare/r-omicsprint/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-matrixstats +- r-multiassayexperiment +- r-raggedexperiment +- r-summarizedexperiment +update_on: +- regex: omicsPrint_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/omicsPrint diff --git a/prepare/r-omixer/PKGBUILD b/prepare/r-omixer/PKGBUILD new file mode 100644 index 0000000000..ec7fef4559 --- /dev/null +++ b/prepare/r-omixer/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Omixer +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-forcats + r-ggplot2 + r-gridextra + r-magrittr + r-readr + r-stringr + r-tibble + r-tidyselect +) +optdepends=( + r-biocstyle + r-knitr + r-magick + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-omixer/lilac.py b/prepare/r-omixer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-omixer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-omixer/lilac.yaml b/prepare/r-omixer/lilac.yaml new file mode 100644 index 0000000000..f91bbeb62c --- /dev/null +++ b/prepare/r-omixer/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-forcats +- r-ggplot2 +- r-gridextra +- r-magrittr +- r-readr +- r-stringr +- r-tibble +- r-tidyselect +update_on: +- regex: Omixer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Omixer diff --git a/prepare/r-omnipathr/PKGBUILD b/prepare/r-omnipathr/PKGBUILD new file mode 100644 index 0000000000..7e3352a291 --- /dev/null +++ b/prepare/r-omnipathr/PKGBUILD @@ -0,0 +1,66 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OmnipathR +_pkgver=3.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='OmniPath web service client and more' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-checkmate + r-crayon + r-curl + r-digest + r-dplyr + r-httr + r-igraph + r-jsonlite + r-later + r-logger + r-magrittr + r-progress + r-purrr + r-rappdirs + r-readr + r-readxl + r-rlang + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-xml2 + r-yaml +) +optdepends=( + r-biocstyle + r-dnet + r-ggplot2 + r-ggraph + r-gprofiler2 + r-knitr + r-mlrmbo + r-parallelmap + r-paramhelpers + r-rgraphviz + r-rmarkdown + r-smoof + r-suprahex + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-omnipathr/lilac.py b/prepare/r-omnipathr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-omnipathr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-omnipathr/lilac.yaml b/prepare/r-omnipathr/lilac.yaml new file mode 100644 index 0000000000..d52fbeba42 --- /dev/null +++ b/prepare/r-omnipathr/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-checkmate +- r-crayon +- r-curl +- r-digest +- r-dplyr +- r-httr +- r-igraph +- r-jsonlite +- r-later +- r-logger +- r-magrittr +- r-progress +- r-purrr +- r-rappdirs +- r-readr +- r-readxl +- r-rlang +- r-stringr +- r-tibble +- r-tidyr +- r-tidyselect +- r-xml2 +- r-yaml +update_on: +- regex: OmnipathR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OmnipathR diff --git a/prepare/r-onassis/PKGBUILD b/prepare/r-onassis/PKGBUILD new file mode 100644 index 0000000000..ec67eb0dec --- /dev/null +++ b/prepare/r-onassis/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Onassis +_pkgver=1.15.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='OnASSIs Ontology Annotation and Semantic SImilarity software' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rjava + r-onassisjavalibs + r-geometadb + r-rsqlite + r-data.table + r-annotationdbi + r-rcurl + r-dt + r-knitr + r-rtsne + r-dendextend + r-ggplot2 + r-ggfortify +) +makedepends=( + git + tar +) +optdepends=( + r-biocstyle + r-rmarkdown + r-htmltools + r-org.hs.eg.db + r-gplots + r-genomicranges + r-kableextra +) +source=("git+https://git.bioconductor.org/packages/${_pkgname}.git") +sha256sums=('SKIP') + +build() { + tar -zcvf ${_pkgname}.tar.gz ${_pkgname} + R CMD INSTALL ${_pkgname}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: + diff --git a/prepare/r-onassis/lilac.py b/prepare/r-onassis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-onassis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-onassis/lilac.yaml b/prepare/r-onassis/lilac.yaml new file mode 100644 index 0000000000..5ae1acd1d7 --- /dev/null +++ b/prepare/r-onassis/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rjava +- r-onassisjavalibs +- r-geometadb +- r-rsqlite +- r-data.table +- r-annotationdbi +- r-rcurl +- r-dt +- r-knitr +- r-rtsne +- r-dendextend +- r-ggplot2 +- r-ggfortify +update_on: +- regex: Version(\d+.\d+.\d+) + source: regex + url: https://bioconductor.org/packages/Onassis diff --git a/prepare/r-onassisjavalibs/PKGBUILD b/prepare/r-onassisjavalibs/PKGBUILD new file mode 100644 index 0000000000..997149d138 --- /dev/null +++ b/prepare/r-onassisjavalibs/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: Java (>= 1.8) +# Maintainer: Guoyi Zhang + +_pkgname=OnassisJavaLibs +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='OnassisJavaLibs, java libraries to run conceptmapper and semantic similarity' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rjava +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-onassisjavalibs/lilac.py b/prepare/r-onassisjavalibs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-onassisjavalibs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-onassisjavalibs/lilac.yaml b/prepare/r-onassisjavalibs/lilac.yaml new file mode 100644 index 0000000000..995f0d7e50 --- /dev/null +++ b/prepare/r-onassisjavalibs/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rjava +update_on: +- regex: OnassisJavaLibs_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OnassisJavaLibs diff --git a/prepare/r-oncomix/PKGBUILD b/prepare/r-oncomix/PKGBUILD new file mode 100644 index 0000000000..82cbad76a2 --- /dev/null +++ b/prepare/r-oncomix/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=oncomix +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-ggrepel + r-mclust + r-rcolorbrewer + r-summarizedexperiment +) +optdepends=( + r-knitr + r-rmarkdown + r-rmysql + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-oncomix/lilac.py b/prepare/r-oncomix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-oncomix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-oncomix/lilac.yaml b/prepare/r-oncomix/lilac.yaml new file mode 100644 index 0000000000..0be3bfad43 --- /dev/null +++ b/prepare/r-oncomix/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-ggrepel +- r-mclust +- r-rcolorbrewer +- r-summarizedexperiment +update_on: +- regex: oncomix_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/oncomix diff --git a/prepare/r-oncoscore/PKGBUILD b/prepare/r-oncoscore/PKGBUILD new file mode 100644 index 0000000000..465c0198ef --- /dev/null +++ b/prepare/r-oncoscore/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OncoScore +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A tool to identify potentially oncogenic genes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-biomart +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-oncoscore/lilac.py b/prepare/r-oncoscore/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-oncoscore/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-oncoscore/lilac.yaml b/prepare/r-oncoscore/lilac.yaml new file mode 100644 index 0000000000..2e5e15ef27 --- /dev/null +++ b/prepare/r-oncoscore/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +update_on: +- regex: OncoScore_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OncoScore diff --git a/prepare/r-oncosimulr/PKGBUILD b/prepare/r-oncosimulr/PKGBUILD new file mode 100644 index 0000000000..0577e59a5e --- /dev/null +++ b/prepare/r-oncosimulr/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OncoSimulR +_pkgver=3.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Forward Genetic Simulation of Cancer Progression with Epistasis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-car + r-data.table + r-dplyr + r-ggplot2 + r-ggrepel + r-graph + r-gtools + r-igraph + r-rcolorbrewer + r-rcpp + r-rgraphviz + r-smatr + r-stringr +) +optdepends=( + r-biocstyle + r-bookdown + r-knitr + r-oncotree + r-pander + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-oncosimulr/lilac.py b/prepare/r-oncosimulr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-oncosimulr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-oncosimulr/lilac.yaml b/prepare/r-oncosimulr/lilac.yaml new file mode 100644 index 0000000000..acaabf1343 --- /dev/null +++ b/prepare/r-oncosimulr/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-car +- r-data.table +- r-dplyr +- r-ggplot2 +- r-ggrepel +- r-graph +- r-gtools +- r-igraph +- r-rcolorbrewer +- r-rcpp +- r-rgraphviz +- r-smatr +- r-stringr +update_on: +- regex: OncoSimulR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OncoSimulR diff --git a/prepare/r-onesense/PKGBUILD b/prepare/r-onesense/PKGBUILD new file mode 100644 index 0000000000..ee5851e752 --- /dev/null +++ b/prepare/r-onesense/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=oneSENSE +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-flowcore + r-gplots + r-plotly + r-rtsne + r-scatterplot3d + r-shiny + r-shinyfiles + r-webshot +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-onesense/lilac.py b/prepare/r-onesense/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-onesense/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-onesense/lilac.yaml b/prepare/r-onesense/lilac.yaml new file mode 100644 index 0000000000..cae5e8affe --- /dev/null +++ b/prepare/r-onesense/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-flowcore +- r-gplots +- r-plotly +- r-rtsne +- r-scatterplot3d +- r-shiny +- r-shinyfiles +- r-webshot +update_on: +- regex: oneSENSE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/oneSENSE diff --git a/prepare/r-onlinefdr/PKGBUILD b/prepare/r-onlinefdr/PKGBUILD new file mode 100644 index 0000000000..803bf487d1 --- /dev/null +++ b/prepare/r-onlinefdr/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=onlineFDR +_pkgver=2.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Online error control' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-ggplot2 + r-progress + r-rcpp + r-rcppprogress + r-tidyr +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-onlinefdr/lilac.py b/prepare/r-onlinefdr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-onlinefdr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-onlinefdr/lilac.yaml b/prepare/r-onlinefdr/lilac.yaml new file mode 100644 index 0000000000..418e39a938 --- /dev/null +++ b/prepare/r-onlinefdr/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-progress +- r-rcpp +- r-rcppprogress +- r-tidyr +update_on: +- regex: onlineFDR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/onlineFDR diff --git a/prepare/r-ontologyindex/PKGBUILD b/prepare/r-ontologyindex/PKGBUILD new file mode 100644 index 0000000000..2dd0a1b399 --- /dev/null +++ b/prepare/r-ontologyindex/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ontologyIndex +_pkgver=2.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for Reading Ontologies into R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ontologyindex/lilac.py b/prepare/r-ontologyindex/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ontologyindex/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ontologyindex/lilac.yaml b/prepare/r-ontologyindex/lilac.yaml new file mode 100644 index 0000000000..f690095944 --- /dev/null +++ b/prepare/r-ontologyindex/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ontologyIndex_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ontologyIndex diff --git a/prepare/r-ontologyplot/PKGBUILD b/prepare/r-ontologyplot/PKGBUILD new file mode 100644 index 0000000000..5b1af33f17 --- /dev/null +++ b/prepare/r-ontologyplot/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ontologyPlot +_pkgver=1.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualising Sets of Ontological Terms' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ontologyindex + r-paintmap + r-rgraphviz +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ontologyplot/lilac.py b/prepare/r-ontologyplot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ontologyplot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ontologyplot/lilac.yaml b/prepare/r-ontologyplot/lilac.yaml new file mode 100644 index 0000000000..e00c4999ef --- /dev/null +++ b/prepare/r-ontologyplot/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ontologyindex +- r-paintmap +- r-rgraphviz +update_on: +- regex: ontologyPlot_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ontologyPlot diff --git a/prepare/r-ontoproc/PKGBUILD b/prepare/r-ontoproc/PKGBUILD new file mode 100644 index 0000000000..ceebb6ca0d --- /dev/null +++ b/prepare/r-ontoproc/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ontoProc +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='processing of ontologies of anatomy, cell lines, and so on' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-annotationhub + r-biobase + r-biocfilecache + r-dplyr + r-dt + r-graph + r-igraph + r-magrittr + r-ontologyindex + r-ontologyplot + r-rgraphviz + r-s4vectors + r-shiny +) +optdepends=( + r-biocstyle + r-celldex + r-knitr + r-org.hs.eg.db + r-org.mm.eg.db + r-rmarkdown + r-singlecellexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ontoproc/lilac.py b/prepare/r-ontoproc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ontoproc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ontoproc/lilac.yaml b/prepare/r-ontoproc/lilac.yaml new file mode 100644 index 0000000000..44bc0134ce --- /dev/null +++ b/prepare/r-ontoproc/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-biobase +- r-biocfilecache +- r-dplyr +- r-dt +- r-graph +- r-igraph +- r-magrittr +- r-ontologyindex +- r-ontologyplot +- r-rgraphviz +- r-s4vectors +- r-shiny +update_on: +- regex: ontoProc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ontoProc diff --git a/prepare/r-opencpu/PKGBUILD b/prepare/r-opencpu/PKGBUILD new file mode 100644 index 0000000000..47f3994b2b --- /dev/null +++ b/prepare/r-opencpu/PKGBUILD @@ -0,0 +1,49 @@ +# system requirements: pandoc, apparmor (optional) +# Maintainer: Guoyi Zhang + +_pkgname=opencpu +_pkgver=2.2.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Producing and Reproducing Results' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-brew + r-curl + r-evaluate + r-httpuv + r-jsonlite + r-knitr + r-mime + r-openssl + r-protolite + r-rappdirs + r-remotes + r-sys + r-webutils + r-zip +) +optdepends=( + r-feather + r-haven + r-pander + r-r.rsp + r-svglite + r-unix +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-opencpu/lilac.py b/prepare/r-opencpu/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-opencpu/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-opencpu/lilac.yaml b/prepare/r-opencpu/lilac.yaml new file mode 100644 index 0000000000..0d90fadb1b --- /dev/null +++ b/prepare/r-opencpu/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-brew +- r-curl +- r-evaluate +- r-httpuv +- r-jsonlite +- r-knitr +- r-mime +- r-openssl +- r-protolite +- r-rappdirs +- r-remotes +- r-sys +- r-webutils +- r-zip +update_on: +- regex: opencpu_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=opencpu diff --git a/prepare/r-opencyto/PKGBUILD b/prepare/r-opencyto/PKGBUILD new file mode 100644 index 0000000000..781cbea468 --- /dev/null +++ b/prepare/r-opencyto/PKGBUILD @@ -0,0 +1,58 @@ +# Maintainer: Guoyi Zhang + +_pkgname=openCyto +_pkgver=2.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Hierarchical Gating Pipeline for flow cytometry data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-biobase + r-biocgenerics + r-clue + r-data.table + r-flowclust + r-flowcore + r-flowstats + r-flowviz + r-flowworkspace + r-graph + r-gtools + r-ks + r-ncdfflow + r-plyr + r-r.utils + r-rbgl + r-rcolorbrewer + r-rcpp + r-rrcov +) +optdepends=( + r-cytoml + r-flowworkspacedata + r-ggcyto + r-knitr + r-markdown + r-parallel + r-rmarkdown + r-testthat + r-tools + r-utils +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-opencyto/lilac.py b/prepare/r-opencyto/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-opencyto/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-opencyto/lilac.yaml b/prepare/r-opencyto/lilac.yaml new file mode 100644 index 0000000000..5b6c1b101a --- /dev/null +++ b/prepare/r-opencyto/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-clue +- r-data.table +- r-flowclust +- r-flowcore +- r-flowstats +- r-flowviz +- r-flowworkspace +- r-graph +- r-gtools +- r-ks +- r-ncdfflow +- r-plyr +- r-r.utils +- r-rbgl +- r-rcolorbrewer +- r-rcpp +- r-rrcov +update_on: +- regex: openCyto_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/openCyto diff --git a/prepare/r-openprimer/PKGBUILD b/prepare/r-openprimer/PKGBUILD new file mode 100644 index 0000000000..19ccf34d54 --- /dev/null +++ b/prepare/r-openprimer/PKGBUILD @@ -0,0 +1,63 @@ +# system requirements: MAFFT (>= 7.305), OligoArrayAux (>= 3.8), ViennaRNA(>= 2.4.1), MELTING (>= 5.1.1), Pandoc (>= 1.12.3) +# Maintainer: Guoyi Zhang + +_pkgname=openPrimeR +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multiplex PCR Primer Design and Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-biocgenerics + r-biostrings + r-decipher + r-digest + r-distr + r-distrex + r-dplyr + r-fitdistrplus + r-foreach + r-genomicranges + r-ggplot2 + r-hmisc + r-iranges + r-lpsolveapi + r-magrittr + r-openxlsx + r-plyr + r-rcolorbrewer + r-reshape2 + r-s4vectors + r-scales + r-seqinr + r-stringdist + r-stringr + r-uniqtag + r-xml +) +optdepends=( + r-devtools + r-doparallel + r-knitr + r-learnr + r-pander + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-openprimer/lilac.py b/prepare/r-openprimer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-openprimer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-openprimer/lilac.yaml b/prepare/r-openprimer/lilac.yaml new file mode 100644 index 0000000000..5700b4a0d7 --- /dev/null +++ b/prepare/r-openprimer/lilac.yaml @@ -0,0 +1,36 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-biocgenerics +- r-biostrings +- r-decipher +- r-digest +- r-distr +- r-distrex +- r-dplyr +- r-fitdistrplus +- r-foreach +- r-genomicranges +- r-ggplot2 +- r-hmisc +- r-iranges +- r-lpsolveapi +- r-magrittr +- r-openxlsx +- r-plyr +- r-rcolorbrewer +- r-reshape2 +- r-s4vectors +- r-scales +- r-seqinr +- r-stringdist +- r-stringr +- r-uniqtag +- r-xml +update_on: +- regex: openPrimeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/openPrimeR diff --git a/prepare/r-openprimerui/PKGBUILD b/prepare/r-openprimerui/PKGBUILD new file mode 100644 index 0000000000..8181c983d0 --- /dev/null +++ b/prepare/r-openprimerui/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=openPrimeRui +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Shiny Application for Multiplex PCR Primer Design and Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dt + r-openprimer + r-rmarkdown + r-shiny + r-shinybs + r-shinyjs +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-openprimerui/lilac.py b/prepare/r-openprimerui/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-openprimerui/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-openprimerui/lilac.yaml b/prepare/r-openprimerui/lilac.yaml new file mode 100644 index 0000000000..662e4691fb --- /dev/null +++ b/prepare/r-openprimerui/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dt +- r-openprimer +- r-rmarkdown +- r-shiny +- r-shinybs +- r-shinyjs +update_on: +- regex: openPrimeRui_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/openPrimeRui diff --git a/prepare/r-openstats/PKGBUILD b/prepare/r-openstats/PKGBUILD new file mode 100644 index 0000000000..fa7d55ba76 --- /dev/null +++ b/prepare/r-openstats/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OpenStats +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-aiccmodavg + r-car + r-hmisc + r-jsonlite + r-knitr + r-rlist + r-summarytools +) +optdepends=( + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-openstats/lilac.py b/prepare/r-openstats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-openstats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-openstats/lilac.yaml b/prepare/r-openstats/lilac.yaml new file mode 100644 index 0000000000..580e6701fa --- /dev/null +++ b/prepare/r-openstats/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aiccmodavg +- r-car +- r-hmisc +- r-jsonlite +- r-knitr +- r-rlist +- r-summarytools +update_on: +- regex: OpenStats_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OpenStats diff --git a/prepare/r-openxlsx/PKGBUILD b/prepare/r-openxlsx/PKGBUILD new file mode 100644 index 0000000000..6d5accda21 --- /dev/null +++ b/prepare/r-openxlsx/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=openxlsx +_pkgver=4.2.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Read, Write and Edit xlsx Files' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-rcpp + r-stringi + r-zip +) +optdepends=( + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-openxlsx/lilac.py b/prepare/r-openxlsx/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-openxlsx/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-openxlsx/lilac.yaml b/prepare/r-openxlsx/lilac.yaml new file mode 100644 index 0000000000..32bd14ed5a --- /dev/null +++ b/prepare/r-openxlsx/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-stringi +- r-zip +update_on: +- regex: openxlsx_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=openxlsx diff --git a/prepare/r-operator.tools/PKGBUILD b/prepare/r-operator.tools/PKGBUILD new file mode 100644 index 0000000000..5c0ecad235 --- /dev/null +++ b/prepare/r-operator.tools/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=operator.tools +_pkgver=1.6.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Utilities for Working with R's Operators" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-magrittr + r-operators + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-operator.tools/lilac.py b/prepare/r-operator.tools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-operator.tools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-operator.tools/lilac.yaml b/prepare/r-operator.tools/lilac.yaml new file mode 100644 index 0000000000..8a270b653b --- /dev/null +++ b/prepare/r-operator.tools/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: operator.tools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=operator.tools diff --git a/prepare/r-opossom/PKGBUILD b/prepare/r-opossom/PKGBUILD new file mode 100644 index 0000000000..fb4ca22dce --- /dev/null +++ b/prepare/r-opossom/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=oposSOM +_pkgver=2.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Comprehensive analysis of transcriptome data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-biobase + r-biomart + r-fastica + r-fdrtool + r-graph + r-igraph + r-pixmap + r-png + r-rcpp + r-rcppparallel + r-rcurl + r-scatterplot3d + r-tsne + r-xml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-opossom/lilac.py b/prepare/r-opossom/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-opossom/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-opossom/lilac.yaml b/prepare/r-opossom/lilac.yaml new file mode 100644 index 0000000000..7d696a0ea1 --- /dev/null +++ b/prepare/r-opossom/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-biobase +- r-biomart +- r-fastica +- r-fdrtool +- r-graph +- r-igraph +- r-pixmap +- r-png +- r-rcpp +- r-rcppparallel +- r-rcurl +- r-scatterplot3d +- r-tsne +- r-xml +update_on: +- regex: oposSOM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/oposSOM diff --git a/prepare/r-oppar/PKGBUILD b/prepare/r-oppar/PKGBUILD new file mode 100644 index 0000000000..ecef6671cc --- /dev/null +++ b/prepare/r-oppar/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=oppar +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Outlier profile and pathway analysis in R' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-gseabase + r-gsva +) +optdepends=( + r-go.db + r-knitr + r-limma + r-org.hs.eg.db + r-parallel + r-rmarkdown + r-snow +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-oppar/lilac.py b/prepare/r-oppar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-oppar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-oppar/lilac.yaml b/prepare/r-oppar/lilac.yaml new file mode 100644 index 0000000000..d880e88d7f --- /dev/null +++ b/prepare/r-oppar/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-gseabase +- r-gsva +update_on: +- regex: oppar_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/oppar diff --git a/prepare/r-oppti/PKGBUILD b/prepare/r-oppti/PKGBUILD new file mode 100644 index 0000000000..2a22d1802c --- /dev/null +++ b/prepare/r-oppti/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=oppti +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Outlier Protein and Phosphosite Target Identifier' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-devtools + r-ggplot2 + r-knitr + r-limma + r-paralleldist + r-pheatmap + r-rcolorbrewer + r-reshape +) +optdepends=( + r-markdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-oppti/lilac.py b/prepare/r-oppti/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-oppti/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-oppti/lilac.yaml b/prepare/r-oppti/lilac.yaml new file mode 100644 index 0000000000..4b74f3af64 --- /dev/null +++ b/prepare/r-oppti/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-devtools +- r-ggplot2 +- r-knitr +- r-limma +- r-paralleldist +- r-pheatmap +- r-rcolorbrewer +- r-reshape +update_on: +- regex: oppti_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/oppti diff --git a/prepare/r-optextras/PKGBUILD b/prepare/r-optextras/PKGBUILD new file mode 100644 index 0000000000..ccfba29039 --- /dev/null +++ b/prepare/r-optextras/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=optextras +_pkgver=2019-12.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools to Support Optimization Possibly with Bounds and Masks' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-numderiv +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-optextras/lilac.py b/prepare/r-optextras/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-optextras/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-optextras/lilac.yaml b/prepare/r-optextras/lilac.yaml new file mode 100644 index 0000000000..4007214ac8 --- /dev/null +++ b/prepare/r-optextras/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-numderiv +update_on: +- regex: optextras_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=optextras diff --git a/prepare/r-optimalflow/PKGBUILD b/prepare/r-optimalflow/PKGBUILD new file mode 100644 index 0000000000..6444e24c0e --- /dev/null +++ b/prepare/r-optimalflow/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=optimalFlow +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='optimalFlow' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-dbscan + r-doparallel + r-dplyr + r-ellipse + r-flowmeans + r-foreach + r-optimalflowdata + r-randomforest + r-rfast + r-rgl + r-rlang + r-robustbase + r-transport +) +optdepends=( + r-biocstyle + r-knitr + r-magick + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-optimalflow/lilac.py b/prepare/r-optimalflow/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-optimalflow/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-optimalflow/lilac.yaml b/prepare/r-optimalflow/lilac.yaml new file mode 100644 index 0000000000..bdafb0f3ec --- /dev/null +++ b/prepare/r-optimalflow/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dbscan +- r-doparallel +- r-dplyr +- r-ellipse +- r-flowmeans +- r-foreach +- r-optimalflowdata +- r-randomforest +- r-rfast +- r-rgl +- r-rlang +- r-robustbase +- r-transport +update_on: +- regex: optimalFlow_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/optimalFlow diff --git a/prepare/r-optimalflowdata/PKGBUILD b/prepare/r-optimalflowdata/PKGBUILD new file mode 100644 index 0000000000..ced549e27d --- /dev/null +++ b/prepare/r-optimalflowdata/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=optimalFlowData +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='optimalFlowData' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-biocstyle + r-knitr + r-magick + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-optimalflowdata/lilac.py b/prepare/r-optimalflowdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-optimalflowdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-optimalflowdata/lilac.yaml b/prepare/r-optimalflowdata/lilac.yaml new file mode 100644 index 0000000000..e14644d216 --- /dev/null +++ b/prepare/r-optimalflowdata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: optimalFlowData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/optimalFlowData diff --git a/prepare/r-optimr/PKGBUILD b/prepare/r-optimr/PKGBUILD new file mode 100644 index 0000000000..51d9f1f458 --- /dev/null +++ b/prepare/r-optimr/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=optimr +_pkgver=2019-12.16 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="A Replacement and Extension of the 'optim' Function" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-numderiv + r-optextras + r-rcgmin + r-rvmmin + r-setrng +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-optimr/lilac.py b/prepare/r-optimr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-optimr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-optimr/lilac.yaml b/prepare/r-optimr/lilac.yaml new file mode 100644 index 0000000000..80c115521f --- /dev/null +++ b/prepare/r-optimr/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-numderiv +- r-optextras +- r-rcgmin +- r-rvmmin +- r-setrng +update_on: +- regex: optimr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=optimr diff --git a/prepare/r-optimx/PKGBUILD b/prepare/r-optimx/PKGBUILD new file mode 100644 index 0000000000..08dd3b8f0b --- /dev/null +++ b/prepare/r-optimx/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=optimx +_pkgver=2021-10.12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Expanded Replacement and Extension of the 'optim' Function" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-numderiv +) +optdepends=( + r-bb + r-dfoptim + r-knitr + r-lbfgs + r-lbfgsb3c + r-minqa + r-rmarkdown + r-setrng + r-subplex + r-ucminf +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-optimx/lilac.py b/prepare/r-optimx/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-optimx/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-optimx/lilac.yaml b/prepare/r-optimx/lilac.yaml new file mode 100644 index 0000000000..a0b83c9c18 --- /dev/null +++ b/prepare/r-optimx/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-numderiv +update_on: +- regex: optimx_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=optimx diff --git a/prepare/r-optparse/PKGBUILD b/prepare/r-optparse/PKGBUILD new file mode 100644 index 0000000000..b07821bb26 --- /dev/null +++ b/prepare/r-optparse/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=optparse +_pkgver=1.7.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Command Line Option Parser' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-getopt +) +optdepends=( + r-knitr + r-stringr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-optparse/lilac.py b/prepare/r-optparse/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-optparse/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-optparse/lilac.yaml b/prepare/r-optparse/lilac.yaml new file mode 100644 index 0000000000..f1390da018 --- /dev/null +++ b/prepare/r-optparse/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-getopt +update_on: +- regex: optparse_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=optparse diff --git a/prepare/r-opweight/PKGBUILD b/prepare/r-opweight/PKGBUILD new file mode 100644 index 0000000000..a237bcecfa --- /dev/null +++ b/prepare/r-opweight/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OPWeight +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Optimal p-value weighting with independent information' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-qvalue + r-tibble +) +optdepends=( + r-airway + r-biocstyle + r-cowplot + r-deseq2 + r-devtools + r-ggplot2 + r-gridextra + r-knitr + r-matrix + r-rmarkdown + r-scales + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-opweight/lilac.py b/prepare/r-opweight/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-opweight/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-opweight/lilac.yaml b/prepare/r-opweight/lilac.yaml new file mode 100644 index 0000000000..92da883617 --- /dev/null +++ b/prepare/r-opweight/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-qvalue +- r-tibble +update_on: +- regex: OPWeight_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OPWeight diff --git a/prepare/r-orcme/PKGBUILD b/prepare/r-orcme/PKGBUILD new file mode 100644 index 0000000000..18fb47e0b3 --- /dev/null +++ b/prepare/r-orcme/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ORCME +_pkgver=2.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Order Restricted Clustering for Microarray Experiments' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-iso +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-orcme/lilac.py b/prepare/r-orcme/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-orcme/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-orcme/lilac.yaml b/prepare/r-orcme/lilac.yaml new file mode 100644 index 0000000000..6dceb071e7 --- /dev/null +++ b/prepare/r-orcme/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-iso +update_on: +- regex: ORCME_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ORCME diff --git a/prepare/r-orderedlist/PKGBUILD b/prepare/r-orderedlist/PKGBUILD new file mode 100644 index 0000000000..c3e2c52f3b --- /dev/null +++ b/prepare/r-orderedlist/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OrderedList +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Similarities of Ordered Gene Lists' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-twilight +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-orderedlist/lilac.py b/prepare/r-orderedlist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-orderedlist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-orderedlist/lilac.yaml b/prepare/r-orderedlist/lilac.yaml new file mode 100644 index 0000000000..6da11da4f7 --- /dev/null +++ b/prepare/r-orderedlist/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-twilight +update_on: +- regex: OrderedList_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OrderedList diff --git a/prepare/r-ore/PKGBUILD b/prepare/r-ore/PKGBUILD new file mode 100644 index 0000000000..a2c9249f06 --- /dev/null +++ b/prepare/r-ore/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ore +_pkgver=1.7.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R Interface to the Onigmo Regular Expression Library' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +optdepends=( + r-covr + r-crayon + r-rex + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENCE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ore/lilac.py b/prepare/r-ore/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ore/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ore/lilac.yaml b/prepare/r-ore/lilac.yaml new file mode 100644 index 0000000000..990f000265 --- /dev/null +++ b/prepare/r-ore/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ore_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ore diff --git a/prepare/r-orfhunter/PKGBUILD b/prepare/r-orfhunter/PKGBUILD new file mode 100644 index 0000000000..87a32b74af --- /dev/null +++ b/prepare/r-orfhunter/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ORFhunteR +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Predict open reading frames in nucleotide sequences' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-bsgenome.hsapiens.ucsc.hg38 + r-data.table + r-peptides + r-randomforest + r-rcpp + r-rtracklayer + r-stringr + r-xfun +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-orfhunter/lilac.py b/prepare/r-orfhunter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-orfhunter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-orfhunter/lilac.yaml b/prepare/r-orfhunter/lilac.yaml new file mode 100644 index 0000000000..8c7b8b4343 --- /dev/null +++ b/prepare/r-orfhunter/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome.hsapiens.ucsc.hg38 +- r-data.table +- r-peptides +- r-randomforest +- r-rcpp +- r-rtracklayer +- r-stringr +- r-xfun +update_on: +- regex: ORFhunteR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ORFhunteR diff --git a/prepare/r-orfik/PKGBUILD b/prepare/r-orfik/PKGBUILD new file mode 100644 index 0000000000..d9e7b037d4 --- /dev/null +++ b/prepare/r-orfik/PKGBUILD @@ -0,0 +1,61 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ORFik +_pkgver=1.14.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Open Reading Frames in Genomics' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-biocgenerics + r-biocparallel + r-biomartr + r-biostrings + r-bsgenome + r-cowplot + r-data.table + r-deseq2 + r-fst + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggally + r-ggplot2 + r-gridextra + r-httr + r-iranges + r-jsonlite + r-r.utils + r-rcpp + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-xml2 +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-orfik/lilac.py b/prepare/r-orfik/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-orfik/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-orfik/lilac.yaml b/prepare/r-orfik/lilac.yaml new file mode 100644 index 0000000000..7d942e4b3b --- /dev/null +++ b/prepare/r-orfik/lilac.yaml @@ -0,0 +1,36 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-biocparallel +- r-biomartr +- r-biostrings +- r-bsgenome +- r-cowplot +- r-data.table +- r-deseq2 +- r-fst +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggally +- r-ggplot2 +- r-gridextra +- r-httr +- r-iranges +- r-jsonlite +- r-r.utils +- r-rcpp +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +- r-xml2 +update_on: +- regex: ORFik_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ORFik diff --git a/prepare/r-org.bt.eg.db/PKGBUILD b/prepare/r-org.bt.eg.db/PKGBUILD new file mode 100644 index 0000000000..5ea7459422 --- /dev/null +++ b/prepare/r-org.bt.eg.db/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=org.Bt.eg.db +_pkgver=3.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genome wide annotation for Bovine' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi +) +optdepends=( + r-annotate + r-dbi + r-runit +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-org.bt.eg.db/lilac.py b/prepare/r-org.bt.eg.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-org.bt.eg.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-org.bt.eg.db/lilac.yaml b/prepare/r-org.bt.eg.db/lilac.yaml new file mode 100644 index 0000000000..0ef5502240 --- /dev/null +++ b/prepare/r-org.bt.eg.db/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +update_on: +- regex: org.Bt.eg.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/org.Bt.eg.db diff --git a/prepare/r-org.dm.eg.db/PKGBUILD b/prepare/r-org.dm.eg.db/PKGBUILD new file mode 100644 index 0000000000..8e8919e574 --- /dev/null +++ b/prepare/r-org.dm.eg.db/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=org.Dm.eg.db +_pkgver=3.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genome wide annotation for Fly' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi +) +optdepends=( + r-annotate + r-dbi + r-runit +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-org.dm.eg.db/lilac.py b/prepare/r-org.dm.eg.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-org.dm.eg.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-org.dm.eg.db/lilac.yaml b/prepare/r-org.dm.eg.db/lilac.yaml new file mode 100644 index 0000000000..766c38244a --- /dev/null +++ b/prepare/r-org.dm.eg.db/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +update_on: +- regex: org.Dm.eg.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/org.Dm.eg.db diff --git a/prepare/r-org.dr.eg.db/PKGBUILD b/prepare/r-org.dr.eg.db/PKGBUILD new file mode 100644 index 0000000000..96a2370caa --- /dev/null +++ b/prepare/r-org.dr.eg.db/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=org.Dr.eg.db +_pkgver=3.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genome wide annotation for Zebrafish' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi +) +optdepends=( + r-annotate + r-dbi + r-runit +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-org.dr.eg.db/lilac.py b/prepare/r-org.dr.eg.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-org.dr.eg.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-org.dr.eg.db/lilac.yaml b/prepare/r-org.dr.eg.db/lilac.yaml new file mode 100644 index 0000000000..be0d130574 --- /dev/null +++ b/prepare/r-org.dr.eg.db/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +update_on: +- regex: org.Dr.eg.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/org.Dr.eg.db diff --git a/prepare/r-org.hs.eg.db/PKGBUILD b/prepare/r-org.hs.eg.db/PKGBUILD new file mode 100644 index 0000000000..df183e0e00 --- /dev/null +++ b/prepare/r-org.hs.eg.db/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=org.Hs.eg.db +_pkgver=3.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genome wide annotation for Human' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi +) +optdepends=( + r-annotate + r-dbi + r-runit +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-org.hs.eg.db/lilac.py b/prepare/r-org.hs.eg.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-org.hs.eg.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-org.hs.eg.db/lilac.yaml b/prepare/r-org.hs.eg.db/lilac.yaml new file mode 100644 index 0000000000..6c62edb00f --- /dev/null +++ b/prepare/r-org.hs.eg.db/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +update_on: +- regex: org.Hs.eg.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/org.Hs.eg.db diff --git a/prepare/r-org.mm.eg.db/PKGBUILD b/prepare/r-org.mm.eg.db/PKGBUILD new file mode 100644 index 0000000000..956d04faec --- /dev/null +++ b/prepare/r-org.mm.eg.db/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=org.Mm.eg.db +_pkgver=3.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genome wide annotation for Mouse' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi +) +optdepends=( + r-annotate + r-dbi + r-runit +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-org.mm.eg.db/lilac.py b/prepare/r-org.mm.eg.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-org.mm.eg.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-org.mm.eg.db/lilac.yaml b/prepare/r-org.mm.eg.db/lilac.yaml new file mode 100644 index 0000000000..337a1c107b --- /dev/null +++ b/prepare/r-org.mm.eg.db/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +update_on: +- regex: org.Mm.eg.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/org.Mm.eg.db diff --git a/prepare/r-org.rn.eg.db/PKGBUILD b/prepare/r-org.rn.eg.db/PKGBUILD new file mode 100644 index 0000000000..6c1d146a94 --- /dev/null +++ b/prepare/r-org.rn.eg.db/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=org.Rn.eg.db +_pkgver=3.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genome wide annotation for Rat' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi +) +optdepends=( + r-annotate + r-dbi + r-runit +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-org.rn.eg.db/lilac.py b/prepare/r-org.rn.eg.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-org.rn.eg.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-org.rn.eg.db/lilac.yaml b/prepare/r-org.rn.eg.db/lilac.yaml new file mode 100644 index 0000000000..54acfb153f --- /dev/null +++ b/prepare/r-org.rn.eg.db/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +update_on: +- regex: org.Rn.eg.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/org.Rn.eg.db diff --git a/prepare/r-org.sc.sgd.db/PKGBUILD b/prepare/r-org.sc.sgd.db/PKGBUILD new file mode 100644 index 0000000000..87d2982966 --- /dev/null +++ b/prepare/r-org.sc.sgd.db/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=org.Sc.sgd.db +_pkgver=3.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genome wide annotation for Yeast' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi +) +optdepends=( + r-annotate + r-dbi + r-runit +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-org.sc.sgd.db/lilac.py b/prepare/r-org.sc.sgd.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-org.sc.sgd.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-org.sc.sgd.db/lilac.yaml b/prepare/r-org.sc.sgd.db/lilac.yaml new file mode 100644 index 0000000000..4c696dbbae --- /dev/null +++ b/prepare/r-org.sc.sgd.db/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +update_on: +- regex: org.Sc.sgd.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/org.Sc.sgd.db diff --git a/prepare/r-organism.dplyr/PKGBUILD b/prepare/r-organism.dplyr/PKGBUILD new file mode 100644 index 0000000000..d48995f25e --- /dev/null +++ b/prepare/r-organism.dplyr/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Organism.dplyr +_pkgver=1.22.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='dplyr-based Access to Bioconductor Annotation Resources' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-annotationfilter + r-biocfilecache + r-dbi + r-dbplyr + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-rlang + r-rsqlite + r-s4vectors + r-tibble +) +optdepends=( + r-biocstyle + r-ggplot2 + r-knitr + r-org.hs.eg.db + r-org.mm.eg.db + r-rmarkdown + r-testthat + r-txdb.hsapiens.ucsc.hg38.knowngene + r-txdb.mmusculus.ucsc.mm10.ensgene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-organism.dplyr/lilac.py b/prepare/r-organism.dplyr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-organism.dplyr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-organism.dplyr/lilac.yaml b/prepare/r-organism.dplyr/lilac.yaml new file mode 100644 index 0000000000..db0a3acb2b --- /dev/null +++ b/prepare/r-organism.dplyr/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationfilter +- r-biocfilecache +- r-dbi +- r-dbplyr +- r-dplyr +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-rlang +- r-rsqlite +- r-s4vectors +- r-tibble +update_on: +- regex: Organism.dplyr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Organism.dplyr diff --git a/prepare/r-organismdbi/PKGBUILD b/prepare/r-organismdbi/PKGBUILD new file mode 100644 index 0000000000..53d8d96f7f --- /dev/null +++ b/prepare/r-organismdbi/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OrganismDbi +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Software to enable the smooth interfacing of different database packages' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biobase + r-biocgenerics + r-biocmanager + r-dbi + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-rbgl + r-s4vectors +) +optdepends=( + r-annotationhub + r-biomart + r-bsgenome.hsapiens.ucsc.hg19 + r-fdb.ucsc.trnas + r-homo.sapiens + r-mirbase.db + r-rattus.norvegicus + r-rmariadb + r-rtracklayer + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-organismdbi/lilac.py b/prepare/r-organismdbi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-organismdbi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-organismdbi/lilac.yaml b/prepare/r-organismdbi/lilac.yaml new file mode 100644 index 0000000000..add205a240 --- /dev/null +++ b/prepare/r-organismdbi/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-biocmanager +- r-dbi +- r-genomicfeatures +- r-genomicranges +- r-graph +- r-iranges +- r-rbgl +- r-s4vectors +update_on: +- regex: OrganismDbi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OrganismDbi diff --git a/prepare/r-orgmassspecr/PKGBUILD b/prepare/r-orgmassspecr/PKGBUILD new file mode 100644 index 0000000000..9e9029303d --- /dev/null +++ b/prepare/r-orgmassspecr/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OrgMassSpecR +_pkgver=0.5-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Organic Mass Spectrometry' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +optdepends=( + r-knitr + r-lattice + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-orgmassspecr/lilac.py b/prepare/r-orgmassspecr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-orgmassspecr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-orgmassspecr/lilac.yaml b/prepare/r-orgmassspecr/lilac.yaml new file mode 100644 index 0000000000..bc8c09408d --- /dev/null +++ b/prepare/r-orgmassspecr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: OrgMassSpecR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=OrgMassSpecR diff --git a/prepare/r-oriclust/PKGBUILD b/prepare/r-oriclust/PKGBUILD new file mode 100644 index 0000000000..4c3bb9a9d5 --- /dev/null +++ b/prepare/r-oriclust/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ORIClust +_pkgver=1.0-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Order-restricted Information Criterion-based Clustering Algorithm' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-oriclust/lilac.py b/prepare/r-oriclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-oriclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-oriclust/lilac.yaml b/prepare/r-oriclust/lilac.yaml new file mode 100644 index 0000000000..ac36c2762b --- /dev/null +++ b/prepare/r-oriclust/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ORIClust_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ORIClust diff --git a/prepare/r-origami/PKGBUILD b/prepare/r-origami/PKGBUILD new file mode 100644 index 0000000000..9cf5fec289 --- /dev/null +++ b/prepare/r-origami/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=origami +_pkgver=1.0.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generalized Framework for Cross-Validation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-assertthat + r-data.table + r-future + r-future.apply + r-listenv +) +optdepends=( + r-class + r-forecast + r-glmnet + r-knitr + r-randomforest + r-rmarkdown + r-stringr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-origami/lilac.py b/prepare/r-origami/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-origami/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-origami/lilac.yaml b/prepare/r-origami/lilac.yaml new file mode 100644 index 0000000000..81c8fd9d27 --- /dev/null +++ b/prepare/r-origami/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-assertthat +- r-data.table +- r-future +- r-future.apply +- r-listenv +update_on: +- regex: origami_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=origami diff --git a/prepare/r-orqa/PKGBUILD b/prepare/r-orqa/PKGBUILD new file mode 100644 index 0000000000..03212ea215 --- /dev/null +++ b/prepare/r-orqa/PKGBUILD @@ -0,0 +1,30 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=orQA +_pkgver=0.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Order Restricted Assessment Of Microarray Titration Experiments' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-genefilter + r-gtools + r-rcpp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-orqa/lilac.py b/prepare/r-orqa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-orqa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-orqa/lilac.yaml b/prepare/r-orqa/lilac.yaml new file mode 100644 index 0000000000..f4e6456320 --- /dev/null +++ b/prepare/r-orqa/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genefilter +- r-gtools +- r-rcpp +update_on: +- regex: orQA_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=orQA diff --git a/prepare/r-orthogene/PKGBUILD b/prepare/r-orthogene/PKGBUILD new file mode 100644 index 0000000000..a9cdc95b3e --- /dev/null +++ b/prepare/r-orthogene/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=orthogene +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interspecies gene mapping' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-babelgene + r-data.table + r-delayedarray + r-delayedmatrixstats + r-dplyr + r-genomeinfodbdata + r-ggplot2 + r-ggpubr + r-gprofiler2 + r-grr + r-homologene + r-jsonlite + r-matrix.utils + r-patchwork + r-repmis +) +optdepends=( + r-badger + r-biocstyle + r-covr + r-here + r-knitr + r-markdown + r-piggyback + r-remotes + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-orthogene/lilac.py b/prepare/r-orthogene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-orthogene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-orthogene/lilac.yaml b/prepare/r-orthogene/lilac.yaml new file mode 100644 index 0000000000..a49fb4fe36 --- /dev/null +++ b/prepare/r-orthogene/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-babelgene +- r-data.table +- r-delayedarray +- r-delayedmatrixstats +- r-dplyr +- r-genomeinfodbdata +- r-ggplot2 +- r-ggpubr +- r-gprofiler2 +- r-grr +- r-homologene +- r-jsonlite +- r-matrix.utils +- r-patchwork +- r-repmis +update_on: +- regex: orthogene_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/orthogene diff --git a/prepare/r-osat/PKGBUILD b/prepare/r-osat/PKGBUILD new file mode 100644 index 0000000000..7738adbfce --- /dev/null +++ b/prepare/r-osat/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OSAT +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='OSAT: Optimal Sample Assignment Tool' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-biobase + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-osat/lilac.py b/prepare/r-osat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-osat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-osat/lilac.yaml b/prepare/r-osat/lilac.yaml new file mode 100644 index 0000000000..4a63ec0320 --- /dev/null +++ b/prepare/r-osat/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: OSAT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OSAT diff --git a/prepare/r-oscope/PKGBUILD b/prepare/r-oscope/PKGBUILD new file mode 100644 index 0000000000..75a7e80431 --- /dev/null +++ b/prepare/r-oscope/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Oscope +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-ebseq + r-testthat +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-oscope/lilac.py b/prepare/r-oscope/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-oscope/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-oscope/lilac.yaml b/prepare/r-oscope/lilac.yaml new file mode 100644 index 0000000000..758fcee9a3 --- /dev/null +++ b/prepare/r-oscope/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-ebseq +- r-testthat +update_on: +- regex: Oscope_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Oscope diff --git a/prepare/r-osfr/PKGBUILD b/prepare/r-osfr/PKGBUILD new file mode 100644 index 0000000000..ed0b690487 --- /dev/null +++ b/prepare/r-osfr/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=osfr +_pkgver=0.2.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Interface to the 'Open Science Framework' ('OSF')" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-crul + r-fs + r-httr + r-jsonlite + r-memoise + r-purrr + r-rlang + r-stringi + r-tibble +) +optdepends=( + r-covr + r-dplyr + r-knitr + r-lintr + r-logger + r-rmarkdown + r-rprojroot + r-spelling + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-osfr/lilac.py b/prepare/r-osfr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-osfr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-osfr/lilac.yaml b/prepare/r-osfr/lilac.yaml new file mode 100644 index 0000000000..aed2a85d50 --- /dev/null +++ b/prepare/r-osfr/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-crul +- r-fs +- r-httr +- r-jsonlite +- r-memoise +- r-purrr +- r-rlang +- r-stringi +- r-tibble +update_on: +- regex: osfr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=osfr diff --git a/prepare/r-otubase/PKGBUILD b/prepare/r-otubase/PKGBUILD new file mode 100644 index 0000000000..43d216fb48 --- /dev/null +++ b/prepare/r-otubase/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OTUbase +_pkgver=1.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Provides structure and functions for the analysis of OTU data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biostrings + r-iranges + r-s4vectors + r-shortread + r-vegan +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-otubase/lilac.py b/prepare/r-otubase/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-otubase/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-otubase/lilac.yaml b/prepare/r-otubase/lilac.yaml new file mode 100644 index 0000000000..514d6233ca --- /dev/null +++ b/prepare/r-otubase/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biostrings +- r-iranges +- r-s4vectors +- r-shortread +- r-vegan +update_on: +- regex: OTUbase_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OTUbase diff --git a/prepare/r-outliers/PKGBUILD b/prepare/r-outliers/PKGBUILD new file mode 100644 index 0000000000..8f69556230 --- /dev/null +++ b/prepare/r-outliers/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=outliers +_pkgver=0.14 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tests for outliers' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-outliers/lilac.py b/prepare/r-outliers/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-outliers/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-outliers/lilac.yaml b/prepare/r-outliers/lilac.yaml new file mode 100644 index 0000000000..43afe1eb55 --- /dev/null +++ b/prepare/r-outliers/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: outliers_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=outliers diff --git a/prepare/r-outrider/PKGBUILD b/prepare/r-outrider/PKGBUILD new file mode 100644 index 0000000000..0be4042ebb --- /dev/null +++ b/prepare/r-outrider/PKGBUILD @@ -0,0 +1,63 @@ +# Maintainer: Guoyi Zhang + +_pkgname=OUTRIDER +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='OUTRIDER - OUTlier in RNA-Seq fInDER' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-bbmisc + r-biocgenerics + r-biocparallel + r-data.table + r-deseq2 + r-generics + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-heatmaply + r-iranges + r-matrixstats + r-pcamethods + r-pheatmap + r-plotly + r-plyr + r-prroc + r-rcolorbrewer + r-rcpp + r-rcpparmadillo + r-reshape2 + r-s4vectors + r-scales + r-summarizedexperiment +) +optdepends=( + r-annotationdbi + r-beeswarm + r-biocstyle + r-covr + r-knitr + r-org.hs.eg.db + r-rmariadb + r-rmarkdown + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-outrider/lilac.py b/prepare/r-outrider/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-outrider/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-outrider/lilac.yaml b/prepare/r-outrider/lilac.yaml new file mode 100644 index 0000000000..f1ab0de57d --- /dev/null +++ b/prepare/r-outrider/lilac.yaml @@ -0,0 +1,33 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bbmisc +- r-biocgenerics +- r-biocparallel +- r-data.table +- r-deseq2 +- r-generics +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-heatmaply +- r-iranges +- r-matrixstats +- r-pcamethods +- r-pheatmap +- r-plotly +- r-plyr +- r-prroc +- r-rcolorbrewer +- r-rcpp +- r-rcpparmadillo +- r-reshape2 +- r-s4vectors +- r-scales +- r-summarizedexperiment +update_on: +- regex: OUTRIDER_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OUTRIDER diff --git a/prepare/r-oveseg/PKGBUILD b/prepare/r-oveseg/PKGBUILD new file mode 100644 index 0000000000..0fa27e5341 --- /dev/null +++ b/prepare/r-oveseg/PKGBUILD @@ -0,0 +1,43 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=OVESEG +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='OVESEG-test to detect tissue/cell-specific markers' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-fdrtool + r-limma + r-rcpp + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-ggplot2 + r-grid + r-gridextra + r-knitr + r-reshape2 + r-rmarkdown + r-scales + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-oveseg/lilac.py b/prepare/r-oveseg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-oveseg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-oveseg/lilac.yaml b/prepare/r-oveseg/lilac.yaml new file mode 100644 index 0000000000..a274e72bf9 --- /dev/null +++ b/prepare/r-oveseg/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-fdrtool +- r-limma +- r-rcpp +- r-summarizedexperiment +update_on: +- regex: OVESEG_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/OVESEG diff --git a/prepare/r-paa/PKGBUILD b/prepare/r-paa/PKGBUILD new file mode 100644 index 0000000000..f4b5156a72 --- /dev/null +++ b/prepare/r-paa/PKGBUILD @@ -0,0 +1,43 @@ +# system requirements: C++ software package Random Jungle +# Maintainer: Guoyi Zhang + +_pkgname=PAA +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PAA (Protein Array Analyzer)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-e1071 + r-gplots + r-gtools + r-limma + r-mrmre + r-randomforest + r-rcpp + r-rocr + r-sva +) +optdepends=( + r-biocgenerics + r-biocstyle + r-runit + r-vsn +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-paa/lilac.py b/prepare/r-paa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-paa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-paa/lilac.yaml b/prepare/r-paa/lilac.yaml new file mode 100644 index 0000000000..215bed2cb0 --- /dev/null +++ b/prepare/r-paa/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-e1071 +- r-gplots +- r-gtools +- r-limma +- r-mrmre +- r-randomforest +- r-rcpp +- r-rocr +- r-sva +update_on: +- regex: PAA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PAA diff --git a/prepare/r-packfinder/PKGBUILD b/prepare/r-packfinder/PKGBUILD new file mode 100644 index 0000000000..3d3232ce15 --- /dev/null +++ b/prepare/r-packfinder/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=packFinder +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='de novo Annotation of Pack-TYPE Transposable Elements' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-biostrings + r-genomicranges + r-iranges + r-kmer + r-s4vectors +) +optdepends=( + r-bioccheck + r-biocstyle + r-biocviews + r-biomartr + r-dendextend + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-packfinder/lilac.py b/prepare/r-packfinder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-packfinder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-packfinder/lilac.yaml b/prepare/r-packfinder/lilac.yaml new file mode 100644 index 0000000000..851c7d36e8 --- /dev/null +++ b/prepare/r-packfinder/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-biostrings +- r-genomicranges +- r-iranges +- r-kmer +- r-s4vectors +update_on: +- regex: packFinder_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/packFinder diff --git a/prepare/r-padma/PKGBUILD b/prepare/r-padma/PKGBUILD new file mode 100644 index 0000000000..991e0c6cdc --- /dev/null +++ b/prepare/r-padma/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=padma +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-factominer + r-multiassayexperiment + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-car + r-cowplot + r-ggplot2 + r-ggrepel + r-keggrest + r-knitr + r-missmda + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-padma/lilac.py b/prepare/r-padma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-padma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-padma/lilac.yaml b/prepare/r-padma/lilac.yaml new file mode 100644 index 0000000000..6b8ce8ccb2 --- /dev/null +++ b/prepare/r-padma/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-factominer +- r-multiassayexperiment +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: padma_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/padma diff --git a/prepare/r-padog/PKGBUILD b/prepare/r-padog/PKGBUILD new file mode 100644 index 0000000000..474fcef71f --- /dev/null +++ b/prepare/r-padog/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PADOG +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biobase + r-dorng + r-foreach + r-gsa + r-hgu133a.db + r-hgu133plus2.db + r-keggdzpathwaysgeo + r-keggrest + r-limma +) +optdepends=( + r-doparallel + r-parallel +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-padog/lilac.py b/prepare/r-padog/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-padog/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-padog/lilac.yaml b/prepare/r-padog/lilac.yaml new file mode 100644 index 0000000000..8a9051d0b6 --- /dev/null +++ b/prepare/r-padog/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-dorng +- r-foreach +- r-gsa +- r-hgu133a.db +- r-hgu133plus2.db +- r-keggdzpathwaysgeo +- r-keggrest +- r-limma +update_on: +- regex: PADOG_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PADOG diff --git a/prepare/r-pagerank/PKGBUILD b/prepare/r-pagerank/PKGBUILD new file mode 100644 index 0000000000..999bfb8dff --- /dev/null +++ b/prepare/r-pagerank/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pageRank +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Temporal and Multiplex PageRank for Gene Regulatory Network Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicranges + r-igraph + r-motifmatchr +) +optdepends=( + r-annotate + r-bcellviper + r-bsgenome.hsapiens.ucsc.hg19 + r-genomicfeatures + r-jaspar2018 + r-org.hs.eg.db + r-tfbstools + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pagerank/lilac.py b/prepare/r-pagerank/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pagerank/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pagerank/lilac.yaml b/prepare/r-pagerank/lilac.yaml new file mode 100644 index 0000000000..76bc6fe160 --- /dev/null +++ b/prepare/r-pagerank/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-igraph +- r-motifmatchr +update_on: +- regex: pageRank_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pageRank diff --git a/prepare/r-paintmap/PKGBUILD b/prepare/r-paintmap/PKGBUILD new file mode 100644 index 0000000000..b563b19a48 --- /dev/null +++ b/prepare/r-paintmap/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=paintmap +_pkgver=1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Plotting Paintmaps' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-paintmap/lilac.py b/prepare/r-paintmap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-paintmap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-paintmap/lilac.yaml b/prepare/r-paintmap/lilac.yaml new file mode 100644 index 0000000000..96c0cdd5b9 --- /dev/null +++ b/prepare/r-paintmap/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: paintmap_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=paintmap diff --git a/prepare/r-pairadise/PKGBUILD b/prepare/r-pairadise/PKGBUILD new file mode 100644 index 0000000000..b9a78e759c --- /dev/null +++ b/prepare/r-pairadise/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PAIRADISE +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PAIRADISE: Paired analysis of differential isoform expression' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-abind + r-biocparallel + r-nloptr + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pairadise/lilac.py b/prepare/r-pairadise/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pairadise/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pairadise/lilac.yaml b/prepare/r-pairadise/lilac.yaml new file mode 100644 index 0000000000..3d4452470f --- /dev/null +++ b/prepare/r-pairadise/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-biocparallel +- r-nloptr +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: PAIRADISE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PAIRADISE diff --git a/prepare/r-paircompviz/PKGBUILD b/prepare/r-paircompviz/PKGBUILD new file mode 100644 index 0000000000..38366e50af --- /dev/null +++ b/prepare/r-paircompviz/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=paircompviz +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multiple comparison test visualization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rgraphviz +) +optdepends=( + r-multcomp + r-plyr + r-reshape + r-rpart + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-paircompviz/lilac.py b/prepare/r-paircompviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-paircompviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-paircompviz/lilac.yaml b/prepare/r-paircompviz/lilac.yaml new file mode 100644 index 0000000000..ee0c13ccbd --- /dev/null +++ b/prepare/r-paircompviz/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rgraphviz +update_on: +- regex: paircompviz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/paircompviz diff --git a/prepare/r-paireddata/PKGBUILD b/prepare/r-paireddata/PKGBUILD new file mode 100644 index 0000000000..f27fbfc02e --- /dev/null +++ b/prepare/r-paireddata/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PairedData +_pkgver=1.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Paired Data Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-gld + r-mvtnorm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-paireddata/lilac.py b/prepare/r-paireddata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-paireddata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-paireddata/lilac.yaml b/prepare/r-paireddata/lilac.yaml new file mode 100644 index 0000000000..024d6e66b8 --- /dev/null +++ b/prepare/r-paireddata/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gld +- r-mvtnorm +update_on: +- regex: PairedData_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=PairedData diff --git a/prepare/r-pairkat/PKGBUILD b/prepare/r-pairkat/PKGBUILD new file mode 100644 index 0000000000..4d3ccd4d06 --- /dev/null +++ b/prepare/r-pairkat/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pairkat +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PaIRKAT' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-compquadform + r-data.table + r-dplyr + r-igraph + r-keggrest + r-magrittr + r-s4vectors + r-summarizedexperiment + r-tibble +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pairkat/lilac.py b/prepare/r-pairkat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pairkat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pairkat/lilac.yaml b/prepare/r-pairkat/lilac.yaml new file mode 100644 index 0000000000..804fa6918e --- /dev/null +++ b/prepare/r-pairkat/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-compquadform +- r-data.table +- r-dplyr +- r-igraph +- r-keggrest +- r-magrittr +- r-s4vectors +- r-summarizedexperiment +- r-tibble +update_on: +- regex: pairkat_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pairkat diff --git a/prepare/r-pairsd3/PKGBUILD b/prepare/r-pairsd3/PKGBUILD new file mode 100644 index 0000000000..15be10fbf5 --- /dev/null +++ b/prepare/r-pairsd3/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pairsD3 +_pkgver=0.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='D3 Scatterplot Matrices' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-htmlwidgets + r-shiny +) +optdepends=( + r-knitr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pairsd3/lilac.py b/prepare/r-pairsd3/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pairsd3/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pairsd3/lilac.yaml b/prepare/r-pairsd3/lilac.yaml new file mode 100644 index 0000000000..ba1c39d438 --- /dev/null +++ b/prepare/r-pairsd3/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmlwidgets +- r-shiny +update_on: +- regex: pairsD3_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pairsD3 diff --git a/prepare/r-pals/PKGBUILD b/prepare/r-pals/PKGBUILD new file mode 100644 index 0000000000..16e9bd8d0b --- /dev/null +++ b/prepare/r-pals/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pals +_pkgver=1.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Color Palettes, Colormaps, and Tools to Evaluate Them' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-colorspace + r-dichromat + r-mapproj + r-maps +) +optdepends=( + r-classint + r-ggplot2 + r-knitr + r-latticeextra + r-reshape2 + r-rgl + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pals/lilac.py b/prepare/r-pals/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pals/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pals/lilac.yaml b/prepare/r-pals/lilac.yaml new file mode 100644 index 0000000000..84aae4dcfa --- /dev/null +++ b/prepare/r-pals/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colorspace +- r-dichromat +- r-mapproj +- r-maps +update_on: +- regex: pals_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pals diff --git a/prepare/r-pamr/PKGBUILD b/prepare/r-pamr/PKGBUILD new file mode 100644 index 0000000000..7178a17d7c --- /dev/null +++ b/prepare/r-pamr/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pamr +_pkgver=1.56.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pam: Prediction Analysis for Microarrays' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pamr/lilac.py b/prepare/r-pamr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pamr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pamr/lilac.yaml b/prepare/r-pamr/lilac.yaml new file mode 100644 index 0000000000..40b737184d --- /dev/null +++ b/prepare/r-pamr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pamr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pamr diff --git a/prepare/r-pandar/PKGBUILD b/prepare/r-pandar/PKGBUILD new file mode 100644 index 0000000000..99864ec425 --- /dev/null +++ b/prepare/r-pandar/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pandaR +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PANDA Algorithm' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-ggplot2 + r-hexbin + r-igraph + r-matrixstats + r-plyr + r-reshape + r-runit +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pandar/lilac.py b/prepare/r-pandar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pandar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pandar/lilac.yaml b/prepare/r-pandar/lilac.yaml new file mode 100644 index 0000000000..1575b6be3d --- /dev/null +++ b/prepare/r-pandar/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-ggplot2 +- r-hexbin +- r-igraph +- r-matrixstats +- r-plyr +- r-reshape +- r-runit +update_on: +- regex: pandaR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pandaR diff --git a/prepare/r-pander/PKGBUILD b/prepare/r-pander/PKGBUILD new file mode 100644 index 0000000000..8163696624 --- /dev/null +++ b/prepare/r-pander/PKGBUILD @@ -0,0 +1,55 @@ +# system requirements: pandoc (https://johnmacfarlane.net/pandoc) forexporting markdown files to other formats. +# Maintainer: Guoyi Zhang + +_pkgname=pander +_pkgver=0.6.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="An R 'Pandoc' Writer" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('AGPL') +depends=( + r + r-digest + r-rcpp +) +optdepends=( + r-data.table + r-descr + r-epi + r-forecast + r-ggplot2 + r-grid + r-gtable + r-knitr + r-lattice + r-logger + r-mass + r-memisc + r-microbenchmark + r-nlme + r-randomforest + r-reshape + r-rmarkdown + r-rms + r-survival + r-sylly + r-sylly.en + r-tables + r-tseries + r-zoo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pander/lilac.py b/prepare/r-pander/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pander/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pander/lilac.yaml b/prepare/r-pander/lilac.yaml new file mode 100644 index 0000000000..8b32d3d61b --- /dev/null +++ b/prepare/r-pander/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-rcpp +update_on: +- regex: pander_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pander diff --git a/prepare/r-panelcn.mops/PKGBUILD b/prepare/r-panelcn.mops/PKGBUILD new file mode 100644 index 0000000000..80cbbed0f9 --- /dev/null +++ b/prepare/r-panelcn.mops/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=panelcn.mops +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CNV detection tool for targeted NGS panel data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-cn.mops + r-genomeinfodb + r-genomicranges + r-iranges + r-rsamtools + r-s4vectors +) +optdepends=( + r-biocgenerics + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-panelcn.mops/lilac.py b/prepare/r-panelcn.mops/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-panelcn.mops/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-panelcn.mops/lilac.yaml b/prepare/r-panelcn.mops/lilac.yaml new file mode 100644 index 0000000000..c38c7e18c7 --- /dev/null +++ b/prepare/r-panelcn.mops/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cn.mops +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rsamtools +- r-s4vectors +update_on: +- regex: panelcn.mops_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/panelcn.mops diff --git a/prepare/r-panp/PKGBUILD b/prepare/r-panp/PKGBUILD new file mode 100644 index 0000000000..820ef32294 --- /dev/null +++ b/prepare/r-panp/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=panp +_pkgver=1.64.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Presence-Absence Calls from Negative Strand Matching Probesets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-biobase +) +optdepends=( + r-gcrma +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-panp/lilac.py b/prepare/r-panp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-panp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-panp/lilac.yaml b/prepare/r-panp/lilac.yaml new file mode 100644 index 0000000000..892cc9b17c --- /dev/null +++ b/prepare/r-panp/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +update_on: +- regex: panp_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/panp diff --git a/prepare/r-panr/PKGBUILD b/prepare/r-panr/PKGBUILD new file mode 100644 index 0000000000..91681281e7 --- /dev/null +++ b/prepare/r-panr/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PANR +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-igraph + r-pvclust + r-reder +) +optdepends=( + r-snow +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-panr/lilac.py b/prepare/r-panr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-panr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-panr/lilac.yaml b/prepare/r-panr/lilac.yaml new file mode 100644 index 0000000000..e943265a85 --- /dev/null +++ b/prepare/r-panr/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +- r-pvclust +- r-reder +update_on: +- regex: PANR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PANR diff --git a/prepare/r-panvizgenerator/PKGBUILD b/prepare/r-panvizgenerator/PKGBUILD new file mode 100644 index 0000000000..bbf78728b1 --- /dev/null +++ b/prepare/r-panvizgenerator/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PanVizGenerator +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generate PanViz visualisations from your pangenome' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-findmyfriends + r-igraph + r-jsonlite + r-pcamethods + r-shiny +) +optdepends=( + r-biocstyle + r-digest + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-panvizgenerator/lilac.py b/prepare/r-panvizgenerator/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-panvizgenerator/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-panvizgenerator/lilac.yaml b/prepare/r-panvizgenerator/lilac.yaml new file mode 100644 index 0000000000..185586df21 --- /dev/null +++ b/prepare/r-panvizgenerator/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-findmyfriends +- r-igraph +- r-jsonlite +- r-pcamethods +- r-shiny +update_on: +- regex: PanVizGenerator_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PanVizGenerator diff --git a/prepare/r-paralleldist/PKGBUILD b/prepare/r-paralleldist/PKGBUILD new file mode 100644 index 0000000000..d53283a972 --- /dev/null +++ b/prepare/r-paralleldist/PKGBUILD @@ -0,0 +1,38 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=parallelDist +_pkgver=0.2.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Parallel Distance Matrix Computation using Multiple Threads' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcpparmadillo + r-rcppparallel +) +optdepends=( + r-dtw + r-ggplot2 + r-proxy + r-rcpparmadillo + r-rcppxptrutils + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-paralleldist/lilac.py b/prepare/r-paralleldist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-paralleldist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-paralleldist/lilac.yaml b/prepare/r-paralleldist/lilac.yaml new file mode 100644 index 0000000000..3d32833349 --- /dev/null +++ b/prepare/r-paralleldist/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcpparmadillo +- r-rcppparallel +update_on: +- regex: parallelDist_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=parallelDist diff --git a/prepare/r-parallellogger/PKGBUILD b/prepare/r-parallellogger/PKGBUILD new file mode 100644 index 0000000000..27eebaec18 --- /dev/null +++ b/prepare/r-parallellogger/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ParallelLogger +_pkgver=2.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Support for Parallel Computation, Logging, and Function Automation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-jsonlite + r-snow + r-xml2 +) +optdepends=( + r-dt + r-knitr + r-mailr + r-rmarkdown + r-shiny + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-parallellogger/lilac.py b/prepare/r-parallellogger/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-parallellogger/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-parallellogger/lilac.yaml b/prepare/r-parallellogger/lilac.yaml new file mode 100644 index 0000000000..b4e3ea5e9b --- /dev/null +++ b/prepare/r-parallellogger/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-jsonlite +- r-snow +- r-xml2 +update_on: +- regex: ParallelLogger_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ParallelLogger diff --git a/prepare/r-parallelly/PKGBUILD b/prepare/r-parallelly/PKGBUILD new file mode 100644 index 0000000000..9760f8ee5e --- /dev/null +++ b/prepare/r-parallelly/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=parallelly +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Enhancing the 'parallel' Package" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-parallelly/lilac.py b/prepare/r-parallelly/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-parallelly/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-parallelly/lilac.yaml b/prepare/r-parallelly/lilac.yaml new file mode 100644 index 0000000000..3e91b66e5a --- /dev/null +++ b/prepare/r-parallelly/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: parallelly_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=parallelly diff --git a/prepare/r-parallelmap/PKGBUILD b/prepare/r-parallelmap/PKGBUILD new file mode 100644 index 0000000000..8503e67bcf --- /dev/null +++ b/prepare/r-parallelmap/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=parallelMap +_pkgver=1.5.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Unified Interface to Parallelization Back-Ends' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-bbmisc + r-checkmate +) +optdepends=( + r-batchjobs + r-batchtools + r-data.table + r-rmpi + r-rpart + r-snow + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-parallelmap/lilac.py b/prepare/r-parallelmap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-parallelmap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-parallelmap/lilac.yaml b/prepare/r-parallelmap/lilac.yaml new file mode 100644 index 0000000000..d355acdad8 --- /dev/null +++ b/prepare/r-parallelmap/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bbmisc +- r-checkmate +update_on: +- regex: parallelMap_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=parallelMap diff --git a/prepare/r-paramhelpers/PKGBUILD b/prepare/r-paramhelpers/PKGBUILD new file mode 100644 index 0000000000..6bb5b4cefe --- /dev/null +++ b/prepare/r-paramhelpers/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ParamHelpers +_pkgver=1.14 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-backports + r-bbmisc + r-checkmate + r-fastmatch +) +optdepends=( + r-akima + r-covr + r-eaf + r-emoa + r-ggally + r-ggplot2 + r-grid + r-gridextra + r-irace + r-lhs + r-plyr + r-reshape2 + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-paramhelpers/lilac.py b/prepare/r-paramhelpers/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-paramhelpers/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-paramhelpers/lilac.yaml b/prepare/r-paramhelpers/lilac.yaml new file mode 100644 index 0000000000..398c5de886 --- /dev/null +++ b/prepare/r-paramhelpers/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-backports +- r-bbmisc +- r-checkmate +- r-fastmatch +update_on: +- regex: ParamHelpers_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ParamHelpers diff --git a/prepare/r-parglms/PKGBUILD b/prepare/r-parglms/PKGBUILD new file mode 100644 index 0000000000..30c030405f --- /dev/null +++ b/prepare/r-parglms/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=parglms +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='support for parallelized estimation of GLMs/GEEs' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-batchjobs + r-biocgenerics + r-doparallel + r-foreach +) +optdepends=( + r-biocstyle + r-genomeinfodb + r-genomicranges + r-gwascat + r-knitr + r-mass + r-rmarkdown + r-runit + r-sandwich +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-parglms/lilac.py b/prepare/r-parglms/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-parglms/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-parglms/lilac.yaml b/prepare/r-parglms/lilac.yaml new file mode 100644 index 0000000000..250f4b1307 --- /dev/null +++ b/prepare/r-parglms/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-batchjobs +- r-biocgenerics +- r-doparallel +- r-foreach +update_on: +- regex: parglms_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/parglms diff --git a/prepare/r-parmigene/PKGBUILD b/prepare/r-parmigene/PKGBUILD new file mode 100644 index 0000000000..e72246a2e7 --- /dev/null +++ b/prepare/r-parmigene/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=parmigene +_pkgver=1.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Parallel Mutual Information Estimation for Gene Network Reconstruction' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('AGPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-parmigene/lilac.py b/prepare/r-parmigene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-parmigene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-parmigene/lilac.yaml b/prepare/r-parmigene/lilac.yaml new file mode 100644 index 0000000000..765f938c31 --- /dev/null +++ b/prepare/r-parmigene/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: parmigene_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=parmigene diff --git a/prepare/r-parody/PKGBUILD b/prepare/r-parody/PKGBUILD new file mode 100644 index 0000000000..1867c2d9a3 --- /dev/null +++ b/prepare/r-parody/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=parody +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Parametric And Resistant Outlier DYtection' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-parody/lilac.py b/prepare/r-parody/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-parody/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-parody/lilac.yaml b/prepare/r-parody/lilac.yaml new file mode 100644 index 0000000000..86c25547c5 --- /dev/null +++ b/prepare/r-parody/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: parody_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/parody diff --git a/prepare/r-partykit/PKGBUILD b/prepare/r-partykit/PKGBUILD new file mode 100644 index 0000000000..184856fa21 --- /dev/null +++ b/prepare/r-partykit/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=partykit +_pkgver=1.2-15 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Toolkit for Recursive Partytioning' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-formula + r-inum + r-libcoin + r-mvtnorm +) +optdepends=( + r-aer + r-coin + r-datasets + r-mlbench + r-parallel + r-party + r-pmml + r-psychotools + r-psychotree + r-randomforest + r-rjava + r-rweka + r-sandwich + r-strucchange + r-th.data + r-vcd + r-xml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-partykit/lilac.py b/prepare/r-partykit/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-partykit/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-partykit/lilac.yaml b/prepare/r-partykit/lilac.yaml new file mode 100644 index 0000000000..27ae4adc55 --- /dev/null +++ b/prepare/r-partykit/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-formula +- r-inum +- r-libcoin +- r-mvtnorm +update_on: +- regex: partykit_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=partykit diff --git a/prepare/r-pasilla/PKGBUILD b/prepare/r-pasilla/PKGBUILD new file mode 100644 index 0000000000..f64fcfb9e5 --- /dev/null +++ b/prepare/r-pasilla/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pasilla +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +optdepends=( + r-biocstyle + r-dexseq + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pasilla/lilac.py b/prepare/r-pasilla/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pasilla/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pasilla/lilac.yaml b/prepare/r-pasilla/lilac.yaml new file mode 100644 index 0000000000..f6131fe572 --- /dev/null +++ b/prepare/r-pasilla/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pasilla_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pasilla diff --git a/prepare/r-past/PKGBUILD b/prepare/r-past/PKGBUILD new file mode 100644 index 0000000000..f75e6e44b5 --- /dev/null +++ b/prepare/r-past/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PAST +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pathway Association Study Tool (PAST)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-doparallel + r-dplyr + r-foreach + r-genomicranges + r-ggplot2 + r-iterators + r-qvalue + r-rlang + r-rtracklayer + r-s4vectors +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-past/lilac.py b/prepare/r-past/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-past/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-past/lilac.yaml b/prepare/r-past/lilac.yaml new file mode 100644 index 0000000000..a831ec40d0 --- /dev/null +++ b/prepare/r-past/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-dplyr +- r-foreach +- r-genomicranges +- r-ggplot2 +- r-iterators +- r-qvalue +- r-rlang +- r-rtracklayer +- r-s4vectors +update_on: +- regex: PAST_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PAST diff --git a/prepare/r-pastecs/PKGBUILD b/prepare/r-pastecs/PKGBUILD new file mode 100644 index 0000000000..4bc89eaf8e --- /dev/null +++ b/prepare/r-pastecs/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pastecs +_pkgver=1.3.21 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Package for Analysis of Space-Time Ecological Series' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-covr + r-svunit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pastecs/lilac.py b/prepare/r-pastecs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pastecs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pastecs/lilac.yaml b/prepare/r-pastecs/lilac.yaml new file mode 100644 index 0000000000..90dcf85f82 --- /dev/null +++ b/prepare/r-pastecs/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pastecs_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pastecs diff --git a/prepare/r-patchwork/PKGBUILD b/prepare/r-patchwork/PKGBUILD new file mode 100644 index 0000000000..313708eb0f --- /dev/null +++ b/prepare/r-patchwork/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=patchwork +_pkgver=1.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The Composer of Plots' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-ggplot2 + r-gtable +) +optdepends=( + r-covr + r-gridextra + r-gridgraphics + r-knitr + r-png + r-ragg + r-rmarkdown + r-testthat + r-vdiffr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-patchwork/lilac.py b/prepare/r-patchwork/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-patchwork/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-patchwork/lilac.yaml b/prepare/r-patchwork/lilac.yaml new file mode 100644 index 0000000000..3fef2e889e --- /dev/null +++ b/prepare/r-patchwork/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gtable +update_on: +- regex: patchwork_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=patchwork diff --git a/prepare/r-path2ppi/PKGBUILD b/prepare/r-path2ppi/PKGBUILD new file mode 100644 index 0000000000..dc45d282e2 --- /dev/null +++ b/prepare/r-path2ppi/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Path2PPI +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Prediction of pathway-related protein-protein interaction networks' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-igraph +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-path2ppi/lilac.py b/prepare/r-path2ppi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-path2ppi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-path2ppi/lilac.yaml b/prepare/r-path2ppi/lilac.yaml new file mode 100644 index 0000000000..0a8dc477b7 --- /dev/null +++ b/prepare/r-path2ppi/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +update_on: +- regex: Path2PPI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Path2PPI diff --git a/prepare/r-pathifier/PKGBUILD b/prepare/r-pathifier/PKGBUILD new file mode 100644 index 0000000000..f440aabe15 --- /dev/null +++ b/prepare/r-pathifier/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pathifier +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quantify deregulation of pathways in cancer' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-princurve + r-r.oo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pathifier/lilac.py b/prepare/r-pathifier/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pathifier/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pathifier/lilac.yaml b/prepare/r-pathifier/lilac.yaml new file mode 100644 index 0000000000..41b52f227e --- /dev/null +++ b/prepare/r-pathifier/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-princurve +- r-r.oo +update_on: +- regex: pathifier_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pathifier diff --git a/prepare/r-pathnet/PKGBUILD b/prepare/r-pathnet/PKGBUILD new file mode 100644 index 0000000000..9834d8dd51 --- /dev/null +++ b/prepare/r-pathnet/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PathNet +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package for pathway analysis using topological information' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biocgenerics + r-pathnetdata + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pathnet/lilac.py b/prepare/r-pathnet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pathnet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pathnet/lilac.yaml b/prepare/r-pathnet/lilac.yaml new file mode 100644 index 0000000000..3d83e994ab --- /dev/null +++ b/prepare/r-pathnet/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: PathNet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PathNet diff --git a/prepare/r-pathostat/PKGBUILD b/prepare/r-pathostat/PKGBUILD new file mode 100644 index 0000000000..17923cebdd --- /dev/null +++ b/prepare/r-pathostat/PKGBUILD @@ -0,0 +1,59 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PathoStat +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PathoStat Statistical Microbiome Analysis Package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-biocstyle + r-complexheatmap + r-corpcor + r-deseq2 + r-devtools + r-dplyr + r-dt + r-edger + r-ggplot2 + r-glmnet + r-gmodels + r-knitr + r-limma + r-matrixstats + r-phyloseq + r-plotly + r-plyr + r-rcolorbrewer + r-rentrez + r-reshape2 + r-rocr + r-scales + r-shiny + r-shinyjs + r-tidyr + r-vegan + r-webshot + r-xml +) +optdepends=( + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pathostat/lilac.py b/prepare/r-pathostat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pathostat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pathostat/lilac.yaml b/prepare/r-pathostat/lilac.yaml new file mode 100644 index 0000000000..ee0b9f56d0 --- /dev/null +++ b/prepare/r-pathostat/lilac.yaml @@ -0,0 +1,38 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-biocstyle +- r-complexheatmap +- r-corpcor +- r-deseq2 +- r-devtools +- r-dplyr +- r-dt +- r-edger +- r-ggplot2 +- r-glmnet +- r-gmodels +- r-knitr +- r-limma +- r-matrixstats +- r-phyloseq +- r-plotly +- r-plyr +- r-rcolorbrewer +- r-rentrez +- r-reshape2 +- r-rocr +- r-scales +- r-shiny +- r-shinyjs +- r-tidyr +- r-vegan +- r-webshot +- r-xml +update_on: +- regex: PathoStat_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PathoStat diff --git a/prepare/r-pathrender/PKGBUILD b/prepare/r-pathrender/PKGBUILD new file mode 100644 index 0000000000..393e6762e3 --- /dev/null +++ b/prepare/r-pathrender/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pathRender +_pkgver=1.62.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Render molecular pathways' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-annotationdbi + r-cmap + r-graph + r-rcolorbrewer + r-rgraphviz +) +optdepends=( + r-all + r-hgu95av2.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pathrender/lilac.py b/prepare/r-pathrender/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pathrender/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pathrender/lilac.yaml b/prepare/r-pathrender/lilac.yaml new file mode 100644 index 0000000000..de0c0dad86 --- /dev/null +++ b/prepare/r-pathrender/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-cmap +- r-graph +- r-rcolorbrewer +- r-rgraphviz +update_on: +- regex: pathRender_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pathRender diff --git a/prepare/r-pathvar/PKGBUILD b/prepare/r-pathvar/PKGBUILD new file mode 100644 index 0000000000..3a9086b3f3 --- /dev/null +++ b/prepare/r-pathvar/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pathVar +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methods to Find Pathways with Significantly Different Variability' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-data.table + r-emt + r-ggplot2 + r-gridextra + r-matching + r-mclust +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pathvar/lilac.py b/prepare/r-pathvar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pathvar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pathvar/lilac.yaml b/prepare/r-pathvar/lilac.yaml new file mode 100644 index 0000000000..8cd4d6ca63 --- /dev/null +++ b/prepare/r-pathvar/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-emt +- r-ggplot2 +- r-gridextra +- r-matching +- r-mclust +update_on: +- regex: pathVar_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pathVar diff --git a/prepare/r-pathview/PKGBUILD b/prepare/r-pathview/PKGBUILD new file mode 100644 index 0000000000..437986566b --- /dev/null +++ b/prepare/r-pathview/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pathview +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='a tool set for pathway based data integration and visualization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-graph + r-kegggraph + r-keggrest + r-org.hs.eg.db + r-png + r-rgraphviz + r-xml +) +optdepends=( + r-biocgenerics + r-gage + r-org.mm.eg.db + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pathview/lilac.py b/prepare/r-pathview/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pathview/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pathview/lilac.yaml b/prepare/r-pathview/lilac.yaml new file mode 100644 index 0000000000..78fa3ec977 --- /dev/null +++ b/prepare/r-pathview/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-graph +- r-kegggraph +- r-keggrest +- r-org.hs.eg.db +- r-png +- r-rgraphviz +- r-xml +update_on: +- regex: pathview_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pathview diff --git a/prepare/r-pathwaypca/PKGBUILD b/prepare/r-pathwaypca/PKGBUILD new file mode 100644 index 0000000000..f4819e6e84 --- /dev/null +++ b/prepare/r-pathwaypca/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pathwayPCA +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-lars +) +optdepends=( + r-airway + r-circlize + r-grdevices + r-knitr + r-rcurl + r-reshape2 + r-rmarkdown + r-summarizedexperiment + r-survminer + r-testthat + r-tidyverse +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pathwaypca/lilac.py b/prepare/r-pathwaypca/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pathwaypca/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pathwaypca/lilac.yaml b/prepare/r-pathwaypca/lilac.yaml new file mode 100644 index 0000000000..7a4323df7c --- /dev/null +++ b/prepare/r-pathwaypca/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lars +update_on: +- regex: pathwayPCA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pathwayPCA diff --git a/prepare/r-paxtoolsr/PKGBUILD b/prepare/r-paxtoolsr/PKGBUILD new file mode 100644 index 0000000000..f9ee810ea2 --- /dev/null +++ b/prepare/r-paxtoolsr/PKGBUILD @@ -0,0 +1,50 @@ +# system requirements: Java (>= 1.6) +# Maintainer: Guoyi Zhang + +_pkgname=paxtoolsr +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Access Pathways from Multiple Databases Through BioPAX and Pathway Commons' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-httr + r-igraph + r-jsonlite + r-plyr + r-r.utils + r-rappdirs + r-readr + r-rjava + r-rjson + r-xml +) +optdepends=( + r-biocstyle + r-clusterprofiler + r-dosnow + r-foreach + r-formatr + r-knitr + r-org.hs.eg.db + r-parallel + r-rcolorbrewer + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-paxtoolsr/lilac.py b/prepare/r-paxtoolsr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-paxtoolsr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-paxtoolsr/lilac.yaml b/prepare/r-paxtoolsr/lilac.yaml new file mode 100644 index 0000000000..2e62996b64 --- /dev/null +++ b/prepare/r-paxtoolsr/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-httr +- r-igraph +- r-jsonlite +- r-plyr +- r-r.utils +- r-rappdirs +- r-readr +- r-rjava +- r-rjson +- r-xml +update_on: +- regex: paxtoolsr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/paxtoolsr diff --git a/prepare/r-pbapply/PKGBUILD b/prepare/r-pbapply/PKGBUILD new file mode 100644 index 0000000000..fefea7fd7d --- /dev/null +++ b/prepare/r-pbapply/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pbapply +_pkgver=1.5-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Adding Progress Bar to '*apply' Functions" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-shiny +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pbapply/lilac.py b/prepare/r-pbapply/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pbapply/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pbapply/lilac.yaml b/prepare/r-pbapply/lilac.yaml new file mode 100644 index 0000000000..38ce4b84ca --- /dev/null +++ b/prepare/r-pbapply/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pbapply_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pbapply diff --git a/prepare/r-pbdzmq/PKGBUILD b/prepare/r-pbdzmq/PKGBUILD new file mode 100644 index 0000000000..151578e55a --- /dev/null +++ b/prepare/r-pbdzmq/PKGBUILD @@ -0,0 +1,27 @@ +# system requirements: Linux, Mac OSX, and Windows, or 'ZeroMQ' library >=4.0.4. Solaris 10 needs 'ZeroMQ' library 4.0.7 and 'OpenCSW'. +# Maintainer: Guoyi Zhang + +_pkgname=pbdZMQ +_pkgver=0.3-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Programming with Big Data -- Interface to 'ZeroMQ'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pbdzmq/lilac.py b/prepare/r-pbdzmq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pbdzmq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pbdzmq/lilac.yaml b/prepare/r-pbdzmq/lilac.yaml new file mode 100644 index 0000000000..33c948fe25 --- /dev/null +++ b/prepare/r-pbdzmq/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pbdZMQ_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pbdZMQ diff --git a/prepare/r-pbkrtest/PKGBUILD b/prepare/r-pbkrtest/PKGBUILD new file mode 100644 index 0000000000..47b4990686 --- /dev/null +++ b/prepare/r-pbkrtest/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pbkrtest +_pkgver=0.5.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for Test in Mixed Models' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-broom + r-dplyr + r-knitr + r-lme4 + r-magrittr + r-numderiv +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pbkrtest/lilac.py b/prepare/r-pbkrtest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pbkrtest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pbkrtest/lilac.yaml b/prepare/r-pbkrtest/lilac.yaml new file mode 100644 index 0000000000..5146d131b9 --- /dev/null +++ b/prepare/r-pbkrtest/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-broom +- r-dplyr +- r-knitr +- r-lme4 +- r-magrittr +- r-numderiv +update_on: +- regex: pbkrtest_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pbkrtest diff --git a/prepare/r-pbmcapply/PKGBUILD b/prepare/r-pbmcapply/PKGBUILD new file mode 100644 index 0000000000..ef517ec702 --- /dev/null +++ b/prepare/r-pbmcapply/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pbmcapply +_pkgver=1.5.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tracking the Progress of Mc*pply with Progress Bar' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pbmcapply/lilac.py b/prepare/r-pbmcapply/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pbmcapply/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pbmcapply/lilac.yaml b/prepare/r-pbmcapply/lilac.yaml new file mode 100644 index 0000000000..ea0abdc23f --- /dev/null +++ b/prepare/r-pbmcapply/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pbmcapply_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pbmcapply diff --git a/prepare/r-pcaexplorer/PKGBUILD b/prepare/r-pcaexplorer/PKGBUILD new file mode 100644 index 0000000000..8d2be0f04d --- /dev/null +++ b/prepare/r-pcaexplorer/PKGBUILD @@ -0,0 +1,64 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pcaExplorer +_pkgver=2.20.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive Visualization of RNA-seq Data Using a Principal Components Approach' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-base64enc + r-biomart + r-deseq2 + r-dt + r-genefilter + r-genomicranges + r-ggplot2 + r-ggrepel + r-go.db + r-gostats + r-heatmaply + r-iranges + r-knitr + r-limma + r-nmf + r-pheatmap + r-plotly + r-plyr + r-rmarkdown + r-s4vectors + r-scales + r-shiny + r-shinyace + r-shinybs + r-shinydashboard + r-summarizedexperiment + r-threejs + r-tidyr + r-topgo +) +optdepends=( + r-airway + r-biocstyle + r-htmltools + r-org.hs.eg.db + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pcaexplorer/lilac.py b/prepare/r-pcaexplorer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pcaexplorer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pcaexplorer/lilac.yaml b/prepare/r-pcaexplorer/lilac.yaml new file mode 100644 index 0000000000..8f18de111e --- /dev/null +++ b/prepare/r-pcaexplorer/lilac.yaml @@ -0,0 +1,39 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-base64enc +- r-biomart +- r-deseq2 +- r-dt +- r-genefilter +- r-genomicranges +- r-ggplot2 +- r-ggrepel +- r-go.db +- r-gostats +- r-heatmaply +- r-iranges +- r-knitr +- r-limma +- r-nmf +- r-pheatmap +- r-plotly +- r-plyr +- r-rmarkdown +- r-s4vectors +- r-scales +- r-shiny +- r-shinyace +- r-shinybs +- r-shinydashboard +- r-summarizedexperiment +- r-threejs +- r-tidyr +- r-topgo +update_on: +- regex: pcaExplorer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pcaExplorer diff --git a/prepare/r-pcalg/PKGBUILD b/prepare/r-pcalg/PKGBUILD new file mode 100644 index 0000000000..b75877ce38 --- /dev/null +++ b/prepare/r-pcalg/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pcalg +_pkgver=2.7-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methods for Graphical Models and Causal Inference' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-bdsmatrix + r-bh + r-clue + r-corpcor + r-fastica + r-ggm + r-graph + r-igraph + r-rbgl + r-rcpp + r-rcpparmadillo + r-robustbase + r-sfsmisc + r-vcd +) +optdepends=( + r-dagitty + r-ggplot2 + r-huge + r-mass + r-matrix + r-mvtnorm + r-rgraphviz +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pcalg/lilac.py b/prepare/r-pcalg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pcalg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pcalg/lilac.yaml b/prepare/r-pcalg/lilac.yaml new file mode 100644 index 0000000000..e8cd33943e --- /dev/null +++ b/prepare/r-pcalg/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-bdsmatrix +- r-bh +- r-clue +- r-corpcor +- r-fastica +- r-ggm +- r-graph +- r-igraph +- r-rbgl +- r-rcpp +- r-rcpparmadillo +- r-robustbase +- r-sfsmisc +- r-vcd +update_on: +- regex: pcalg_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pcalg diff --git a/prepare/r-pcamethods/PKGBUILD b/prepare/r-pcamethods/PKGBUILD new file mode 100644 index 0000000000..cfb8bbd7fb --- /dev/null +++ b/prepare/r-pcamethods/PKGBUILD @@ -0,0 +1,35 @@ +# system requirements: Rcpp +# Maintainer: Guoyi Zhang + +_pkgname=pcaMethods +_pkgver=1.86.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A collection of PCA methods' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-rcpp +) +optdepends=( + r-ggplot2 + r-lattice + r-matrixstats +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pcamethods/lilac.py b/prepare/r-pcamethods/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pcamethods/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pcamethods/lilac.yaml b/prepare/r-pcamethods/lilac.yaml new file mode 100644 index 0000000000..80d7f5610a --- /dev/null +++ b/prepare/r-pcamethods/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-rcpp +update_on: +- regex: pcaMethods_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pcaMethods diff --git a/prepare/r-pcan/PKGBUILD b/prepare/r-pcan/PKGBUILD new file mode 100644 index 0000000000..0c653896de --- /dev/null +++ b/prepare/r-pcan/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PCAN +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Phenotype Consensus ANalysis (PCAN)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CCPL:by-nc-sa') +depends=( + r + r-biocparallel +) +optdepends=( + r-biocstyle + r-knitr + r-reactome.db + r-rmarkdown + r-stringdb +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pcan/lilac.py b/prepare/r-pcan/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pcan/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pcan/lilac.yaml b/prepare/r-pcan/lilac.yaml new file mode 100644 index 0000000000..fb99a556d8 --- /dev/null +++ b/prepare/r-pcan/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +update_on: +- regex: PCAN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PCAN diff --git a/prepare/r-pcapp/PKGBUILD b/prepare/r-pcapp/PKGBUILD new file mode 100644 index 0000000000..f442747d14 --- /dev/null +++ b/prepare/r-pcapp/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pcaPP +_pkgver=1.9-74 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Robust PCA by Projection Pursuit' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mvtnorm +) +optdepends=( + r-robustbase +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pcapp/lilac.py b/prepare/r-pcapp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pcapp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pcapp/lilac.yaml b/prepare/r-pcapp/lilac.yaml new file mode 100644 index 0000000000..ee55f87e61 --- /dev/null +++ b/prepare/r-pcapp/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mvtnorm +update_on: +- regex: pcaPP_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pcaPP diff --git a/prepare/r-pcatools/PKGBUILD b/prepare/r-pcatools/PKGBUILD new file mode 100644 index 0000000000..20f4350f89 --- /dev/null +++ b/prepare/r-pcatools/PKGBUILD @@ -0,0 +1,57 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=PCAtools +_pkgver=2.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PCAtools: Everything Principal Components Analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-beachmat + r-bh + r-biocparallel + r-biocsingular + r-cowplot + r-delayedarray + r-delayedmatrixstats + r-dqrng + r-ggplot2 + r-ggrepel + r-rcpp + r-reshape2 +) +optdepends=( + r-airway + r-beachmat + r-biobase + r-biocgenerics + r-deseq2 + r-geoquery + r-ggalt + r-ggplotify + r-hgu133a.db + r-knitr + r-magrittr + r-org.hs.eg.db + r-rmarkdown + r-rmtstat + r-scran + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pcatools/lilac.py b/prepare/r-pcatools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pcatools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pcatools/lilac.yaml b/prepare/r-pcatools/lilac.yaml new file mode 100644 index 0000000000..7201297b57 --- /dev/null +++ b/prepare/r-pcatools/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beachmat +- r-bh +- r-biocparallel +- r-biocsingular +- r-cowplot +- r-delayedarray +- r-delayedmatrixstats +- r-dqrng +- r-ggplot2 +- r-ggrepel +- r-rcpp +- r-reshape2 +update_on: +- regex: PCAtools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PCAtools diff --git a/prepare/r-pcxn/PKGBUILD b/prepare/r-pcxn/PKGBUILD new file mode 100644 index 0000000000..6d3532b5f5 --- /dev/null +++ b/prepare/r-pcxn/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pcxn +_pkgver=2.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Exploring, analyzing and visualizing functions utilizing the pcxnData package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-pcxndata + r-pheatmap +) +optdepends=( + r-annotate + r-igraph + r-org.hs.eg.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pcxn/lilac.py b/prepare/r-pcxn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pcxn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pcxn/lilac.yaml b/prepare/r-pcxn/lilac.yaml new file mode 100644 index 0000000000..9a6c828ad5 --- /dev/null +++ b/prepare/r-pcxn/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-pcxndata +- r-pheatmap +update_on: +- regex: pcxn_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pcxn diff --git a/prepare/r-pcxndata/PKGBUILD b/prepare/r-pcxndata/PKGBUILD new file mode 100644 index 0000000000..fe3cc684ee --- /dev/null +++ b/prepare/r-pcxndata/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pcxnData +_pkgver=2.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Correlation coefficients and p values between pre-defined pathway/gene sets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-pcxn +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pcxndata/lilac.py b/prepare/r-pcxndata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pcxndata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pcxndata/lilac.yaml b/prepare/r-pcxndata/lilac.yaml new file mode 100644 index 0000000000..74ffef31e2 --- /dev/null +++ b/prepare/r-pcxndata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pcxnData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pcxnData diff --git a/prepare/r-pd.mapping50k.xba240/PKGBUILD b/prepare/r-pd.mapping50k.xba240/PKGBUILD new file mode 100644 index 0000000000..9ab7bbb97b --- /dev/null +++ b/prepare/r-pd.mapping50k.xba240/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pd.mapping50k.xba240 +_pkgver=3.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Platform Design Info for Affymetrix Mapping50K_Xba240' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-dbi + r-iranges + r-oligo + r-oligoclasses + r-rsqlite + r-s4vectors +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pd.mapping50k.xba240/lilac.py b/prepare/r-pd.mapping50k.xba240/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pd.mapping50k.xba240/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pd.mapping50k.xba240/lilac.yaml b/prepare/r-pd.mapping50k.xba240/lilac.yaml new file mode 100644 index 0000000000..3979df997d --- /dev/null +++ b/prepare/r-pd.mapping50k.xba240/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-dbi +- r-iranges +- r-oligo +- r-oligoclasses +- r-rsqlite +- r-s4vectors +update_on: +- regex: pd.mapping50k.xba240_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pd.mapping50k.xba240 diff --git a/prepare/r-pdatk/PKGBUILD b/prepare/r-pdatk/PKGBUILD new file mode 100644 index 0000000000..74d1200e14 --- /dev/null +++ b/prepare/r-pdatk/PKGBUILD @@ -0,0 +1,63 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PDATK +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pancreatic Ductal Adenocarcinoma Tool-Kit' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-biocparallel + r-caret + r-clusterrepro + r-consensusclusterplus + r-coregx + r-data.table + r-dplyr + r-genefu + r-ggplot2 + r-ggplotify + r-igraph + r-matrixgenerics + r-matrixstats + r-multiassayexperiment + r-piano + r-plyr + r-proc + r-rcolorbrewer + r-reportroc + r-rlang + r-s4vectors + r-scales + r-summarizedexperiment + r-survcomp + r-survminer + r-switchbox + r-verification +) +optdepends=( + r-biocstyle + r-hdf5array + r-knitr + r-msigdbr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pdatk/lilac.py b/prepare/r-pdatk/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pdatk/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pdatk/lilac.yaml b/prepare/r-pdatk/lilac.yaml new file mode 100644 index 0000000000..a60f71f8c1 --- /dev/null +++ b/prepare/r-pdatk/lilac.yaml @@ -0,0 +1,37 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-caret +- r-clusterrepro +- r-consensusclusterplus +- r-coregx +- r-data.table +- r-dplyr +- r-genefu +- r-ggplot2 +- r-ggplotify +- r-igraph +- r-matrixgenerics +- r-matrixstats +- r-multiassayexperiment +- r-piano +- r-plyr +- r-proc +- r-rcolorbrewer +- r-reportroc +- r-rlang +- r-s4vectors +- r-scales +- r-summarizedexperiment +- r-survcomp +- r-survminer +- r-switchbox +- r-verification +update_on: +- regex: PDATK_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PDATK diff --git a/prepare/r-pdftools/PKGBUILD b/prepare/r-pdftools/PKGBUILD new file mode 100644 index 0000000000..c6cfec9c51 --- /dev/null +++ b/prepare/r-pdftools/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: Poppler C++ API: libpoppler-cpp-dev (deb) orpoppler-cpp-devel (rpm). The unit tests also require the'poppler-data' package (rpm/deb) +# Maintainer: Guoyi Zhang + +_pkgname=pdftools +_pkgver=3.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Text Extraction, Rendering and Converting of PDF Documents' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-qpdf + r-rcpp +) +optdepends=( + r-jpeg + r-png + r-tesseract + r-testthat + r-webp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pdftools/lilac.py b/prepare/r-pdftools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pdftools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pdftools/lilac.yaml b/prepare/r-pdftools/lilac.yaml new file mode 100644 index 0000000000..224f8ffff9 --- /dev/null +++ b/prepare/r-pdftools/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-qpdf +- r-rcpp +update_on: +- regex: pdftools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pdftools diff --git a/prepare/r-pdinfobuilder/PKGBUILD b/prepare/r-pdinfobuilder/PKGBUILD new file mode 100644 index 0000000000..730155b5fa --- /dev/null +++ b/prepare/r-pdinfobuilder/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pdInfoBuilder +_pkgver=1.58.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Platform Design Information Package Builder' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-affxparser + r-biobase + r-biocgenerics + r-biostrings + r-dbi + r-iranges + r-oligo + r-oligoclasses + r-rsqlite + r-s4vectors +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pdinfobuilder/lilac.py b/prepare/r-pdinfobuilder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pdinfobuilder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pdinfobuilder/lilac.yaml b/prepare/r-pdinfobuilder/lilac.yaml new file mode 100644 index 0000000000..03ba8485f1 --- /dev/null +++ b/prepare/r-pdinfobuilder/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affxparser +- r-biobase +- r-biocgenerics +- r-biostrings +- r-dbi +- r-iranges +- r-oligo +- r-oligoclasses +- r-rsqlite +- r-s4vectors +update_on: +- regex: pdInfoBuilder_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pdInfoBuilder diff --git a/prepare/r-pdist/PKGBUILD b/prepare/r-pdist/PKGBUILD new file mode 100644 index 0000000000..08c1528be9 --- /dev/null +++ b/prepare/r-pdist/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pdist +_pkgver=1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Partitioned Distance Function' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pdist/lilac.py b/prepare/r-pdist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pdist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pdist/lilac.yaml b/prepare/r-pdist/lilac.yaml new file mode 100644 index 0000000000..0cded5c0d0 --- /dev/null +++ b/prepare/r-pdist/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pdist_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pdist diff --git a/prepare/r-peacoqc/PKGBUILD b/prepare/r-peacoqc/PKGBUILD new file mode 100644 index 0000000000..acfb7d0413 --- /dev/null +++ b/prepare/r-peacoqc/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PeacoQC +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Peak-based selection of high quality cytometry data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-circlize + r-complexheatmap + r-flowcore + r-flowworkspace + r-ggplot2 + r-gridextra + r-plyr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-peacoqc/lilac.py b/prepare/r-peacoqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-peacoqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-peacoqc/lilac.yaml b/prepare/r-peacoqc/lilac.yaml new file mode 100644 index 0000000000..217f49129e --- /dev/null +++ b/prepare/r-peacoqc/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circlize +- r-complexheatmap +- r-flowcore +- r-flowworkspace +- r-ggplot2 +- r-gridextra +- r-plyr +update_on: +- regex: PeacoQC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PeacoQC diff --git a/prepare/r-peakpanther/PKGBUILD b/prepare/r-peakpanther/PKGBUILD new file mode 100644 index 0000000000..0554f6e5da --- /dev/null +++ b/prepare/r-peakpanther/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=peakPantheR +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Peak Picking and Annotation of High Resolution Experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-doparallel + r-dt + r-foreach + r-ggplot2 + r-gridextra + r-minpack.lm + r-msnbase + r-mzr + r-pracma + r-scales + r-shiny + r-shinycssloaders + r-shinythemes + r-stringr + r-xml +) +optdepends=( + r-biocstyle + r-faahko + r-knitr + r-msdata + r-pander + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-peakpanther/lilac.py b/prepare/r-peakpanther/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-peakpanther/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-peakpanther/lilac.yaml b/prepare/r-peakpanther/lilac.yaml new file mode 100644 index 0000000000..91de9a75fd --- /dev/null +++ b/prepare/r-peakpanther/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-dt +- r-foreach +- r-ggplot2 +- r-gridextra +- r-minpack.lm +- r-msnbase +- r-mzr +- r-pracma +- r-scales +- r-shiny +- r-shinycssloaders +- r-shinythemes +- r-stringr +- r-xml +update_on: +- regex: peakPantheR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/peakPantheR diff --git a/prepare/r-peca/PKGBUILD b/prepare/r-peca/PKGBUILD new file mode 100644 index 0000000000..cbf16b75f8 --- /dev/null +++ b/prepare/r-peca/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PECA +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Probe-level Expression Change Averaging' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-aroma.affymetrix + r-aroma.core + r-genefilter + r-limma + r-preprocesscore + r-rots +) +optdepends=( + r-spikein +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-peca/lilac.py b/prepare/r-peca/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-peca/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-peca/lilac.yaml b/prepare/r-peca/lilac.yaml new file mode 100644 index 0000000000..a09d53332f --- /dev/null +++ b/prepare/r-peca/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-aroma.affymetrix +- r-aroma.core +- r-genefilter +- r-limma +- r-preprocesscore +- r-rots +update_on: +- regex: PECA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PECA diff --git a/prepare/r-peco/PKGBUILD b/prepare/r-peco/PKGBUILD new file mode 100644 index 0000000000..4b5b19ddf5 --- /dev/null +++ b/prepare/r-peco/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=peco +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-circular + r-conicfit + r-doparallel + r-foreach + r-genlasso + r-scater + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-peco/lilac.py b/prepare/r-peco/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-peco/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-peco/lilac.yaml b/prepare/r-peco/lilac.yaml new file mode 100644 index 0000000000..661d14445d --- /dev/null +++ b/prepare/r-peco/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-circular +- r-conicfit +- r-doparallel +- r-foreach +- r-genlasso +- r-scater +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: peco_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/peco diff --git a/prepare/r-penalized/PKGBUILD b/prepare/r-penalized/PKGBUILD new file mode 100644 index 0000000000..194cc837d8 --- /dev/null +++ b/prepare/r-penalized/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=penalized +_pkgver=0.9-51 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation in GLMs and in the Cox Model' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-globaltest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-penalized/lilac.py b/prepare/r-penalized/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-penalized/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-penalized/lilac.yaml b/prepare/r-penalized/lilac.yaml new file mode 100644 index 0000000000..c38d0e2ecc --- /dev/null +++ b/prepare/r-penalized/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: penalized_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=penalized diff --git a/prepare/r-pengls/PKGBUILD b/prepare/r-pengls/PKGBUILD new file mode 100644 index 0000000000..f1afec9da3 --- /dev/null +++ b/prepare/r-pengls/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pengls +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fit Penalised Generalised Least Squares models' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-glmnet +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pengls/lilac.py b/prepare/r-pengls/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pengls/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pengls/lilac.yaml b/prepare/r-pengls/lilac.yaml new file mode 100644 index 0000000000..6b7ec49fbc --- /dev/null +++ b/prepare/r-pengls/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-glmnet +update_on: +- regex: pengls_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pengls diff --git a/prepare/r-pepsnmr/PKGBUILD b/prepare/r-pepsnmr/PKGBUILD new file mode 100644 index 0000000000..13d18528a0 --- /dev/null +++ b/prepare/r-pepsnmr/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PepsNMR +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pre-process 1H-NMR FID signals' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-gridextra + r-matrixstats + r-ptw + r-reshape2 +) +optdepends=( + r-biocstyle + r-knitr + r-markdown + r-pepsnmrdata + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pepsnmr/lilac.py b/prepare/r-pepsnmr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pepsnmr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pepsnmr/lilac.yaml b/prepare/r-pepsnmr/lilac.yaml new file mode 100644 index 0000000000..1fbb2dfd93 --- /dev/null +++ b/prepare/r-pepsnmr/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gridextra +- r-matrixstats +- r-ptw +- r-reshape2 +update_on: +- regex: PepsNMR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PepsNMR diff --git a/prepare/r-pepstat/PKGBUILD b/prepare/r-pepstat/PKGBUILD new file mode 100644 index 0000000000..114a2f2ec9 --- /dev/null +++ b/prepare/r-pepstat/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pepStat +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical analysis of peptide microarrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-data.table + r-fields + r-genomicranges + r-ggplot2 + r-iranges + r-limma + r-plyr +) +optdepends=( + r-knitr + r-pepdat + r-pviz + r-shiny +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pepstat/lilac.py b/prepare/r-pepstat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pepstat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pepstat/lilac.yaml b/prepare/r-pepstat/lilac.yaml new file mode 100644 index 0000000000..ee4c83dee8 --- /dev/null +++ b/prepare/r-pepstat/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-data.table +- r-fields +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-limma +- r-plyr +update_on: +- regex: pepStat_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pepStat diff --git a/prepare/r-peptides/PKGBUILD b/prepare/r-peptides/PKGBUILD new file mode 100644 index 0000000000..721eaf30a4 --- /dev/null +++ b/prepare/r-peptides/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Peptides +_pkgver=2.4.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-peptides/lilac.py b/prepare/r-peptides/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-peptides/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-peptides/lilac.yaml b/prepare/r-peptides/lilac.yaml new file mode 100644 index 0000000000..4c173152bc --- /dev/null +++ b/prepare/r-peptides/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: Peptides_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Peptides diff --git a/prepare/r-pepxmltab/PKGBUILD b/prepare/r-pepxmltab/PKGBUILD new file mode 100644 index 0000000000..3fa09d1895 --- /dev/null +++ b/prepare/r-pepxmltab/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pepXMLTab +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Parsing pepXML files and filter based on peptide FDR.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-xml +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pepxmltab/lilac.py b/prepare/r-pepxmltab/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pepxmltab/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pepxmltab/lilac.yaml b/prepare/r-pepxmltab/lilac.yaml new file mode 100644 index 0000000000..126f274ae2 --- /dev/null +++ b/prepare/r-pepxmltab/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-xml +update_on: +- regex: pepXMLTab_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pepXMLTab diff --git a/prepare/r-perfect/PKGBUILD b/prepare/r-perfect/PKGBUILD new file mode 100644 index 0000000000..cd1bed38b8 --- /dev/null +++ b/prepare/r-perfect/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PERFect +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Permutation filtration for microbiome data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-fitdistrplus + r-ggplot2 + r-phyloseq + r-psych + r-sn + r-zoo +) +optdepends=( + r-ggpubr + r-kableextra + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-perfect/lilac.py b/prepare/r-perfect/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-perfect/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-perfect/lilac.yaml b/prepare/r-perfect/lilac.yaml new file mode 100644 index 0000000000..53e2ee0435 --- /dev/null +++ b/prepare/r-perfect/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fitdistrplus +- r-ggplot2 +- r-phyloseq +- r-psych +- r-sn +- r-zoo +update_on: +- regex: PERFect_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PERFect diff --git a/prepare/r-performanceanalytics/PKGBUILD b/prepare/r-performanceanalytics/PKGBUILD new file mode 100644 index 0000000000..cda19b5425 --- /dev/null +++ b/prepare/r-performanceanalytics/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PerformanceAnalytics +_pkgver=2.0.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Econometric Tools for Performance and Risk Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-quadprog + r-xts + r-zoo +) +optdepends=( + r-dygraphs + r-gamlss + r-gamlss.dist + r-ggplot2 + r-ggpubr + r-googlevis + r-gridextra + r-hmisc + r-mass + r-plotly + r-quantmod + r-quantreg + r-r.rsp + r-rcolorbrewer + r-robstattm + r-robustbase + r-rpese + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-performanceanalytics/lilac.py b/prepare/r-performanceanalytics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-performanceanalytics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-performanceanalytics/lilac.yaml b/prepare/r-performanceanalytics/lilac.yaml new file mode 100644 index 0000000000..3e1b451b02 --- /dev/null +++ b/prepare/r-performanceanalytics/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-quadprog +- r-xts +- r-zoo +update_on: +- regex: PerformanceAnalytics_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=PerformanceAnalytics diff --git a/prepare/r-periodicdna/PKGBUILD b/prepare/r-periodicdna/PKGBUILD new file mode 100644 index 0000000000..81f320318f --- /dev/null +++ b/prepare/r-periodicdna/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=periodicDNA +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Set of tools to identify periodic occurrences of k-mers in DNA sequences' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-biostrings + r-bsgenome + r-cowplot + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-magrittr + r-rtracklayer + r-s4vectors + r-zoo +) +optdepends=( + r-bsgenome.celegans.ucsc.ce11 + r-bsgenome.dmelanogaster.ucsc.dm6 + r-bsgenome.drerio.ucsc.danrer10 + r-bsgenome.hsapiens.ucsc.hg38 + r-bsgenome.mmusculus.ucsc.mm10 + r-bsgenome.scerevisiae.ucsc.saccer3 + r-covr + r-knitr + r-pkgdown + r-reticulate + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-periodicdna/lilac.py b/prepare/r-periodicdna/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-periodicdna/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-periodicdna/lilac.yaml b/prepare/r-periodicdna/lilac.yaml new file mode 100644 index 0000000000..fa85ac4680 --- /dev/null +++ b/prepare/r-periodicdna/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-cowplot +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-magrittr +- r-rtracklayer +- r-s4vectors +- r-zoo +update_on: +- regex: periodicDNA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/periodicDNA diff --git a/prepare/r-permute/PKGBUILD b/prepare/r-permute/PKGBUILD new file mode 100644 index 0000000000..629b9a86f5 --- /dev/null +++ b/prepare/r-permute/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=permute +_pkgver=0.9-5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for Generating Restricted Permutations of Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-parallel + r-testthat + r-vegan +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-permute/lilac.py b/prepare/r-permute/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-permute/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-permute/lilac.yaml b/prepare/r-permute/lilac.yaml new file mode 100644 index 0000000000..47e1c2578e --- /dev/null +++ b/prepare/r-permute/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: permute_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=permute diff --git a/prepare/r-perturbatr/PKGBUILD b/prepare/r-perturbatr/PKGBUILD new file mode 100644 index 0000000000..961a218066 --- /dev/null +++ b/prepare/r-perturbatr/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=perturbatr +_pkgver=1.13.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Analysis of High-Throughput Genetic Perturbation Screens' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-diffusr + r-doparallel + r-dplyr + r-foreach + r-formula.tools + r-ggplot2 + r-igraph + r-lazyeval + r-lme4 + r-magrittr + r-rlang + r-scales + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-lintr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-perturbatr/lilac.py b/prepare/r-perturbatr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-perturbatr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-perturbatr/lilac.yaml b/prepare/r-perturbatr/lilac.yaml new file mode 100644 index 0000000000..b80d4dfa50 --- /dev/null +++ b/prepare/r-perturbatr/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-diffusr +- r-doparallel +- r-dplyr +- r-foreach +- r-formula.tools +- r-ggplot2 +- r-igraph +- r-lazyeval +- r-lme4 +- r-magrittr +- r-rlang +- r-scales +- r-tibble +- r-tidyr +update_on: +- regex: perturbatr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/perturbatr diff --git a/prepare/r-pfam.db/PKGBUILD b/prepare/r-pfam.db/PKGBUILD new file mode 100644 index 0000000000..428cc340b2 --- /dev/null +++ b/prepare/r-pfam.db/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PFAM.db +_pkgver=3.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A set of protein ID mappings for PFAM' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi +) +optdepends=( + r-dbi +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pfam.db/lilac.py b/prepare/r-pfam.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pfam.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pfam.db/lilac.yaml b/prepare/r-pfam.db/lilac.yaml new file mode 100644 index 0000000000..5277d537f3 --- /dev/null +++ b/prepare/r-pfam.db/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +update_on: +- regex: PFAM.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PFAM.db diff --git a/prepare/r-pfp/PKGBUILD b/prepare/r-pfp/PKGBUILD new file mode 100644 index 0000000000..22b3065682 --- /dev/null +++ b/prepare/r-pfp/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PFP +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pathway Fingerprint Framework in R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-clusterprofiler + r-ggplot2 + r-graph + r-igraph + r-kegggraph + r-magrittr + r-plyr + r-tidyr +) +optdepends=( + r-knitr + r-org.hs.eg.db + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pfp/lilac.py b/prepare/r-pfp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pfp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pfp/lilac.yaml b/prepare/r-pfp/lilac.yaml new file mode 100644 index 0000000000..e20fe43a8a --- /dev/null +++ b/prepare/r-pfp/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clusterprofiler +- r-ggplot2 +- r-graph +- r-igraph +- r-kegggraph +- r-magrittr +- r-plyr +- r-tidyr +update_on: +- regex: PFP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PFP diff --git a/prepare/r-pgca/PKGBUILD b/prepare/r-pgca/PKGBUILD new file mode 100644 index 0000000000..70141f7b6e --- /dev/null +++ b/prepare/r-pgca/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pgca +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pgca/lilac.py b/prepare/r-pgca/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pgca/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pgca/lilac.yaml b/prepare/r-pgca/lilac.yaml new file mode 100644 index 0000000000..0dd540b0d5 --- /dev/null +++ b/prepare/r-pgca/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pgca_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pgca diff --git a/prepare/r-phangorn/PKGBUILD b/prepare/r-phangorn/PKGBUILD new file mode 100644 index 0000000000..900f2f8ed6 --- /dev/null +++ b/prepare/r-phangorn/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=phangorn +_pkgver=2.8.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Phylogenetic Reconstruction and Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-fastmatch + r-igraph + r-quadprog + r-rcpp +) +optdepends=( + r-biostrings + r-knitr + r-magick + r-prettydoc + r-rgl + r-rmarkdown + r-seqinr + r-seqlogo + r-tinytest + r-xtable +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phangorn/lilac.py b/prepare/r-phangorn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phangorn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phangorn/lilac.yaml b/prepare/r-phangorn/lilac.yaml new file mode 100644 index 0000000000..6e8a909ce0 --- /dev/null +++ b/prepare/r-phangorn/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-fastmatch +- r-igraph +- r-quadprog +- r-rcpp +update_on: +- regex: phangorn_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=phangorn diff --git a/prepare/r-phantasus/PKGBUILD b/prepare/r-phantasus/PKGBUILD new file mode 100644 index 0000000000..10a5c77c34 --- /dev/null +++ b/prepare/r-phantasus/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=phantasus +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visual and interactive gene expression analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-assertthat + r-biobase + r-ccapp + r-curl + r-deseq2 + r-fgsea + r-geoquery + r-ggplot2 + r-gtable + r-htmltools + r-httpuv + r-httr + r-jsonlite + r-limma + r-opencpu + r-pheatmap + r-protolite + r-rhdf5 + r-rook + r-scales + r-stringr + r-svglite +) +optdepends=( + r-biocstyle + r-data.table + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phantasus/lilac.py b/prepare/r-phantasus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phantasus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phantasus/lilac.yaml b/prepare/r-phantasus/lilac.yaml new file mode 100644 index 0000000000..39b67346e8 --- /dev/null +++ b/prepare/r-phantasus/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-assertthat +- r-biobase +- r-ccapp +- r-curl +- r-deseq2 +- r-fgsea +- r-geoquery +- r-ggplot2 +- r-gtable +- r-htmltools +- r-httpuv +- r-httr +- r-jsonlite +- r-limma +- r-opencpu +- r-pheatmap +- r-protolite +- r-rhdf5 +- r-rook +- r-scales +- r-stringr +- r-svglite +update_on: +- regex: phantasus_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/phantasus diff --git a/prepare/r-pharmacogx/PKGBUILD b/prepare/r-pharmacogx/PKGBUILD new file mode 100644 index 0000000000..3b574e9ba3 --- /dev/null +++ b/prepare/r-pharmacogx/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PharmacoGx +_pkgver=2.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Large-Scale Pharmacogenomic Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-catools + r-checkmate + r-coregx + r-data.table + r-downloader + r-ggplot2 + r-glue + r-jsonlite + r-magicaxis + r-multiassayexperiment + r-rcolorbrewer + r-reshape2 + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-crayon + r-knitcitations + r-knitr + r-markdown + r-pander + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pharmacogx/lilac.py b/prepare/r-pharmacogx/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pharmacogx/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pharmacogx/lilac.yaml b/prepare/r-pharmacogx/lilac.yaml new file mode 100644 index 0000000000..73b0ed5c41 --- /dev/null +++ b/prepare/r-pharmacogx/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-catools +- r-checkmate +- r-coregx +- r-data.table +- r-downloader +- r-ggplot2 +- r-glue +- r-jsonlite +- r-magicaxis +- r-multiassayexperiment +- r-rcolorbrewer +- r-reshape2 +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: PharmacoGx_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PharmacoGx diff --git a/prepare/r-phastcons100way.ucsc.hg19/PKGBUILD b/prepare/r-phastcons100way.ucsc.hg19/PKGBUILD new file mode 100644 index 0000000000..43b687be29 --- /dev/null +++ b/prepare/r-phastcons100way.ucsc.hg19/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=phastCons100way.UCSC.hg19 +_pkgver=3.7.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='UCSC phastCons conservation scores for hg19' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bsgenome + r-genomeinfodb + r-genomicranges + r-genomicscores + r-iranges + r-s4vectors +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phastcons100way.ucsc.hg19/lilac.py b/prepare/r-phastcons100way.ucsc.hg19/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phastcons100way.ucsc.hg19/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phastcons100way.ucsc.hg19/lilac.yaml b/prepare/r-phastcons100way.ucsc.hg19/lilac.yaml new file mode 100644 index 0000000000..2f7d56166b --- /dev/null +++ b/prepare/r-phastcons100way.ucsc.hg19/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +- r-genomeinfodb +- r-genomicranges +- r-genomicscores +- r-iranges +- r-s4vectors +update_on: +- regex: phastCons100way.UCSC.hg19_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/phastCons100way.UCSC.hg19 diff --git a/prepare/r-phastcons100way.ucsc.hg38/PKGBUILD b/prepare/r-phastcons100way.ucsc.hg38/PKGBUILD new file mode 100644 index 0000000000..809668bb08 --- /dev/null +++ b/prepare/r-phastcons100way.ucsc.hg38/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=phastCons100way.UCSC.hg38 +_pkgver=3.7.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='UCSC phastCons conservation scores for hg38' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bsgenome + r-genomeinfodb + r-genomicranges + r-genomicscores + r-iranges + r-s4vectors +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phastcons100way.ucsc.hg38/lilac.py b/prepare/r-phastcons100way.ucsc.hg38/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phastcons100way.ucsc.hg38/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phastcons100way.ucsc.hg38/lilac.yaml b/prepare/r-phastcons100way.ucsc.hg38/lilac.yaml new file mode 100644 index 0000000000..bdc7878b75 --- /dev/null +++ b/prepare/r-phastcons100way.ucsc.hg38/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome +- r-genomeinfodb +- r-genomicranges +- r-genomicscores +- r-iranges +- r-s4vectors +update_on: +- regex: phastCons100way.UCSC.hg38_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/phastCons100way.UCSC.hg38 diff --git a/prepare/r-phater/PKGBUILD b/prepare/r-phater/PKGBUILD new file mode 100644 index 0000000000..4345d535b1 --- /dev/null +++ b/prepare/r-phater/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=phateR +_pkgver=1.0.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PHATE - Potential of Heat-Diffusion for Affinity-Based Transition Embedding' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-memoise + r-reticulate +) +optdepends=( + r-cowplot + r-gridgraphics +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phater/lilac.py b/prepare/r-phater/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phater/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phater/lilac.yaml b/prepare/r-phater/lilac.yaml new file mode 100644 index 0000000000..a67dae6005 --- /dev/null +++ b/prepare/r-phater/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-memoise +- r-reticulate +update_on: +- regex: phateR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=phateR diff --git a/prepare/r-pheatmap/PKGBUILD b/prepare/r-pheatmap/PKGBUILD new file mode 100644 index 0000000000..fcd8cc4f5b --- /dev/null +++ b/prepare/r-pheatmap/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pheatmap +_pkgver=1.0.12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pretty Heatmaps' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-gtable + r-rcolorbrewer + r-scales +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pheatmap/lilac.py b/prepare/r-pheatmap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pheatmap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pheatmap/lilac.yaml b/prepare/r-pheatmap/lilac.yaml new file mode 100644 index 0000000000..36068820f9 --- /dev/null +++ b/prepare/r-pheatmap/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gtable +- r-rcolorbrewer +- r-scales +update_on: +- regex: pheatmap_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pheatmap diff --git a/prepare/r-phemd/PKGBUILD b/prepare/r-phemd/PKGBUILD new file mode 100644 index 0000000000..0f1cd613da --- /dev/null +++ b/prepare/r-phemd/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=phemd +_pkgver=1.9.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Phenotypic EMD for comparison of single-cell samples' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-cowplot + r-destiny + r-ggplot2 + r-igraph + r-maptree + r-monocle + r-phater + r-pheatmap + r-pracma + r-rann + r-rcolorbrewer + r-reticulate + r-rtsne + r-s4vectors + r-scatterplot3d + r-seurat + r-singlecellexperiment + r-summarizedexperiment + r-transport + r-vgam +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phemd/lilac.py b/prepare/r-phemd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phemd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phemd/lilac.yaml b/prepare/r-phemd/lilac.yaml new file mode 100644 index 0000000000..74cd65a17a --- /dev/null +++ b/prepare/r-phemd/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-cowplot +- r-destiny +- r-ggplot2 +- r-igraph +- r-maptree +- r-monocle +- r-phater +- r-pheatmap +- r-pracma +- r-rann +- r-rcolorbrewer +- r-reticulate +- r-rtsne +- r-s4vectors +- r-scatterplot3d +- r-seurat +- r-singlecellexperiment +- r-summarizedexperiment +- r-transport +- r-vgam +update_on: +- regex: phemd_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/phemd diff --git a/prepare/r-phenogeneranker/PKGBUILD b/prepare/r-phenogeneranker/PKGBUILD new file mode 100644 index 0000000000..d823076c4d --- /dev/null +++ b/prepare/r-phenogeneranker/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PhenoGeneRanker +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PhenoGeneRanker: A gene and phenotype prioritization tool' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CCPL:by-nc-sa') +depends=( + r + r-doparallel + r-dplyr + r-foreach + r-igraph +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phenogeneranker/lilac.py b/prepare/r-phenogeneranker/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phenogeneranker/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phenogeneranker/lilac.yaml b/prepare/r-phenogeneranker/lilac.yaml new file mode 100644 index 0000000000..29572d5b32 --- /dev/null +++ b/prepare/r-phenogeneranker/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-dplyr +- r-foreach +- r-igraph +update_on: +- regex: PhenoGeneRanker_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PhenoGeneRanker diff --git a/prepare/r-phenopath/PKGBUILD b/prepare/r-phenopath/PKGBUILD new file mode 100644 index 0000000000..aeb55b92c4 --- /dev/null +++ b/prepare/r-phenopath/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=phenopath +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genomic trajectories with heterogeneous genetic and environmental backgrounds' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Apache') +depends=( + r + r-dplyr + r-ggplot2 + r-rcpp + r-summarizedexperiment + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-forcats + r-knitr + r-rmarkdown + r-singlecellexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phenopath/lilac.py b/prepare/r-phenopath/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phenopath/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phenopath/lilac.yaml b/prepare/r-phenopath/lilac.yaml new file mode 100644 index 0000000000..b43c7ce043 --- /dev/null +++ b/prepare/r-phenopath/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-rcpp +- r-summarizedexperiment +- r-tibble +- r-tidyr +update_on: +- regex: phenopath_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/phenopath diff --git a/prepare/r-phenotest/PKGBUILD b/prepare/r-phenotest/PKGBUILD new file mode 100644 index 0000000000..cb56afe287 --- /dev/null +++ b/prepare/r-phenotest/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=phenoTest +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotate + r-annotationdbi + r-biobase + r-biomart + r-bma + r-category + r-ellipse + r-genefilter + r-ggplot2 + r-gplots + r-gseabase + r-heatplus + r-hgu133a.db + r-hmisc + r-hopach + r-limma + r-xtable +) +optdepends=( + r-go.db + r-gseabase + r-org.ce.eg.db + r-org.dm.eg.db + r-org.hs.eg.db + r-org.mm.eg.db + r-org.rn.eg.db + r-parallel +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phenotest/lilac.py b/prepare/r-phenotest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phenotest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phenotest/lilac.yaml b/prepare/r-phenotest/lilac.yaml new file mode 100644 index 0000000000..961af57921 --- /dev/null +++ b/prepare/r-phenotest/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-biobase +- r-biomart +- r-bma +- r-category +- r-ellipse +- r-genefilter +- r-ggplot2 +- r-gplots +- r-gseabase +- r-heatplus +- r-hgu133a.db +- r-hmisc +- r-hopach +- r-limma +- r-xtable +update_on: +- regex: phenoTest_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/phenoTest diff --git a/prepare/r-phenstat/PKGBUILD b/prepare/r-phenstat/PKGBUILD new file mode 100644 index 0000000000..06d08e6ccd --- /dev/null +++ b/prepare/r-phenstat/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PhenStat +_pkgver=2.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical analysis of phenotypic data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-car + r-corrplot + r-ggplot2 + r-graph + r-knitr + r-lme4 + r-logistf + r-msgps + r-nortest + r-pingr + r-reshape + r-smoothwin +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phenstat/lilac.py b/prepare/r-phenstat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phenstat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phenstat/lilac.yaml b/prepare/r-phenstat/lilac.yaml new file mode 100644 index 0000000000..3e693635e5 --- /dev/null +++ b/prepare/r-phenstat/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-car +- r-corrplot +- r-ggplot2 +- r-graph +- r-knitr +- r-lme4 +- r-logistf +- r-msgps +- r-nortest +- r-pingr +- r-reshape +- r-smoothwin +update_on: +- regex: PhenStat_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PhenStat diff --git a/prepare/r-philentropy/PKGBUILD b/prepare/r-philentropy/PKGBUILD new file mode 100644 index 0000000000..813f5af700 --- /dev/null +++ b/prepare/r-philentropy/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=philentropy +_pkgver=0.5.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Similarity and Distance Quantification Between Probability Functions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-rcpp +) +optdepends=( + r-knitr + r-markdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-philentropy/lilac.py b/prepare/r-philentropy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-philentropy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-philentropy/lilac.yaml b/prepare/r-philentropy/lilac.yaml new file mode 100644 index 0000000000..13caaab223 --- /dev/null +++ b/prepare/r-philentropy/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-rcpp +update_on: +- regex: philentropy_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=philentropy diff --git a/prepare/r-philr/PKGBUILD b/prepare/r-philr/PKGBUILD new file mode 100644 index 0000000000..95dbd42f30 --- /dev/null +++ b/prepare/r-philr/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=philr +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Phylogenetic partitioning based ILR transform for metagenomics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-ggplot2 + r-ggtree + r-phangorn + r-tidyr +) +optdepends=( + r-biocstyle + r-dplyr + r-ecodist + r-glmnet + r-knitr + r-mia + r-phyloseq + r-rmarkdown + r-summarizedexperiment + r-testthat + r-treesummarizedexperiment +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-philr/lilac.py b/prepare/r-philr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-philr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-philr/lilac.yaml b/prepare/r-philr/lilac.yaml new file mode 100644 index 0000000000..844ff300d5 --- /dev/null +++ b/prepare/r-philr/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-ggplot2 +- r-ggtree +- r-phangorn +- r-tidyr +update_on: +- regex: philr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/philr diff --git a/prepare/r-phipdata/PKGBUILD b/prepare/r-phipdata/PKGBUILD new file mode 100644 index 0000000000..ee5083cc37 --- /dev/null +++ b/prepare/r-phipdata/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PhIPData +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Container for PhIP-Seq Experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-cli + r-edger + r-genomicranges + r-iranges + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-covr + r-dplyr + r-knitr + r-readr + r-rmarkdown + r-testthat + r-withr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phipdata/lilac.py b/prepare/r-phipdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phipdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phipdata/lilac.yaml b/prepare/r-phipdata/lilac.yaml new file mode 100644 index 0000000000..7c4623aba5 --- /dev/null +++ b/prepare/r-phipdata/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-cli +- r-edger +- r-genomicranges +- r-iranges +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: PhIPData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PhIPData diff --git a/prepare/r-phosphonormalizer/PKGBUILD b/prepare/r-phosphonormalizer/PKGBUILD new file mode 100644 index 0000000000..ad5d435ae8 --- /dev/null +++ b/prepare/r-phosphonormalizer/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=phosphonormalizer +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Compensates for the bias introduced by median normalization in' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-matrixstats + r-plyr +) +optdepends=( + r-knitr + r-msnbase + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phosphonormalizer/lilac.py b/prepare/r-phosphonormalizer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phosphonormalizer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phosphonormalizer/lilac.yaml b/prepare/r-phosphonormalizer/lilac.yaml new file mode 100644 index 0000000000..3a8446a209 --- /dev/null +++ b/prepare/r-phosphonormalizer/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-matrixstats +- r-plyr +update_on: +- regex: phosphonormalizer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/phosphonormalizer diff --git a/prepare/r-phosr/PKGBUILD b/prepare/r-phosr/PKGBUILD new file mode 100644 index 0000000000..f14fa631e4 --- /dev/null +++ b/prepare/r-phosr/PKGBUILD @@ -0,0 +1,65 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PhosR +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A set of methods and tools for comprehensive analysis of phosphoproteomics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-circlize + r-dendextend + r-dplyr + r-e1071 + r-ggally + r-ggdendro + r-ggplot2 + r-ggpubr + r-ggtext + r-igraph + r-limma + r-network + r-pcamethods + r-pheatmap + r-preprocesscore + r-rcolorbrewer + r-reshape2 + r-rlang + r-ruv + r-s4vectors + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-annotate + r-biocstyle + r-calibrate + r-cluer + r-directpa + r-knitr + r-org.mm.eg.db + r-org.rn.eg.db + r-reactome.db + r-rgl + r-rmarkdown + r-sna + r-stringr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phosr/lilac.py b/prepare/r-phosr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phosr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phosr/lilac.yaml b/prepare/r-phosr/lilac.yaml new file mode 100644 index 0000000000..c06d3711dc --- /dev/null +++ b/prepare/r-phosr/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-circlize +- r-dendextend +- r-dplyr +- r-e1071 +- r-ggally +- r-ggdendro +- r-ggplot2 +- r-ggpubr +- r-ggtext +- r-igraph +- r-limma +- r-network +- r-pcamethods +- r-pheatmap +- r-preprocesscore +- r-rcolorbrewer +- r-reshape2 +- r-rlang +- r-ruv +- r-s4vectors +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: PhosR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PhosR diff --git a/prepare/r-phyclust/PKGBUILD b/prepare/r-phyclust/PKGBUILD new file mode 100644 index 0000000000..18a094bef0 --- /dev/null +++ b/prepare/r-phyclust/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=phyclust +_pkgver=0.1-30 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Phylogenetic Clustering (Phyloclustering)' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ape +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phyclust/lilac.py b/prepare/r-phyclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phyclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phyclust/lilac.yaml b/prepare/r-phyclust/lilac.yaml new file mode 100644 index 0000000000..d6734c36bc --- /dev/null +++ b/prepare/r-phyclust/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +update_on: +- regex: phyclust_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=phyclust diff --git a/prepare/r-phylobase/PKGBUILD b/prepare/r-phylobase/PKGBUILD new file mode 100644 index 0000000000..b757f8ade3 --- /dev/null +++ b/prepare/r-phylobase/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=phylobase +_pkgver=0.8.10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Base Package for Phylogenetic Structures and Comparative Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ade4 + r-ape + r-rcpp + r-rncl + r-rnexml +) +optdepends=( + r-knitr + r-mass + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phylobase/lilac.py b/prepare/r-phylobase/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phylobase/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phylobase/lilac.yaml b/prepare/r-phylobase/lilac.yaml new file mode 100644 index 0000000000..3425cc786e --- /dev/null +++ b/prepare/r-phylobase/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ade4 +- r-ape +- r-rcpp +- r-rncl +- r-rnexml +update_on: +- regex: phylobase_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=phylobase diff --git a/prepare/r-phylogram/PKGBUILD b/prepare/r-phylogram/PKGBUILD new file mode 100644 index 0000000000..7560e9e76c --- /dev/null +++ b/prepare/r-phylogram/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=phylogram +_pkgver=2.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dendrograms for Evolutionary Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ape +) +optdepends=( + r-dendextend + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phylogram/lilac.py b/prepare/r-phylogram/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phylogram/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phylogram/lilac.yaml b/prepare/r-phylogram/lilac.yaml new file mode 100644 index 0000000000..35957519e9 --- /dev/null +++ b/prepare/r-phylogram/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +update_on: +- regex: phylogram_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=phylogram diff --git a/prepare/r-phyloprofile/PKGBUILD b/prepare/r-phyloprofile/PKGBUILD new file mode 100644 index 0000000000..b54be902de --- /dev/null +++ b/prepare/r-phyloprofile/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PhyloProfile +_pkgver=1.8.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PhyloProfile' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-ape + r-biocstyle + r-biodist + r-biostrings + r-colourpicker + r-data.table + r-dt + r-energy + r-experimenthub + r-ggplot2 + r-gridextra + r-omadb + r-pbapply + r-plyr + r-rcolorbrewer + r-rcurl + r-shiny + r-shinybs + r-shinyjs + r-xml2 + r-yaml + r-zoo +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phyloprofile/lilac.py b/prepare/r-phyloprofile/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phyloprofile/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phyloprofile/lilac.yaml b/prepare/r-phyloprofile/lilac.yaml new file mode 100644 index 0000000000..d25f4b4337 --- /dev/null +++ b/prepare/r-phyloprofile/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-biocstyle +- r-biodist +- r-biostrings +- r-colourpicker +- r-data.table +- r-dt +- r-energy +- r-experimenthub +- r-ggplot2 +- r-gridextra +- r-omadb +- r-pbapply +- r-plyr +- r-rcolorbrewer +- r-rcurl +- r-shiny +- r-shinybs +- r-shinyjs +- r-xml2 +- r-yaml +- r-zoo +update_on: +- regex: PhyloProfile_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PhyloProfile diff --git a/prepare/r-phyloseq/PKGBUILD b/prepare/r-phyloseq/PKGBUILD new file mode 100644 index 0000000000..2d93903263 --- /dev/null +++ b/prepare/r-phyloseq/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=phyloseq +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Handling and analysis of high-throughput microbiome census data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-ade4 + r-ape + r-biobase + r-biocgenerics + r-biomformat + r-biostrings + r-data.table + r-foreach + r-ggplot2 + r-igraph + r-multtest + r-plyr + r-reshape2 + r-scales + r-vegan +) +optdepends=( + r-biocstyle + r-deseq2 + r-doparallel + r-genefilter + r-knitr + r-magrittr + r-metagenomeseq + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-phyloseq/lilac.py b/prepare/r-phyloseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-phyloseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-phyloseq/lilac.yaml b/prepare/r-phyloseq/lilac.yaml new file mode 100644 index 0000000000..46cc683818 --- /dev/null +++ b/prepare/r-phyloseq/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ade4 +- r-ape +- r-biobase +- r-biocgenerics +- r-biomformat +- r-biostrings +- r-data.table +- r-foreach +- r-ggplot2 +- r-igraph +- r-multtest +- r-plyr +- r-reshape2 +- r-scales +- r-vegan +update_on: +- regex: phyloseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/phyloseq diff --git a/prepare/r-pi/PKGBUILD b/prepare/r-pi/PKGBUILD new file mode 100644 index 0000000000..9917c839ed --- /dev/null +++ b/prepare/r-pi/PKGBUILD @@ -0,0 +1,68 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Pi +_pkgver=2.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-caret + r-dnet + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggnetwork + r-ggplot2 + r-ggrepel + r-glmnet + r-igraph + r-iranges + r-osfr + r-plot3d + r-purrr + r-randomforest + r-rcircos + r-readr + r-rocr + r-scales + r-suprahex + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-data.tree + r-doparallel + r-fgsea + r-foreach + r-ggally + r-ggbio + r-ggforce + r-ggpubr + r-gridextra + r-gviz + r-jsonlite + r-knitr + r-png + r-rcolorbrewer + r-rmarkdown + r-rtracklayer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pi/lilac.py b/prepare/r-pi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pi/lilac.yaml b/prepare/r-pi/lilac.yaml new file mode 100644 index 0000000000..8accd64240 --- /dev/null +++ b/prepare/r-pi/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-caret +- r-dnet +- r-dplyr +- r-genomeinfodb +- r-genomicranges +- r-ggnetwork +- r-ggplot2 +- r-ggrepel +- r-glmnet +- r-igraph +- r-iranges +- r-osfr +- r-plot3d +- r-purrr +- r-randomforest +- r-rcircos +- r-readr +- r-rocr +- r-scales +- r-suprahex +- r-tibble +- r-tidyr +update_on: +- regex: Pi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Pi diff --git a/prepare/r-piano/PKGBUILD b/prepare/r-piano/PKGBUILD new file mode 100644 index 0000000000..86e6d315c9 --- /dev/null +++ b/prepare/r-piano/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=piano +_pkgver=2.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Platform for integrative analysis of omics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-dt + r-fgsea + r-gplots + r-htmlwidgets + r-igraph + r-marray + r-relations + r-scales + r-shiny + r-shinydashboard + r-shinyjs + r-visnetwork +) +optdepends=( + r-affy + r-affyplm + r-annotationdbi + r-biocstyle + r-biomart + r-gtools + r-knitr + r-limma + r-plier + r-plotrix + r-rmarkdown + r-rsbml + r-snowfall + r-yeast2.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-piano/lilac.py b/prepare/r-piano/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-piano/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-piano/lilac.yaml b/prepare/r-piano/lilac.yaml new file mode 100644 index 0000000000..2f194e3309 --- /dev/null +++ b/prepare/r-piano/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-dt +- r-fgsea +- r-gplots +- r-htmlwidgets +- r-igraph +- r-marray +- r-relations +- r-scales +- r-shiny +- r-shinydashboard +- r-shinyjs +- r-visnetwork +update_on: +- regex: piano_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/piano diff --git a/prepare/r-picante/PKGBUILD b/prepare/r-picante/PKGBUILD new file mode 100644 index 0000000000..9a62df5c1e --- /dev/null +++ b/prepare/r-picante/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=picante +_pkgver=1.8.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integrating Phylogenies and Ecology' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-vegan +) +optdepends=( + r-brglm + r-circular + r-corpcor + r-quantreg +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-picante/lilac.py b/prepare/r-picante/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-picante/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-picante/lilac.yaml b/prepare/r-picante/lilac.yaml new file mode 100644 index 0000000000..e0cb8fd79c --- /dev/null +++ b/prepare/r-picante/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-vegan +update_on: +- regex: picante_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=picante diff --git a/prepare/r-pickgene/PKGBUILD b/prepare/r-pickgene/PKGBUILD new file mode 100644 index 0000000000..a78476109b --- /dev/null +++ b/prepare/r-pickgene/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pickgene +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Adaptive Gene Picking for Microarray Expression Data Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pickgene/lilac.py b/prepare/r-pickgene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pickgene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pickgene/lilac.yaml b/prepare/r-pickgene/lilac.yaml new file mode 100644 index 0000000000..6c6b869b39 --- /dev/null +++ b/prepare/r-pickgene/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pickgene_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pickgene diff --git a/prepare/r-pics/PKGBUILD b/prepare/r-pics/PKGBUILD new file mode 100644 index 0000000000..947dd5e9a0 --- /dev/null +++ b/prepare/r-pics/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PICS +_pkgver=2.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Probabilistic inference of ChIP-seq' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-genomicalignments + r-genomicranges + r-iranges + r-rsamtools +) +optdepends=( + r-knitr + r-parallel + r-rtracklayer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pics/lilac.py b/prepare/r-pics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pics/lilac.yaml b/prepare/r-pics/lilac.yaml new file mode 100644 index 0000000000..14f669d42d --- /dev/null +++ b/prepare/r-pics/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-rsamtools +update_on: +- regex: PICS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PICS diff --git a/prepare/r-pigengene/PKGBUILD b/prepare/r-pigengene/PKGBUILD new file mode 100644 index 0000000000..c0c55afded --- /dev/null +++ b/prepare/r-pigengene/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Pigengene +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Infers biological signatures from gene expression data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocstyle + r-bnlearn + r-c50 + r-clusterprofiler + r-dbi + r-dplyr + r-gdata + r-ggplot2 + r-go.db + r-graph + r-impute + r-matrixstats + r-openxlsx + r-partykit + r-pheatmap + r-preprocesscore + r-reactomepa + r-rgraphviz + r-wgcna +) +optdepends=( + r-annotationdbi + r-biomart + r-dose + r-energy + r-knitr + r-org.hs.eg.db + r-org.mm.eg.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pigengene/lilac.py b/prepare/r-pigengene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pigengene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pigengene/lilac.yaml b/prepare/r-pigengene/lilac.yaml new file mode 100644 index 0000000000..1dd53164f4 --- /dev/null +++ b/prepare/r-pigengene/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocstyle +- r-bnlearn +- r-c50 +- r-clusterprofiler +- r-dbi +- r-dplyr +- r-gdata +- r-ggplot2 +- r-go.db +- r-graph +- r-impute +- r-matrixstats +- r-openxlsx +- r-partykit +- r-pheatmap +- r-preprocesscore +- r-reactomepa +- r-rgraphviz +- r-wgcna +update_on: +- regex: Pigengene_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Pigengene diff --git a/prepare/r-pinfsc50/PKGBUILD b/prepare/r-pinfsc50/PKGBUILD new file mode 100644 index 0000000000..3d013ca0d9 --- /dev/null +++ b/prepare/r-pinfsc50/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pinfsc50 +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Sequence ('FASTA'), Annotation ('GFF') and Variants ('VCF') for 17 Samples of 'P. Infestans" and 1 'P. Mirabilis'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pinfsc50/lilac.py b/prepare/r-pinfsc50/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pinfsc50/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pinfsc50/lilac.yaml b/prepare/r-pinfsc50/lilac.yaml new file mode 100644 index 0000000000..9b2b26d57f --- /dev/null +++ b/prepare/r-pinfsc50/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pinfsc50_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pinfsc50 diff --git a/prepare/r-ping/PKGBUILD b/prepare/r-ping/PKGBUILD new file mode 100644 index 0000000000..5338621099 --- /dev/null +++ b/prepare/r-ping/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PING +_pkgver=2.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-bsgenome + r-fda + r-genomicranges + r-gviz + r-iranges + r-pics + r-s4vectors +) +optdepends=( + r-parallel + r-rtracklayer + r-shortread +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ping/lilac.py b/prepare/r-ping/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ping/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ping/lilac.yaml b/prepare/r-ping/lilac.yaml new file mode 100644 index 0000000000..7faf32463c --- /dev/null +++ b/prepare/r-ping/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-bsgenome +- r-fda +- r-genomicranges +- r-gviz +- r-iranges +- r-pics +- r-s4vectors +update_on: +- regex: PING_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PING diff --git a/prepare/r-pingr/PKGBUILD b/prepare/r-pingr/PKGBUILD new file mode 100644 index 0000000000..5d4e862571 --- /dev/null +++ b/prepare/r-pingr/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pingr +_pkgver=2.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Check if a Remote Computer is Up' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-processx +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pingr/lilac.py b/prepare/r-pingr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pingr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pingr/lilac.yaml b/prepare/r-pingr/lilac.yaml new file mode 100644 index 0000000000..ae1f4dd642 --- /dev/null +++ b/prepare/r-pingr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-processx +update_on: +- regex: pingr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pingr diff --git a/prepare/r-pipecomp/PKGBUILD b/prepare/r-pipecomp/PKGBUILD new file mode 100644 index 0000000000..28429c63a2 --- /dev/null +++ b/prepare/r-pipecomp/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pipeComp +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='pipeComp pipeline benchmarking framework' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-aricode + r-biocparallel + r-circlize + r-clue + r-complexheatmap + r-cowplot + r-dplyr + r-ggplot2 + r-intrinsicdimension + r-knitr + r-matrixstats + r-randomcolor + r-rcolorbrewer + r-reshape2 + r-rtsne + r-s4vectors + r-scales + r-scater + r-scran + r-seurat + r-singlecellexperiment + r-summarizedexperiment + r-uwot + r-viridislite +) +optdepends=( + r-biocstyle + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pipecomp/lilac.py b/prepare/r-pipecomp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pipecomp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pipecomp/lilac.yaml b/prepare/r-pipecomp/lilac.yaml new file mode 100644 index 0000000000..66445ed715 --- /dev/null +++ b/prepare/r-pipecomp/lilac.yaml @@ -0,0 +1,33 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aricode +- r-biocparallel +- r-circlize +- r-clue +- r-complexheatmap +- r-cowplot +- r-dplyr +- r-ggplot2 +- r-intrinsicdimension +- r-knitr +- r-matrixstats +- r-randomcolor +- r-rcolorbrewer +- r-reshape2 +- r-rtsne +- r-s4vectors +- r-scales +- r-scater +- r-scran +- r-seurat +- r-singlecellexperiment +- r-summarizedexperiment +- r-uwot +- r-viridislite +update_on: +- regex: pipeComp_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pipeComp diff --git a/prepare/r-pipeframe/PKGBUILD b/prepare/r-pipeframe/PKGBUILD new file mode 100644 index 0000000000..1833f0120c --- /dev/null +++ b/prepare/r-pipeframe/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pipeFrame +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pipeline framework for bioinformatics in R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-bsgenome + r-digest + r-genomeinfodb + r-magrittr + r-rmarkdown + r-visnetwork +) +optdepends=( + r-biocmanager + r-knitr + r-rtracklayer + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pipeframe/lilac.py b/prepare/r-pipeframe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pipeframe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pipeframe/lilac.yaml b/prepare/r-pipeframe/lilac.yaml new file mode 100644 index 0000000000..0075d1ecd2 --- /dev/null +++ b/prepare/r-pipeframe/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome +- r-digest +- r-genomeinfodb +- r-magrittr +- r-rmarkdown +- r-visnetwork +update_on: +- regex: pipeFrame_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pipeFrame diff --git a/prepare/r-pixmap/PKGBUILD b/prepare/r-pixmap/PKGBUILD new file mode 100644 index 0000000000..9432a85289 --- /dev/null +++ b/prepare/r-pixmap/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pixmap +_pkgver=0.4-12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bitmap Images / Pixel Maps' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pixmap/lilac.py b/prepare/r-pixmap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pixmap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pixmap/lilac.yaml b/prepare/r-pixmap/lilac.yaml new file mode 100644 index 0000000000..a0845e90c4 --- /dev/null +++ b/prepare/r-pixmap/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pixmap_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pixmap diff --git a/prepare/r-pkgbuild/PKGBUILD b/prepare/r-pkgbuild/PKGBUILD new file mode 100644 index 0000000000..60f94bb0f2 --- /dev/null +++ b/prepare/r-pkgbuild/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pkgbuild +_pkgver=1.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Find Tools Needed to Build R Packages' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-callr + r-cli + r-crayon + r-desc + r-prettyunits + r-r6 + r-rprojroot + r-withr +) +optdepends=( + r-covr + r-cpp11 + r-rcpp + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pkgbuild/lilac.py b/prepare/r-pkgbuild/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pkgbuild/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pkgbuild/lilac.yaml b/prepare/r-pkgbuild/lilac.yaml new file mode 100644 index 0000000000..4a3bc878df --- /dev/null +++ b/prepare/r-pkgbuild/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-callr +- r-cli +- r-crayon +- r-desc +- r-prettyunits +- r-r6 +- r-rprojroot +- r-withr +update_on: +- regex: pkgbuild_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pkgbuild diff --git a/prepare/r-pkgdeptools/PKGBUILD b/prepare/r-pkgdeptools/PKGBUILD new file mode 100644 index 0000000000..0c5ab4e055 --- /dev/null +++ b/prepare/r-pkgdeptools/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pkgDepTools +_pkgver=1.60.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Package Dependency Tools' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-graph + r-rbgl +) +optdepends=( + r-biobase + r-biocmanager + r-rcurl + r-rgraphviz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pkgdeptools/lilac.py b/prepare/r-pkgdeptools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pkgdeptools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pkgdeptools/lilac.yaml b/prepare/r-pkgdeptools/lilac.yaml new file mode 100644 index 0000000000..b6d50beea3 --- /dev/null +++ b/prepare/r-pkgdeptools/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +- r-rbgl +update_on: +- regex: pkgDepTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pkgDepTools diff --git a/prepare/r-pkgload/PKGBUILD b/prepare/r-pkgload/PKGBUILD new file mode 100644 index 0000000000..3291a1929f --- /dev/null +++ b/prepare/r-pkgload/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pkgload +_pkgver=1.2.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Simulate Package Installation and Attach' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-cli + r-crayon + r-desc + r-rlang + r-rprojroot + r-rstudioapi + r-withr +) +optdepends=( + r-bitops + r-covr + r-pkgbuild + r-rcpp + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pkgload/lilac.py b/prepare/r-pkgload/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pkgload/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pkgload/lilac.yaml b/prepare/r-pkgload/lilac.yaml new file mode 100644 index 0000000000..ac537b8dcf --- /dev/null +++ b/prepare/r-pkgload/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cli +- r-crayon +- r-desc +- r-rlang +- r-rprojroot +- r-rstudioapi +- r-withr +update_on: +- regex: pkgload_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pkgload diff --git a/prepare/r-pkgmaker/PKGBUILD b/prepare/r-pkgmaker/PKGBUILD new file mode 100644 index 0000000000..3325552185 --- /dev/null +++ b/prepare/r-pkgmaker/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pkgmaker +_pkgver=0.32.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Development Utilities for R Packages' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-digest + r-registry + r-stringr + r-withr + r-xtable +) +optdepends=( + r-biobase + r-datasets + r-devtools + r-knitr + r-markdown + r-rbibutils + r-rmarkdown + r-roxygen2 + r-runit + r-testthat + r-yaml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pkgmaker/lilac.py b/prepare/r-pkgmaker/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pkgmaker/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pkgmaker/lilac.yaml b/prepare/r-pkgmaker/lilac.yaml new file mode 100644 index 0000000000..fe7ce95468 --- /dev/null +++ b/prepare/r-pkgmaker/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-digest +- r-registry +- r-stringr +- r-withr +- r-xtable +update_on: +- regex: pkgmaker_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pkgmaker diff --git a/prepare/r-planet/PKGBUILD b/prepare/r-planet/PKGBUILD new file mode 100644 index 0000000000..693542917e --- /dev/null +++ b/prepare/r-planet/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=planet +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Placental DNA methylation analysis tools' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-magrittr + r-tibble +) +optdepends=( + r-epidish + r-ggplot2 + r-knitr + r-minfi + r-rmarkdown + r-scales + r-testthat + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-planet/lilac.py b/prepare/r-planet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-planet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-planet/lilac.yaml b/prepare/r-planet/lilac.yaml new file mode 100644 index 0000000000..1a1c396a20 --- /dev/null +++ b/prepare/r-planet/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-magrittr +- r-tibble +update_on: +- regex: planet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/planet diff --git a/prepare/r-plethy/PKGBUILD b/prepare/r-plethy/PKGBUILD new file mode 100644 index 0000000000..22ac05b844 --- /dev/null +++ b/prepare/r-plethy/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=plethy +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R framework for exploration and analysis of respirometry data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-dbi + r-ggplot2 + r-iranges + r-plyr + r-rcolorbrewer + r-reshape2 + r-rsqlite + r-s4vectors + r-streamer +) +optdepends=( + r-biocstyle + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-plethy/lilac.py b/prepare/r-plethy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-plethy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-plethy/lilac.yaml b/prepare/r-plethy/lilac.yaml new file mode 100644 index 0000000000..1fab7d4b69 --- /dev/null +++ b/prepare/r-plethy/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-dbi +- r-ggplot2 +- r-iranges +- r-plyr +- r-rcolorbrewer +- r-reshape2 +- r-rsqlite +- r-s4vectors +- r-streamer +update_on: +- regex: plethy_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/plethy diff --git a/prepare/r-plgem/PKGBUILD b/prepare/r-plgem/PKGBUILD new file mode 100644 index 0000000000..06c7e0843c --- /dev/null +++ b/prepare/r-plgem/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=plgem +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-plgem/lilac.py b/prepare/r-plgem/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-plgem/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-plgem/lilac.yaml b/prepare/r-plgem/lilac.yaml new file mode 100644 index 0000000000..58af638948 --- /dev/null +++ b/prepare/r-plgem/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: plgem_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/plgem diff --git a/prepare/r-plier/PKGBUILD b/prepare/r-plier/PKGBUILD new file mode 100644 index 0000000000..8970a7d203 --- /dev/null +++ b/prepare/r-plier/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=plier +_pkgver=1.64.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Implements the Affymetrix PLIER algorithm' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-plier/lilac.py b/prepare/r-plier/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-plier/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-plier/lilac.yaml b/prepare/r-plier/lilac.yaml new file mode 100644 index 0000000000..240aa5c2a6 --- /dev/null +++ b/prepare/r-plier/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +update_on: +- regex: plier_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/plier diff --git a/prepare/r-plogo2/PKGBUILD b/prepare/r-plogo2/PKGBUILD new file mode 100644 index 0000000000..8b22bab574 --- /dev/null +++ b/prepare/r-plogo2/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PloGO2 +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Plot Gene Ontology and KEGG pathway Annotation and Abundance' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-go.db + r-gostats + r-httr + r-openxlsx + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-plogo2/lilac.py b/prepare/r-plogo2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-plogo2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-plogo2/lilac.yaml b/prepare/r-plogo2/lilac.yaml new file mode 100644 index 0000000000..ad7c96f95d --- /dev/null +++ b/prepare/r-plogo2/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-go.db +- r-gostats +- r-httr +- r-openxlsx +- r-xtable +update_on: +- regex: PloGO2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PloGO2 diff --git a/prepare/r-plot3d/PKGBUILD b/prepare/r-plot3d/PKGBUILD new file mode 100644 index 0000000000..b81dad8711 --- /dev/null +++ b/prepare/r-plot3d/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=plot3D +_pkgver=1.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Plotting Multi-Dimensional Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-misc3d +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-plot3d/lilac.py b/prepare/r-plot3d/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-plot3d/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-plot3d/lilac.yaml b/prepare/r-plot3d/lilac.yaml new file mode 100644 index 0000000000..6bb865b589 --- /dev/null +++ b/prepare/r-plot3d/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-misc3d +update_on: +- regex: plot3D_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=plot3D diff --git a/prepare/r-plotgardener/PKGBUILD b/prepare/r-plotgardener/PKGBUILD new file mode 100644 index 0000000000..99d0c93b21 --- /dev/null +++ b/prepare/r-plotgardener/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Guoyi Zhang + +_pkgname=plotgardener +_pkgver=1.0.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Coordinate-Based Genomic Visualization Package for R' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-curl + r-data.table + r-dplyr + r-ggplotify + r-plyranges + r-purrr + r-rcolorbrewer + r-rcpp + r-rlang + r-strawr +) +optdepends=( + r-annotationdbi + r-annotationhub + r-bsgenome + r-bsgenome.hsapiens.ucsc.hg19 + r-complexheatmap + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-interactionset + r-iranges + r-knitr + r-org.hs.eg.db + r-plotgardenerdata + r-png + r-rmarkdown + r-rtracklayer + r-scales + r-showtext + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-plotgardener/lilac.py b/prepare/r-plotgardener/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-plotgardener/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-plotgardener/lilac.yaml b/prepare/r-plotgardener/lilac.yaml new file mode 100644 index 0000000000..47cacce244 --- /dev/null +++ b/prepare/r-plotgardener/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-data.table +- r-dplyr +- r-ggplotify +- r-plyranges +- r-purrr +- r-rcolorbrewer +- r-rcpp +- r-rlang +- r-strawr +update_on: +- regex: plotgardener_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/plotgardener diff --git a/prepare/r-plotgrouper/PKGBUILD b/prepare/r-plotgrouper/PKGBUILD new file mode 100644 index 0000000000..b98751ed93 --- /dev/null +++ b/prepare/r-plotgrouper/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=plotGrouper +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Shiny app GUI wrapper for ggplot with built-in statistical analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-colourpicker + r-dplyr + r-egg + r-ggplot2 + r-ggpubr + r-gridextra + r-gtable + r-hmisc + r-magrittr + r-readr + r-readxl + r-rlang + r-scales + r-shiny + r-shinythemes + r-stringr + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-htmltools + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-plotgrouper/lilac.py b/prepare/r-plotgrouper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-plotgrouper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-plotgrouper/lilac.yaml b/prepare/r-plotgrouper/lilac.yaml new file mode 100644 index 0000000000..fb6affcb63 --- /dev/null +++ b/prepare/r-plotgrouper/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colourpicker +- r-dplyr +- r-egg +- r-ggplot2 +- r-ggpubr +- r-gridextra +- r-gtable +- r-hmisc +- r-magrittr +- r-readr +- r-readxl +- r-rlang +- r-scales +- r-shiny +- r-shinythemes +- r-stringr +- r-tibble +- r-tidyr +update_on: +- regex: plotGrouper_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/plotGrouper diff --git a/prepare/r-plotly/PKGBUILD b/prepare/r-plotly/PKGBUILD new file mode 100644 index 0000000000..8939030c39 --- /dev/null +++ b/prepare/r-plotly/PKGBUILD @@ -0,0 +1,78 @@ +# Maintainer: Guoyi Zhang + +_pkgname=plotly +_pkgver=4.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Create Interactive Web Graphics via 'plotly.js'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-base64enc + r-crosstalk + r-data.table + r-digest + r-dplyr + r-ggplot2 + r-htmltools + r-htmlwidgets + r-httr + r-jsonlite + r-lazyeval + r-magrittr + r-promises + r-purrr + r-rcolorbrewer + r-rlang + r-scales + r-tibble + r-tidyr + r-vctrs + r-viridislite +) +optdepends=( + r-broom + r-cairo + r-curl + r-dendextend + r-devtools + r-forcats + r-ggally + r-ggthemes + r-hexbin + r-irdisplay + r-knitr + r-listviewer + r-maps + r-maptools + r-mass + r-palmerpenguins + r-plotlygeoassets + r-png + r-processx + r-reticulate + r-rgeos + r-rmarkdown + r-rversions + r-sf + r-shiny + r-shinytest + r-testthat + r-webshot +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-plotly/lilac.py b/prepare/r-plotly/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-plotly/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-plotly/lilac.yaml b/prepare/r-plotly/lilac.yaml new file mode 100644 index 0000000000..e75035fd8b --- /dev/null +++ b/prepare/r-plotly/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-crosstalk +- r-data.table +- r-digest +- r-dplyr +- r-ggplot2 +- r-htmltools +- r-htmlwidgets +- r-httr +- r-jsonlite +- r-lazyeval +- r-magrittr +- r-promises +- r-purrr +- r-rcolorbrewer +- r-rlang +- r-scales +- r-tibble +- r-tidyr +- r-vctrs +- r-viridislite +update_on: +- regex: plotly_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=plotly diff --git a/prepare/r-plotmo/PKGBUILD b/prepare/r-plotmo/PKGBUILD new file mode 100644 index 0000000000..44ba3eb5b5 --- /dev/null +++ b/prepare/r-plotmo/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=plotmo +_pkgver=3.6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Plot a Model's Residuals, Response, and Partial Dependence Plots" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-formula + r-plotrix + r-teachingdemos +) +optdepends=( + r-c50 + r-earth + r-gbm + r-glmnet + r-glmnetutils + r-mass + r-mlr + r-neuralnet + r-partykit + r-pre + r-rpart + r-rpart.plot +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-plotmo/lilac.py b/prepare/r-plotmo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-plotmo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-plotmo/lilac.yaml b/prepare/r-plotmo/lilac.yaml new file mode 100644 index 0000000000..929b114478 --- /dev/null +++ b/prepare/r-plotmo/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-formula +- r-plotrix +- r-teachingdemos +update_on: +- regex: plotmo_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=plotmo diff --git a/prepare/r-plotrix/PKGBUILD b/prepare/r-plotrix/PKGBUILD new file mode 100644 index 0000000000..ba799cf1cf --- /dev/null +++ b/prepare/r-plotrix/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=plotrix +_pkgver=3.8-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Various Plotting Functions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-plotrix/lilac.py b/prepare/r-plotrix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-plotrix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-plotrix/lilac.yaml b/prepare/r-plotrix/lilac.yaml new file mode 100644 index 0000000000..23b8712c53 --- /dev/null +++ b/prepare/r-plotrix/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: plotrix_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=plotrix diff --git a/prepare/r-plotroc/PKGBUILD b/prepare/r-plotroc/PKGBUILD new file mode 100644 index 0000000000..e713011463 --- /dev/null +++ b/prepare/r-plotroc/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=plotROC +_pkgver=2.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generate Useful ROC Curve Charts for Print and Interactive Use' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-ggplot2 + r-gridsvg + r-plyr + r-rlang + r-shiny +) +optdepends=( + r-knitr + r-rmarkdown + r-stringr + r-survivalroc + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-plotroc/lilac.py b/prepare/r-plotroc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-plotroc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-plotroc/lilac.yaml b/prepare/r-plotroc/lilac.yaml new file mode 100644 index 0000000000..62587e97f4 --- /dev/null +++ b/prepare/r-plotroc/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gridsvg +- r-plyr +- r-rlang +- r-shiny +update_on: +- regex: plotROC_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=plotROC diff --git a/prepare/r-plpe/PKGBUILD b/prepare/r-plpe/PKGBUILD new file mode 100644 index 0000000000..be679a8bb5 --- /dev/null +++ b/prepare/r-plpe/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PLPE +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Local Pooled Error Test for Differential Expression with Paired High-throughput Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-lpe +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-plpe/lilac.py b/prepare/r-plpe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-plpe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-plpe/lilac.yaml b/prepare/r-plpe/lilac.yaml new file mode 100644 index 0000000000..034ec4a151 --- /dev/null +++ b/prepare/r-plpe/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-lpe +update_on: +- regex: PLPE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PLPE diff --git a/prepare/r-pls/PKGBUILD b/prepare/r-pls/PKGBUILD new file mode 100644 index 0000000000..6364e09aaf --- /dev/null +++ b/prepare/r-pls/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pls +_pkgver=2.8-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Partial Least Squares and Principal Component Regression' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-mass + r-parallel + r-rmpi + r-runit + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pls/lilac.py b/prepare/r-pls/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pls/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pls/lilac.yaml b/prepare/r-pls/lilac.yaml new file mode 100644 index 0000000000..8768ec456f --- /dev/null +++ b/prepare/r-pls/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pls_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pls diff --git a/prepare/r-plsgenomics/PKGBUILD b/prepare/r-plsgenomics/PKGBUILD new file mode 100644 index 0000000000..05618f355b --- /dev/null +++ b/prepare/r-plsgenomics/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=plsgenomics +_pkgver=1.5-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PLS Analyses for Genomics' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-fields + r-plyr + r-reshape2 + r-rhpcblasctl +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-plsgenomics/lilac.py b/prepare/r-plsgenomics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-plsgenomics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-plsgenomics/lilac.yaml b/prepare/r-plsgenomics/lilac.yaml new file mode 100644 index 0000000000..ed2242862e --- /dev/null +++ b/prepare/r-plsgenomics/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fields +- r-plyr +- r-reshape2 +- r-rhpcblasctl +update_on: +- regex: plsgenomics_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=plsgenomics diff --git a/prepare/r-plsvarsel/PKGBUILD b/prepare/r-plsvarsel/PKGBUILD new file mode 100644 index 0000000000..52b047a04d --- /dev/null +++ b/prepare/r-plsvarsel/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=plsVarSel +_pkgver=0.9.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Variable Selection in Partial Least Squares' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bdsmatrix + r-genalg + r-msqc + r-mvtnorm + r-pls + r-praznik + r-progress +) +optdepends=( + r-rmpi +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-plsvarsel/lilac.py b/prepare/r-plsvarsel/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-plsvarsel/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-plsvarsel/lilac.yaml b/prepare/r-plsvarsel/lilac.yaml new file mode 100644 index 0000000000..d3aebed85d --- /dev/null +++ b/prepare/r-plsvarsel/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bdsmatrix +- r-genalg +- r-msqc +- r-mvtnorm +- r-pls +- r-praznik +- r-progress +update_on: +- regex: plsVarSel_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=plsVarSel diff --git a/prepare/r-plyr/PKGBUILD b/prepare/r-plyr/PKGBUILD new file mode 100644 index 0000000000..5a38114023 --- /dev/null +++ b/prepare/r-plyr/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=plyr +_pkgver=1.8.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Splitting, Applying and Combining Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-rcpp +) +optdepends=( + r-abind + r-covr + r-doparallel + r-foreach + r-iterators + r-itertools + r-tcltk + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-plyr/lilac.py b/prepare/r-plyr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-plyr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-plyr/lilac.yaml b/prepare/r-plyr/lilac.yaml new file mode 100644 index 0000000000..16df8a22a5 --- /dev/null +++ b/prepare/r-plyr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: plyr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=plyr diff --git a/prepare/r-plyranges/PKGBUILD b/prepare/r-plyranges/PKGBUILD new file mode 100644 index 0000000000..5cf46f4445 --- /dev/null +++ b/prepare/r-plyranges/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=plyranges +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A fluent interface for manipulating GenomicRanges' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-dplyr + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-magrittr + r-rlang + r-rsamtools + r-rtracklayer + r-s4vectors + r-tidyselect +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-covr + r-ggplot2 + r-helloranges + r-hellorangesdata + r-knitr + r-pasillabamsubset + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-plyranges/lilac.py b/prepare/r-plyranges/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-plyranges/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-plyranges/lilac.yaml b/prepare/r-plyranges/lilac.yaml new file mode 100644 index 0000000000..7b7e87e7d1 --- /dev/null +++ b/prepare/r-plyranges/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-dplyr +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-magrittr +- r-rlang +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-tidyselect +update_on: +- regex: plyranges_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/plyranges diff --git a/prepare/r-pma/PKGBUILD b/prepare/r-pma/PKGBUILD new file mode 100644 index 0000000000..890161b012 --- /dev/null +++ b/prepare/r-pma/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PMA +_pkgver=1.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Penalized Multivariate Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pma/lilac.py b/prepare/r-pma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pma/lilac.yaml b/prepare/r-pma/lilac.yaml new file mode 100644 index 0000000000..e44337a439 --- /dev/null +++ b/prepare/r-pma/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: PMA_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=PMA diff --git a/prepare/r-pmcmrplus/PKGBUILD b/prepare/r-pmcmrplus/PKGBUILD new file mode 100644 index 0000000000..d4a44a06da --- /dev/null +++ b/prepare/r-pmcmrplus/PKGBUILD @@ -0,0 +1,48 @@ +# system requirements: gmp (>= 4.2.3), mpfr (>= 3.0.0) | file README.md +# Maintainer: Guoyi Zhang + +_pkgname=PMCMRplus +_pkgver=1.9.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Calculate Pairwise Multiple Comparisons of Mean Rank Sums Extended' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bwstest + r-gmp + r-ksamples + r-multcompview + r-mvtnorm + r-rmpfr + r-suppdists +) +optdepends=( + r-car + r-e1071 + r-graphics + r-knitr + r-multcomp + r-nsm3 + r-pwr + r-rmarkdown + r-xtable +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pmcmrplus/lilac.py b/prepare/r-pmcmrplus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pmcmrplus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pmcmrplus/lilac.yaml b/prepare/r-pmcmrplus/lilac.yaml new file mode 100644 index 0000000000..e7f1b85374 --- /dev/null +++ b/prepare/r-pmcmrplus/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bwstest +- r-gmp +- r-ksamples +- r-multcompview +- r-mvtnorm +- r-rmpfr +- r-suppdists +update_on: +- regex: PMCMRplus_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=PMCMRplus diff --git a/prepare/r-pmm/PKGBUILD b/prepare/r-pmm/PKGBUILD new file mode 100644 index 0000000000..69879dc2ac --- /dev/null +++ b/prepare/r-pmm/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pmm +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Parallel Mixed Model' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-lme4 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pmm/lilac.py b/prepare/r-pmm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pmm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pmm/lilac.yaml b/prepare/r-pmm/lilac.yaml new file mode 100644 index 0000000000..f0abc13f6e --- /dev/null +++ b/prepare/r-pmm/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lme4 +update_on: +- regex: pmm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pmm diff --git a/prepare/r-pmp/PKGBUILD b/prepare/r-pmp/PKGBUILD new file mode 100644 index 0000000000..c85191674d --- /dev/null +++ b/prepare/r-pmp/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pmp +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Peak Matrix Processing and signal batch correction for metabolomics datasets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-impute + r-matrixstats + r-missforest + r-pcamethods + r-reshape2 + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-covr + r-gridextra + r-knitr + r-magick + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pmp/lilac.py b/prepare/r-pmp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pmp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pmp/lilac.yaml b/prepare/r-pmp/lilac.yaml new file mode 100644 index 0000000000..35ac07eefe --- /dev/null +++ b/prepare/r-pmp/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-impute +- r-matrixstats +- r-missforest +- r-pcamethods +- r-reshape2 +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: pmp_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pmp diff --git a/prepare/r-podcall/PKGBUILD b/prepare/r-podcall/PKGBUILD new file mode 100644 index 0000000000..fde071d7f3 --- /dev/null +++ b/prepare/r-podcall/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PoDCall +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Positive Droplet Calling for DNA Methylation Droplet Digital PCR' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-diptest + r-dt + r-ggplot2 + r-gridextra + r-laplacesdemon + r-mclust + r-purrr + r-readr + r-rlist + r-shiny + r-shinyjs +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-podcall/lilac.py b/prepare/r-podcall/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-podcall/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-podcall/lilac.yaml b/prepare/r-podcall/lilac.yaml new file mode 100644 index 0000000000..d1bc4b8af0 --- /dev/null +++ b/prepare/r-podcall/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-diptest +- r-dt +- r-ggplot2 +- r-gridextra +- r-laplacesdemon +- r-mclust +- r-purrr +- r-readr +- r-rlist +- r-shiny +- r-shinyjs +update_on: +- regex: PoDCall_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PoDCall diff --git a/prepare/r-podkat/PKGBUILD b/prepare/r-podkat/PKGBUILD new file mode 100644 index 0000000000..ca3cd66fe8 --- /dev/null +++ b/prepare/r-podkat/PKGBUILD @@ -0,0 +1,46 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=podkat +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Position-Dependent Kernel Association Test' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-iranges + r-rcpp + r-rhtslib + r-rsamtools +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg38.masked + r-bsgenome.mmusculus.ucsc.mm10.masked + r-gwastools + r-knitr + r-summarizedexperiment + r-txdb.hsapiens.ucsc.hg38.knowngene + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-podkat/lilac.py b/prepare/r-podkat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-podkat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-podkat/lilac.yaml b/prepare/r-podkat/lilac.yaml new file mode 100644 index 0000000000..d69b8136ce --- /dev/null +++ b/prepare/r-podkat/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rcpp +- r-rhtslib +- r-rsamtools +update_on: +- regex: podkat_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/podkat diff --git a/prepare/r-pogos/PKGBUILD b/prepare/r-pogos/PKGBUILD new file mode 100644 index 0000000000..811e70dcad --- /dev/null +++ b/prepare/r-pogos/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pogos +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PharmacOGenomics Ontology Support' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ggplot2 + r-httr + r-ontoproc + r-rjson + r-s4vectors + r-shiny +) +optdepends=( + r-dt + r-knitr + r-ontologyplot + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pogos/lilac.py b/prepare/r-pogos/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pogos/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pogos/lilac.yaml b/prepare/r-pogos/lilac.yaml new file mode 100644 index 0000000000..2a32c4b2d9 --- /dev/null +++ b/prepare/r-pogos/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-httr +- r-ontoproc +- r-rjson +- r-s4vectors +- r-shiny +update_on: +- regex: pogos_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pogos diff --git a/prepare/r-poibin/PKGBUILD b/prepare/r-poibin/PKGBUILD new file mode 100644 index 0000000000..d4f8422248 --- /dev/null +++ b/prepare/r-poibin/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=poibin +_pkgver=1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The Poisson Binomial Distribution' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-poibin/lilac.py b/prepare/r-poibin/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-poibin/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-poibin/lilac.yaml b/prepare/r-poibin/lilac.yaml new file mode 100644 index 0000000000..0e44895c96 --- /dev/null +++ b/prepare/r-poibin/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: poibin_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=poibin diff --git a/prepare/r-poiclaclu/PKGBUILD b/prepare/r-poiclaclu/PKGBUILD new file mode 100644 index 0000000000..cfd86544a6 --- /dev/null +++ b/prepare/r-poiclaclu/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PoiClaClu +_pkgver=1.0.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Classification and Clustering of Sequencing Data Based on a Poisson Model' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-poiclaclu/lilac.py b/prepare/r-poiclaclu/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-poiclaclu/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-poiclaclu/lilac.yaml b/prepare/r-poiclaclu/lilac.yaml new file mode 100644 index 0000000000..70d2509fbd --- /dev/null +++ b/prepare/r-poiclaclu/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: PoiClaClu_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=PoiClaClu diff --git a/prepare/r-poissonbinomial/PKGBUILD b/prepare/r-poissonbinomial/PKGBUILD new file mode 100644 index 0000000000..b3b40519f3 --- /dev/null +++ b/prepare/r-poissonbinomial/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: fftw3 (>= 3.3) +# Maintainer: Guoyi Zhang + +_pkgname=PoissonBinomial +_pkgver=1.2.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Efficient Computation of Ordinary and Generalized Poisson Binomial Distributions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-knitr + r-microbenchmark + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-poissonbinomial/lilac.py b/prepare/r-poissonbinomial/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-poissonbinomial/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-poissonbinomial/lilac.yaml b/prepare/r-poissonbinomial/lilac.yaml new file mode 100644 index 0000000000..b2e49e90e7 --- /dev/null +++ b/prepare/r-poissonbinomial/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: PoissonBinomial_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=PoissonBinomial diff --git a/prepare/r-polspline/PKGBUILD b/prepare/r-polspline/PKGBUILD new file mode 100644 index 0000000000..e462caa061 --- /dev/null +++ b/prepare/r-polspline/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=polspline +_pkgver=1.1.19 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Polynomial Spline Routines' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-polspline/lilac.py b/prepare/r-polspline/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-polspline/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-polspline/lilac.yaml b/prepare/r-polspline/lilac.yaml new file mode 100644 index 0000000000..c7f2044b20 --- /dev/null +++ b/prepare/r-polspline/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: polspline_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=polspline diff --git a/prepare/r-polychrome/PKGBUILD b/prepare/r-polychrome/PKGBUILD new file mode 100644 index 0000000000..23a2f044cc --- /dev/null +++ b/prepare/r-polychrome/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Polychrome +_pkgver=1.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Qualitative Palettes with Many Colors' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-colorspace + r-scatterplot3d +) +optdepends=( + r-ggplot2 + r-knitr + r-rcolorbrewer + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-polychrome/lilac.py b/prepare/r-polychrome/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-polychrome/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-polychrome/lilac.yaml b/prepare/r-polychrome/lilac.yaml new file mode 100644 index 0000000000..84e6f63d00 --- /dev/null +++ b/prepare/r-polychrome/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colorspace +- r-scatterplot3d +update_on: +- regex: Polychrome_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Polychrome diff --git a/prepare/r-polyclip/PKGBUILD b/prepare/r-polyclip/PKGBUILD new file mode 100644 index 0000000000..820fb51f03 --- /dev/null +++ b/prepare/r-polyclip/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=polyclip +_pkgver=1.10-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Polygon Clipping' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-polyclip/lilac.py b/prepare/r-polyclip/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-polyclip/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-polyclip/lilac.yaml b/prepare/r-polyclip/lilac.yaml new file mode 100644 index 0000000000..c5408754d7 --- /dev/null +++ b/prepare/r-polyclip/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: polyclip_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=polyclip diff --git a/prepare/r-polyester/PKGBUILD b/prepare/r-polyester/PKGBUILD new file mode 100644 index 0000000000..152f7b6311 --- /dev/null +++ b/prepare/r-polyester/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=polyester +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Simulate RNA-seq reads' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-iranges + r-limma + r-logspline + r-s4vectors + r-zlibbioc +) +optdepends=( + r-ballgown + r-knitr + r-markdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-polyester/lilac.py b/prepare/r-polyester/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-polyester/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-polyester/lilac.yaml b/prepare/r-polyester/lilac.yaml new file mode 100644 index 0000000000..8b411d6a16 --- /dev/null +++ b/prepare/r-polyester/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-iranges +- r-limma +- r-logspline +- r-s4vectors +- r-zlibbioc +update_on: +- regex: polyester_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/polyester diff --git a/prepare/r-polylabelr/PKGBUILD b/prepare/r-polylabelr/PKGBUILD new file mode 100644 index 0000000000..40d01aea61 --- /dev/null +++ b/prepare/r-polylabelr/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=polylabelr +_pkgver=0.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Find the Pole of Inaccessibility (Visual Center) of a Polygon' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-rcpp +) +optdepends=( + r-covr + r-sf + r-spelling + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-polylabelr/lilac.py b/prepare/r-polylabelr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-polylabelr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-polylabelr/lilac.yaml b/prepare/r-polylabelr/lilac.yaml new file mode 100644 index 0000000000..6bd2b33d4d --- /dev/null +++ b/prepare/r-polylabelr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: polylabelr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=polylabelr diff --git a/prepare/r-polynom/PKGBUILD b/prepare/r-polynom/PKGBUILD new file mode 100644 index 0000000000..c2e2a82ee4 --- /dev/null +++ b/prepare/r-polynom/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=polynom +_pkgver=1.4-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-polynom/lilac.py b/prepare/r-polynom/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-polynom/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-polynom/lilac.yaml b/prepare/r-polynom/lilac.yaml new file mode 100644 index 0000000000..775bcb6e12 --- /dev/null +++ b/prepare/r-polynom/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: polynom_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=polynom diff --git a/prepare/r-polynomf/PKGBUILD b/prepare/r-polynomf/PKGBUILD new file mode 100644 index 0000000000..02a7d732ee --- /dev/null +++ b/prepare/r-polynomf/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PolynomF +_pkgver=2.0-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Polynomials in R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-polynomf/lilac.py b/prepare/r-polynomf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-polynomf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-polynomf/lilac.yaml b/prepare/r-polynomf/lilac.yaml new file mode 100644 index 0000000000..60d220ff52 --- /dev/null +++ b/prepare/r-polynomf/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: PolynomF_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=PolynomF diff --git a/prepare/r-polyphen.hsapiens.dbsnp131/PKGBUILD b/prepare/r-polyphen.hsapiens.dbsnp131/PKGBUILD new file mode 100644 index 0000000000..0bb762f4f6 --- /dev/null +++ b/prepare/r-polyphen.hsapiens.dbsnp131/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PolyPhen.Hsapiens.dbSNP131 +_pkgver=1.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PolyPhen Predictions for Homo sapiens dbSNP build 131' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-rsqlite + r-variantannotation +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-polyphen.hsapiens.dbsnp131/lilac.py b/prepare/r-polyphen.hsapiens.dbsnp131/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-polyphen.hsapiens.dbsnp131/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-polyphen.hsapiens.dbsnp131/lilac.yaml b/prepare/r-polyphen.hsapiens.dbsnp131/lilac.yaml new file mode 100644 index 0000000000..c994deb574 --- /dev/null +++ b/prepare/r-polyphen.hsapiens.dbsnp131/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-rsqlite +- r-variantannotation +update_on: +- regex: PolyPhen.Hsapiens.dbSNP131_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PolyPhen.Hsapiens.dbSNP131 diff --git a/prepare/r-poma/PKGBUILD b/prepare/r-poma/PKGBUILD new file mode 100644 index 0000000000..164d70aff7 --- /dev/null +++ b/prepare/r-poma/PKGBUILD @@ -0,0 +1,61 @@ +# Maintainer: Guoyi Zhang + +_pkgname=POMA +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='User-friendly Workflow for Metabolomics and Proteomics Data Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-broom + r-caret + r-clisymbols + r-complexheatmap + r-crayon + r-dplyr + r-e1071 + r-ggcorrplot + r-ggplot2 + r-ggraph + r-ggrepel + r-glasso + r-glmnet + r-impute + r-knitr + r-limma + r-magrittr + r-mixomics + r-msnbase + r-patchwork + r-qpdf + r-randomforest + r-rankprod + r-rmarkdown + r-tibble + r-tidyr + r-vegan +) +optdepends=( + r-biobase + r-biocstyle + r-covr + r-plotly + r-testthat + r-tidyverse +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-poma/lilac.py b/prepare/r-poma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-poma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-poma/lilac.yaml b/prepare/r-poma/lilac.yaml new file mode 100644 index 0000000000..8f01af7123 --- /dev/null +++ b/prepare/r-poma/lilac.yaml @@ -0,0 +1,36 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-broom +- r-caret +- r-clisymbols +- r-complexheatmap +- r-crayon +- r-dplyr +- r-e1071 +- r-ggcorrplot +- r-ggplot2 +- r-ggraph +- r-ggrepel +- r-glasso +- r-glmnet +- r-impute +- r-knitr +- r-limma +- r-magrittr +- r-mixomics +- r-msnbase +- r-patchwork +- r-qpdf +- r-randomforest +- r-rankprod +- r-rmarkdown +- r-tibble +- r-tidyr +- r-vegan +update_on: +- regex: POMA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/POMA diff --git a/prepare/r-posterior/PKGBUILD b/prepare/r-posterior/PKGBUILD new file mode 100644 index 0000000000..badfd1b350 --- /dev/null +++ b/prepare/r-posterior/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=posterior +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Working with Posterior Distributions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-abind + r-checkmate + r-distributional + r-matrixstats + r-pillar + r-rlang + r-tensora + r-tibble + r-vctrs +) +optdepends=( + r-caret + r-dplyr + r-e1071 + r-gbm + r-knitr + r-randomforest + r-rmarkdown + r-testthat + r-tidyr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-posterior/lilac.py b/prepare/r-posterior/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-posterior/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-posterior/lilac.yaml b/prepare/r-posterior/lilac.yaml new file mode 100644 index 0000000000..ef736dca71 --- /dev/null +++ b/prepare/r-posterior/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-checkmate +- r-distributional +- r-matrixstats +- r-pillar +- r-rlang +- r-tensora +- r-tibble +- r-vctrs +update_on: +- regex: posterior_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=posterior diff --git a/prepare/r-potra/PKGBUILD b/prepare/r-potra/PKGBUILD new file mode 100644 index 0000000000..87e9344350 --- /dev/null +++ b/prepare/r-potra/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PoTRA +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PoTRA: Pathways of Topological Rank Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biocgenerics + r-graph + r-graphite + r-igraph + r-org.hs.eg.db +) +optdepends=( + r-biocstyle + r-colr + r-knitr + r-metap + r-repmis + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-potra/lilac.py b/prepare/r-potra/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-potra/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-potra/lilac.yaml b/prepare/r-potra/lilac.yaml new file mode 100644 index 0000000000..a4c8302835 --- /dev/null +++ b/prepare/r-potra/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-graph +- r-graphite +- r-igraph +- r-org.hs.eg.db +update_on: +- regex: PoTRA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PoTRA diff --git a/prepare/r-powerlaw/PKGBUILD b/prepare/r-powerlaw/PKGBUILD new file mode 100644 index 0000000000..ecad02f9fc --- /dev/null +++ b/prepare/r-powerlaw/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=poweRlaw +_pkgver=0.70.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Heavy Tailed Distributions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-pracma +) +optdepends=( + r-covr + r-knitr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-powerlaw/lilac.py b/prepare/r-powerlaw/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-powerlaw/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-powerlaw/lilac.yaml b/prepare/r-powerlaw/lilac.yaml new file mode 100644 index 0000000000..0cebd0484b --- /dev/null +++ b/prepare/r-powerlaw/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-pracma +update_on: +- regex: poweRlaw_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=poweRlaw diff --git a/prepare/r-powertcr/PKGBUILD b/prepare/r-powertcr/PKGBUILD new file mode 100644 index 0000000000..ac911eef28 --- /dev/null +++ b/prepare/r-powertcr/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=powerTCR +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Model-Based Comparative Analysis of the TCR Repertoire' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-cubature + r-doparallel + r-evmix + r-foreach + r-magrittr + r-purrr + r-truncdist + r-vegan + r-vgam +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-powertcr/lilac.py b/prepare/r-powertcr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-powertcr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-powertcr/lilac.yaml b/prepare/r-powertcr/lilac.yaml new file mode 100644 index 0000000000..848e3ec73a --- /dev/null +++ b/prepare/r-powertcr/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cubature +- r-doparallel +- r-evmix +- r-foreach +- r-magrittr +- r-purrr +- r-truncdist +- r-vegan +- r-vgam +update_on: +- regex: powerTCR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/powerTCR diff --git a/prepare/r-powsc/PKGBUILD b/prepare/r-powsc/PKGBUILD new file mode 100644 index 0000000000..ef82ef9b06 --- /dev/null +++ b/prepare/r-powsc/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=POWSC +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Simulation, power evaluation, and sample size recommendation for single cell RNA-seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-ggplot2 + r-limma + r-mast + r-pheatmap + r-rcolorbrewer + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-powsc/lilac.py b/prepare/r-powsc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-powsc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-powsc/lilac.yaml b/prepare/r-powsc/lilac.yaml new file mode 100644 index 0000000000..43dd7d640e --- /dev/null +++ b/prepare/r-powsc/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-ggplot2 +- r-limma +- r-mast +- r-pheatmap +- r-rcolorbrewer +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: POWSC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/POWSC diff --git a/prepare/r-ppclust/PKGBUILD b/prepare/r-ppclust/PKGBUILD new file mode 100644 index 0000000000..91d1069068 --- /dev/null +++ b/prepare/r-ppclust/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ppclust +_pkgver=1.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Probabilistic and Possibilistic Cluster Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-inaparc +) +optdepends=( + r-cluster + r-factoextra + r-fclust + r-knitr + r-rmarkdown + r-vegclust +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ppclust/lilac.py b/prepare/r-ppclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ppclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ppclust/lilac.yaml b/prepare/r-ppclust/lilac.yaml new file mode 100644 index 0000000000..57e4db6893 --- /dev/null +++ b/prepare/r-ppclust/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-inaparc +update_on: +- regex: ppclust_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ppclust diff --git a/prepare/r-ppcor/PKGBUILD b/prepare/r-ppcor/PKGBUILD new file mode 100644 index 0000000000..78fbc24986 --- /dev/null +++ b/prepare/r-ppcor/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ppcor +_pkgver=1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Partial and Semi-Partial (Part) Correlation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ppcor/lilac.py b/prepare/r-ppcor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ppcor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ppcor/lilac.yaml b/prepare/r-ppcor/lilac.yaml new file mode 100644 index 0000000000..6228db9e60 --- /dev/null +++ b/prepare/r-ppcor/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ppcor_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ppcor diff --git a/prepare/r-ppcseq/PKGBUILD b/prepare/r-ppcseq/PKGBUILD new file mode 100644 index 0000000000..adb924bf36 --- /dev/null +++ b/prepare/r-ppcseq/PKGBUILD @@ -0,0 +1,53 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=ppcseq +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-benchmarkme + r-bh + r-dplyr + r-edger + r-foreach + r-furrr + r-future + r-ggplot2 + r-lifecycle + r-magrittr + r-purrr + r-rcpp + r-rcppeigen + r-rlang + r-rstan + r-rstantools + r-stanheaders + r-tibble + r-tidybayes + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ppcseq/lilac.py b/prepare/r-ppcseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ppcseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ppcseq/lilac.yaml b/prepare/r-ppcseq/lilac.yaml new file mode 100644 index 0000000000..26572a533c --- /dev/null +++ b/prepare/r-ppcseq/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-benchmarkme +- r-bh +- r-dplyr +- r-edger +- r-foreach +- r-furrr +- r-future +- r-ggplot2 +- r-lifecycle +- r-magrittr +- r-purrr +- r-rcpp +- r-rcppeigen +- r-rlang +- r-rstan +- r-rstantools +- r-stanheaders +- r-tibble +- r-tidybayes +- r-tidyr +update_on: +- regex: ppcseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ppcseq diff --git a/prepare/r-ppinfer/PKGBUILD b/prepare/r-ppinfer/PKGBUILD new file mode 100644 index 0000000000..5b692a0f70 --- /dev/null +++ b/prepare/r-ppinfer/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PPInfer +_pkgver=1.20.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Inferring functionally related proteins using protein interaction networks' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biomart + r-fgsea + r-ggplot2 + r-httr + r-igraph + r-kernlab + r-stringdb + r-yeastexpdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ppinfer/lilac.py b/prepare/r-ppinfer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ppinfer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ppinfer/lilac.yaml b/prepare/r-ppinfer/lilac.yaml new file mode 100644 index 0000000000..bc4202ccf6 --- /dev/null +++ b/prepare/r-ppinfer/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-fgsea +- r-ggplot2 +- r-httr +- r-igraph +- r-kernlab +- r-stringdb +- r-yeastexpdata +update_on: +- regex: PPInfer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PPInfer diff --git a/prepare/r-ppistats/PKGBUILD b/prepare/r-ppistats/PKGBUILD new file mode 100644 index 0000000000..ce7d400e6f --- /dev/null +++ b/prepare/r-ppistats/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ppiStats +_pkgver=1.60.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Protein-Protein Interaction Statistical Package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-category + r-graph + r-rcolorbrewer +) +optdepends=( + r-ppidata + r-scisi + r-xtable + r-yeastexpdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ppistats/lilac.py b/prepare/r-ppistats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ppistats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ppistats/lilac.yaml b/prepare/r-ppistats/lilac.yaml new file mode 100644 index 0000000000..dc60a3fe14 --- /dev/null +++ b/prepare/r-ppistats/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-category +- r-graph +- r-rcolorbrewer +update_on: +- regex: ppiStats_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ppiStats diff --git a/prepare/r-pqsfinder/PKGBUILD b/prepare/r-pqsfinder/PKGBUILD new file mode 100644 index 0000000000..2dba1a7b32 --- /dev/null +++ b/prepare/r-pqsfinder/PKGBUILD @@ -0,0 +1,46 @@ +# system requirements: GNU make, C++11 +# Maintainer: Guoyi Zhang + +_pkgname=pqsfinder +_pkgver=2.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identification of potential quadruplex forming sequences' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-bh + r-biostrings + r-genomicranges + r-iranges + r-rcpp + r-s4vectors +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg38 + r-ggplot2 + r-gviz + r-knitr + r-rmarkdown + r-rtracklayer + r-stringi + r-stringr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pqsfinder/lilac.py b/prepare/r-pqsfinder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pqsfinder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pqsfinder/lilac.yaml b/prepare/r-pqsfinder/lilac.yaml new file mode 100644 index 0000000000..c3f7e3789e --- /dev/null +++ b/prepare/r-pqsfinder/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-biostrings +- r-genomicranges +- r-iranges +- r-rcpp +- r-s4vectors +update_on: +- regex: pqsfinder_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pqsfinder diff --git a/prepare/r-prabclus/PKGBUILD b/prepare/r-prabclus/PKGBUILD new file mode 100644 index 0000000000..bb4e0bb4f3 --- /dev/null +++ b/prepare/r-prabclus/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=prabclus +_pkgver=2.3-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mclust +) +optdepends=( + r-bootstrap + r-foreign + r-maptools + r-mvtnorm + r-spatialreg + r-spdep +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-prabclus/lilac.py b/prepare/r-prabclus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-prabclus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-prabclus/lilac.yaml b/prepare/r-prabclus/lilac.yaml new file mode 100644 index 0000000000..c7c6f40b80 --- /dev/null +++ b/prepare/r-prabclus/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mclust +update_on: +- regex: prabclus_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=prabclus diff --git a/prepare/r-pracma/PKGBUILD b/prepare/r-pracma/PKGBUILD new file mode 100644 index 0000000000..f0f5950728 --- /dev/null +++ b/prepare/r-pracma/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pracma +_pkgver=2.3.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Practical Numerical Math Functions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-nlcoptim + r-quadprog +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pracma/lilac.py b/prepare/r-pracma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pracma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pracma/lilac.yaml b/prepare/r-pracma/lilac.yaml new file mode 100644 index 0000000000..495e2139b9 --- /dev/null +++ b/prepare/r-pracma/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pracma_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pracma diff --git a/prepare/r-praise/PKGBUILD b/prepare/r-praise/PKGBUILD new file mode 100644 index 0000000000..8855cbea11 --- /dev/null +++ b/prepare/r-praise/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=praise +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Praise Users' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-praise/lilac.py b/prepare/r-praise/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-praise/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-praise/lilac.yaml b/prepare/r-praise/lilac.yaml new file mode 100644 index 0000000000..428eaeb58c --- /dev/null +++ b/prepare/r-praise/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: praise_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=praise diff --git a/prepare/r-pram/PKGBUILD b/prepare/r-pram/PKGBUILD new file mode 100644 index 0000000000..f97fc458f9 --- /dev/null +++ b/prepare/r-pram/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pram +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pooling RNA-seq datasets for assembling transcript models' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-data.table + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-rsamtools + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pram/lilac.py b/prepare/r-pram/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pram/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pram/lilac.yaml b/prepare/r-pram/lilac.yaml new file mode 100644 index 0000000000..94310220bb --- /dev/null +++ b/prepare/r-pram/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-data.table +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-rsamtools +- r-rtracklayer +- r-s4vectors +update_on: +- regex: pram_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pram diff --git a/prepare/r-praznik/PKGBUILD b/prepare/r-praznik/PKGBUILD new file mode 100644 index 0000000000..058f4a0251 --- /dev/null +++ b/prepare/r-praznik/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=praznik +_pkgver=10.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Information-Based Feature Selection and Scoring' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-praznik/lilac.py b/prepare/r-praznik/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-praznik/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-praznik/lilac.yaml b/prepare/r-praznik/lilac.yaml new file mode 100644 index 0000000000..cad05682e1 --- /dev/null +++ b/prepare/r-praznik/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: praznik_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=praznik diff --git a/prepare/r-prebs/PKGBUILD b/prepare/r-prebs/PKGBUILD new file mode 100644 index 0000000000..2f7f1b4454 --- /dev/null +++ b/prepare/r-prebs/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=prebs +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Probe region expression estimation for RNA-seq data for improved microarray comparability' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-affy + r-biobase + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-rpa + r-s4vectors +) +optdepends=( + r-hgu133plus2cdf + r-hgu133plus2probe + r-prebsdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-prebs/lilac.py b/prepare/r-prebs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-prebs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-prebs/lilac.yaml b/prepare/r-prebs/lilac.yaml new file mode 100644 index 0000000000..e8b1c9badd --- /dev/null +++ b/prepare/r-prebs/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-rpa +- r-s4vectors +update_on: +- regex: prebs_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/prebs diff --git a/prepare/r-precisetad/PKGBUILD b/prepare/r-precisetad/PKGBUILD new file mode 100644 index 0000000000..12a2004898 --- /dev/null +++ b/prepare/r-precisetad/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=preciseTAD +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='preciseTAD: A machine learning framework for precise TAD boundary prediction' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-caret + r-dbscan + r-dosnow + r-e1071 + r-foreach + r-genomicranges + r-gtools + r-iranges + r-modelmetrics + r-pbapply + r-proc + r-prroc + r-randomforest + r-rcgh + r-s4vectors +) +optdepends=( + r-bioccheck + r-biocmanager + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-precisetad/lilac.py b/prepare/r-precisetad/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-precisetad/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-precisetad/lilac.yaml b/prepare/r-precisetad/lilac.yaml new file mode 100644 index 0000000000..aa93d13716 --- /dev/null +++ b/prepare/r-precisetad/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-caret +- r-dbscan +- r-dosnow +- r-e1071 +- r-foreach +- r-genomicranges +- r-gtools +- r-iranges +- r-modelmetrics +- r-pbapply +- r-proc +- r-prroc +- r-randomforest +- r-rcgh +- r-s4vectors +update_on: +- regex: preciseTAD_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/preciseTAD diff --git a/prepare/r-precisiontrialdrawer/PKGBUILD b/prepare/r-precisiontrialdrawer/PKGBUILD new file mode 100644 index 0000000000..ed80eff4b6 --- /dev/null +++ b/prepare/r-precisiontrialdrawer/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PrecisionTrialDrawer +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Tool to Analyze and Design NGS Based Custom Gene Panels' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-biomart + r-brglm + r-cgdsr + r-data.table + r-dt + r-genomicranges + r-ggplot2 + r-ggrepel + r-googlevis + r-httr + r-iranges + r-jsonlite + r-lowmacaannotation + r-magrittr + r-matrixstats + r-rcolorbrewer + r-reshape2 + r-s4vectors + r-shiny + r-shinybs + r-stringr + r-xml +) +optdepends=( + r-biocstyle + r-dplyr + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-precisiontrialdrawer/lilac.py b/prepare/r-precisiontrialdrawer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-precisiontrialdrawer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-precisiontrialdrawer/lilac.yaml b/prepare/r-precisiontrialdrawer/lilac.yaml new file mode 100644 index 0000000000..e0a79f0dcc --- /dev/null +++ b/prepare/r-precisiontrialdrawer/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-biomart +- r-brglm +- r-cgdsr +- r-data.table +- r-dt +- r-genomicranges +- r-ggplot2 +- r-ggrepel +- r-googlevis +- r-httr +- r-iranges +- r-jsonlite +- r-lowmacaannotation +- r-magrittr +- r-matrixstats +- r-rcolorbrewer +- r-reshape2 +- r-s4vectors +- r-shiny +- r-shinybs +- r-stringr +- r-xml +update_on: +- regex: PrecisionTrialDrawer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PrecisionTrialDrawer diff --git a/prepare/r-precrec/PKGBUILD b/prepare/r-precrec/PKGBUILD new file mode 100644 index 0000000000..1d3597a50a --- /dev/null +++ b/prepare/r-precrec/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=precrec +_pkgver=0.12.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Calculate Accurate Precision-Recall and ROC (Receiver Operator Characteristics) Curves' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-data.table + r-ggplot2 + r-gridextra + r-rcpp + r-withr +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-precrec/lilac.py b/prepare/r-precrec/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-precrec/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-precrec/lilac.yaml b/prepare/r-precrec/lilac.yaml new file mode 100644 index 0000000000..aa42b740b8 --- /dev/null +++ b/prepare/r-precrec/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-data.table +- r-ggplot2 +- r-gridextra +- r-rcpp +- r-withr +update_on: +- regex: precrec_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=precrec diff --git a/prepare/r-preda/PKGBUILD b/prepare/r-preda/PKGBUILD new file mode 100644 index 0000000000..50342ee13a --- /dev/null +++ b/prepare/r-preda/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PREDA +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Position Related Data Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotate + r-biobase + r-lokern + r-multtest +) +optdepends=( + r-affy + r-catools + r-limma + r-predasampledata + r-quantsmooth + r-qvalue + r-rmpi + r-rsprng +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-preda/lilac.py b/prepare/r-preda/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-preda/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-preda/lilac.yaml b/prepare/r-preda/lilac.yaml new file mode 100644 index 0000000000..4848e80fc4 --- /dev/null +++ b/prepare/r-preda/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-biobase +- r-lokern +- r-multtest +update_on: +- regex: PREDA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PREDA diff --git a/prepare/r-predictionet/PKGBUILD b/prepare/r-predictionet/PKGBUILD new file mode 100644 index 0000000000..a31b295c99 --- /dev/null +++ b/prepare/r-predictionet/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=predictionet +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Inference for predictive networks designed for (but not limited to) genomic data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-catnet + r-igraph + r-penalized + r-rbgl +) +optdepends=( + r-knitr + r-minet + r-network +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-predictionet/lilac.py b/prepare/r-predictionet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-predictionet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-predictionet/lilac.yaml b/prepare/r-predictionet/lilac.yaml new file mode 100644 index 0000000000..1b70dade59 --- /dev/null +++ b/prepare/r-predictionet/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-catnet +- r-igraph +- r-penalized +- r-rbgl +update_on: +- regex: predictionet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/predictionet diff --git a/prepare/r-preprocesscore/PKGBUILD b/prepare/r-preprocesscore/PKGBUILD new file mode 100644 index 0000000000..9c0c9342cb --- /dev/null +++ b/prepare/r-preprocesscore/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=preprocessCore +_pkgver=1.56.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A collection of pre-processing functions' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-preprocesscore/lilac.py b/prepare/r-preprocesscore/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-preprocesscore/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-preprocesscore/lilac.yaml b/prepare/r-preprocesscore/lilac.yaml new file mode 100644 index 0000000000..05da5a6b7e --- /dev/null +++ b/prepare/r-preprocesscore/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: preprocessCore_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/preprocessCore diff --git a/prepare/r-preseqr/PKGBUILD b/prepare/r-preseqr/PKGBUILD new file mode 100644 index 0000000000..a0291bd81a --- /dev/null +++ b/prepare/r-preseqr/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=preseqR +_pkgver=4.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Predicting Species Accumulation Curves' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-polynom +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-preseqr/lilac.py b/prepare/r-preseqr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-preseqr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-preseqr/lilac.yaml b/prepare/r-preseqr/lilac.yaml new file mode 100644 index 0000000000..8feba4438a --- /dev/null +++ b/prepare/r-preseqr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-polynom +update_on: +- regex: preseqR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=preseqR diff --git a/prepare/r-prettydoc/PKGBUILD b/prepare/r-prettydoc/PKGBUILD new file mode 100644 index 0000000000..065434a938 --- /dev/null +++ b/prepare/r-prettydoc/PKGBUILD @@ -0,0 +1,32 @@ +# system requirements: pandoc (>= 1.12.3) +# Maintainer: Guoyi Zhang + +_pkgname=prettydoc +_pkgver=0.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Creating Pretty Documents from R Markdown' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-rmarkdown +) +optdepends=( + r-kernsmooth + r-knitr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-prettydoc/lilac.py b/prepare/r-prettydoc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-prettydoc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-prettydoc/lilac.yaml b/prepare/r-prettydoc/lilac.yaml new file mode 100644 index 0000000000..4d4712719b --- /dev/null +++ b/prepare/r-prettydoc/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rmarkdown +update_on: +- regex: prettydoc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=prettydoc diff --git a/prepare/r-primirtss/PKGBUILD b/prepare/r-primirtss/PKGBUILD new file mode 100644 index 0000000000..f052505978 --- /dev/null +++ b/prepare/r-primirtss/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=primirTSS +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Prediction of pri-miRNA Transcription Start Site' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-bsgenome.hsapiens.ucsc.hg38 + r-dplyr + r-genomicranges + r-genomicscores + r-gviz + r-iranges + r-jaspar2018 + r-phastcons100way.ucsc.hg38 + r-purrr + r-r.utils + r-rtracklayer + r-s4vectors + r-shiny + r-stringr + r-tfbstools + r-tibble + r-tidyr +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-primirtss/lilac.py b/prepare/r-primirtss/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-primirtss/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-primirtss/lilac.yaml b/prepare/r-primirtss/lilac.yaml new file mode 100644 index 0000000000..4ab32610ba --- /dev/null +++ b/prepare/r-primirtss/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-bsgenome.hsapiens.ucsc.hg38 +- r-dplyr +- r-genomicranges +- r-genomicscores +- r-gviz +- r-iranges +- r-jaspar2018 +- r-phastcons100way.ucsc.hg38 +- r-purrr +- r-r.utils +- r-rtracklayer +- r-s4vectors +- r-shiny +- r-stringr +- r-tfbstools +- r-tibble +- r-tidyr +update_on: +- regex: primirTSS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/primirTSS diff --git a/prepare/r-primme/PKGBUILD b/prepare/r-primme/PKGBUILD new file mode 100644 index 0000000000..a37692e4d6 --- /dev/null +++ b/prepare/r-primme/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: A POSIX system. Currently Linux and OS X are knownto work. GNU make. +# Maintainer: Guoyi Zhang + +_pkgname=PRIMME +_pkgver=3.2-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Eigenvalues and Singular Values and Vectors from Large Matrices' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-matrix +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-primme/lilac.py b/prepare/r-primme/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-primme/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-primme/lilac.yaml b/prepare/r-primme/lilac.yaml new file mode 100644 index 0000000000..e3f3f22c1d --- /dev/null +++ b/prepare/r-primme/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: PRIMME_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=PRIMME diff --git a/prepare/r-prince/PKGBUILD b/prepare/r-prince/PKGBUILD new file mode 100644 index 0000000000..e22976e5d0 --- /dev/null +++ b/prepare/r-prince/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PrInCE +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Predicting Interactomes from Co-Elution' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-dplyr + r-forecast + r-hmisc + r-liblinear + r-magrittr + r-msnbase + r-naivebayes + r-progress + r-purrr + r-ranger + r-rdpack + r-robustbase + r-speedglm + r-tester + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-prince/lilac.py b/prepare/r-prince/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-prince/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-prince/lilac.yaml b/prepare/r-prince/lilac.yaml new file mode 100644 index 0000000000..27dcf7fb33 --- /dev/null +++ b/prepare/r-prince/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-dplyr +- r-forecast +- r-hmisc +- r-liblinear +- r-magrittr +- r-msnbase +- r-naivebayes +- r-progress +- r-purrr +- r-ranger +- r-rdpack +- r-robustbase +- r-speedglm +- r-tester +- r-tidyr +update_on: +- regex: PrInCE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PrInCE diff --git a/prepare/r-princurve/PKGBUILD b/prepare/r-princurve/PKGBUILD new file mode 100644 index 0000000000..083063b348 --- /dev/null +++ b/prepare/r-princurve/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=princurve +_pkgver=2.1.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fit a Principal Curve in Arbitrary Dimension' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-devtools + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-princurve/lilac.py b/prepare/r-princurve/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-princurve/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-princurve/lilac.yaml b/prepare/r-princurve/lilac.yaml new file mode 100644 index 0000000000..bd0b27f3ba --- /dev/null +++ b/prepare/r-princurve/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: princurve_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=princurve diff --git a/prepare/r-proactiv/PKGBUILD b/prepare/r-proactiv/PKGBUILD new file mode 100644 index 0000000000..06fb1dd336 --- /dev/null +++ b/prepare/r-proactiv/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=proActiv +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimate Promoter Activity from RNA-Seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-biocparallel + r-data.table + r-deseq2 + r-dplyr + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-gplots + r-iranges + r-rlang + r-s4vectors + r-scales + r-summarizedexperiment + r-tibble +) +optdepends=( + r-gridextra + r-knitr + r-rmarkdown + r-rtsne + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-proactiv/lilac.py b/prepare/r-proactiv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-proactiv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-proactiv/lilac.yaml b/prepare/r-proactiv/lilac.yaml new file mode 100644 index 0000000000..f1bafb6036 --- /dev/null +++ b/prepare/r-proactiv/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocparallel +- r-data.table +- r-deseq2 +- r-dplyr +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-gplots +- r-iranges +- r-rlang +- r-s4vectors +- r-scales +- r-summarizedexperiment +- r-tibble +update_on: +- regex: proActiv_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/proActiv diff --git a/prepare/r-probamr/PKGBUILD b/prepare/r-probamr/PKGBUILD new file mode 100644 index 0000000000..e78e9115a4 --- /dev/null +++ b/prepare/r-probamr/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=proBAMr +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generating SAM file for PSMs in shotgun proteomics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biostrings + r-genomicfeatures + r-genomicranges + r-iranges + r-rtracklayer +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-probamr/lilac.py b/prepare/r-probamr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-probamr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-probamr/lilac.yaml b/prepare/r-probamr/lilac.yaml new file mode 100644 index 0000000000..512d6fe210 --- /dev/null +++ b/prepare/r-probamr/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biostrings +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-rtracklayer +update_on: +- regex: proBAMr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/proBAMr diff --git a/prepare/r-probatch/PKGBUILD b/prepare/r-probatch/PKGBUILD new file mode 100644 index 0000000000..ffe9ccab5d --- /dev/null +++ b/prepare/r-probatch/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Guoyi Zhang + +_pkgname=proBatch +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Diagnostics and Corrections of Batch Effects in Proteomics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-corrplot + r-data.table + r-dplyr + r-ggfortify + r-ggplot2 + r-lazyeval + r-lubridate + r-magrittr + r-pheatmap + r-preprocesscore + r-purrr + r-pvca + r-rcolorbrewer + r-reshape2 + r-rlang + r-scales + r-sva + r-tibble + r-tidyr + r-viridis + r-wesanderson + r-wgcna +) +optdepends=( + r-devtools + r-ggpubr + r-gridextra + r-gtable + r-knitr + r-rmarkdown + r-roxygen2 + r-spelling + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-probatch/lilac.py b/prepare/r-probatch/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-probatch/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-probatch/lilac.yaml b/prepare/r-probatch/lilac.yaml new file mode 100644 index 0000000000..1c7e77712c --- /dev/null +++ b/prepare/r-probatch/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-corrplot +- r-data.table +- r-dplyr +- r-ggfortify +- r-ggplot2 +- r-lazyeval +- r-lubridate +- r-magrittr +- r-pheatmap +- r-preprocesscore +- r-purrr +- r-pvca +- r-rcolorbrewer +- r-reshape2 +- r-rlang +- r-scales +- r-sva +- r-tibble +- r-tidyr +- r-viridis +- r-wesanderson +- r-wgcna +update_on: +- regex: proBatch_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/proBatch diff --git a/prepare/r-proc/PKGBUILD b/prepare/r-proc/PKGBUILD new file mode 100644 index 0000000000..82ffdcf641 --- /dev/null +++ b/prepare/r-proc/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pROC +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Display and Analyze ROC Curves' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-plyr + r-rcpp +) +optdepends=( + r-doparallel + r-ggplot2 + r-logcondens + r-mass + r-microbenchmark + r-tcltk + r-testthat + r-vdiffr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-proc/lilac.py b/prepare/r-proc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-proc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-proc/lilac.yaml b/prepare/r-proc/lilac.yaml new file mode 100644 index 0000000000..76ad870a89 --- /dev/null +++ b/prepare/r-proc/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-plyr +- r-rcpp +update_on: +- regex: pROC_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pROC diff --git a/prepare/r-process/PKGBUILD b/prepare/r-process/PKGBUILD new file mode 100644 index 0000000000..aed16b1bb0 --- /dev/null +++ b/prepare/r-process/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PROcess +_pkgver=1.70.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Ciphergen SELDI-TOF Processing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-icens +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-process/lilac.py b/prepare/r-process/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-process/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-process/lilac.yaml b/prepare/r-process/lilac.yaml new file mode 100644 index 0000000000..af014f8489 --- /dev/null +++ b/prepare/r-process/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-icens +update_on: +- regex: PROcess_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PROcess diff --git a/prepare/r-processx/PKGBUILD b/prepare/r-processx/PKGBUILD new file mode 100644 index 0000000000..1bb5d8f394 --- /dev/null +++ b/prepare/r-processx/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=processx +_pkgver=3.5.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Execute and Control System Processes' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-ps + r-r6 +) +optdepends=( + r-callr + r-cli + r-codetools + r-covr + r-curl + r-debugme + r-parallel + r-testthat + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-processx/lilac.py b/prepare/r-processx/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-processx/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-processx/lilac.yaml b/prepare/r-processx/lilac.yaml new file mode 100644 index 0000000000..e3e16eea57 --- /dev/null +++ b/prepare/r-processx/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ps +- r-r6 +update_on: +- regex: processx_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=processx diff --git a/prepare/r-procoil/PKGBUILD b/prepare/r-procoil/PKGBUILD new file mode 100644 index 0000000000..683f327a83 --- /dev/null +++ b/prepare/r-procoil/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=procoil +_pkgver=2.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Prediction of Oligomerization of Coiled Coil Proteins' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-kebabs + r-s4vectors +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-procoil/lilac.py b/prepare/r-procoil/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-procoil/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-procoil/lilac.yaml b/prepare/r-procoil/lilac.yaml new file mode 100644 index 0000000000..1430030b1a --- /dev/null +++ b/prepare/r-procoil/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-kebabs +- r-s4vectors +update_on: +- regex: procoil_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/procoil diff --git a/prepare/r-proda/PKGBUILD b/prepare/r-proda/PKGBUILD new file mode 100644 index 0000000000..60ba9362cc --- /dev/null +++ b/prepare/r-proda/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=proDA +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential Abundance Analysis of Label-Free Mass Spectrometry Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-extradistr + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-dep + r-dplyr + r-knitr + r-limma + r-msnbase + r-numderiv + r-pheatmap + r-readr + r-rmarkdown + r-stringr + r-testthat + r-tibble + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-proda/lilac.py b/prepare/r-proda/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-proda/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-proda/lilac.yaml b/prepare/r-proda/lilac.yaml new file mode 100644 index 0000000000..235505a3e5 --- /dev/null +++ b/prepare/r-proda/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-extradistr +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: proDA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/proDA diff --git a/prepare/r-prodlim/PKGBUILD b/prepare/r-prodlim/PKGBUILD new file mode 100644 index 0000000000..172ab0d7ea --- /dev/null +++ b/prepare/r-prodlim/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=prodlim +_pkgver=2019.11.13 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Product-Limit Estimation for Censored Event History Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-lava + r-rcpp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-prodlim/lilac.py b/prepare/r-prodlim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-prodlim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-prodlim/lilac.yaml b/prepare/r-prodlim/lilac.yaml new file mode 100644 index 0000000000..59c8e12b82 --- /dev/null +++ b/prepare/r-prodlim/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lava +- r-rcpp +update_on: +- regex: prodlim_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=prodlim diff --git a/prepare/r-profia/PKGBUILD b/prepare/r-profia/PKGBUILD new file mode 100644 index 0000000000..4db6db6cc7 --- /dev/null +++ b/prepare/r-profia/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=proFIA +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Preprocessing of FIA-HRMS data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CeCILL') +depends=( + r + r-biobase + r-biocparallel + r-minpack.lm + r-missforest + r-pracma + r-ropls + r-xcms +) +optdepends=( + r-biocgenerics + r-knitr + r-plasfia +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-profia/lilac.py b/prepare/r-profia/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-profia/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-profia/lilac.yaml b/prepare/r-profia/lilac.yaml new file mode 100644 index 0000000000..4843983952 --- /dev/null +++ b/prepare/r-profia/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocparallel +- r-minpack.lm +- r-missforest +- r-pracma +- r-ropls +- r-xcms +update_on: +- regex: proFIA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/proFIA diff --git a/prepare/r-profilemodel/PKGBUILD b/prepare/r-profilemodel/PKGBUILD new file mode 100644 index 0000000000..12464c3c61 --- /dev/null +++ b/prepare/r-profilemodel/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=profileModel +_pkgver=0.6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Profiling Inference Functions for Various Model Classes' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-gnm + r-mass +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-profilemodel/lilac.py b/prepare/r-profilemodel/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-profilemodel/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-profilemodel/lilac.yaml b/prepare/r-profilemodel/lilac.yaml new file mode 100644 index 0000000000..dbc4535a12 --- /dev/null +++ b/prepare/r-profilemodel/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: profileModel_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=profileModel diff --git a/prepare/r-profileplyr/PKGBUILD b/prepare/r-profileplyr/PKGBUILD new file mode 100644 index 0000000000..b0d5708196 --- /dev/null +++ b/prepare/r-profileplyr/PKGBUILD @@ -0,0 +1,65 @@ +# Maintainer: Guoyi Zhang + +_pkgname=profileplyr +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization and annotation of read signal over genomic ranges with profileplyr' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-cairo + r-chipseeker + r-circlize + r-complexheatmap + r-dplyr + r-enrichedheatmap + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-magrittr + r-org.hs.eg.db + r-org.mm.eg.db + r-pheatmap + r-r.utils + r-rgreat + r-rjson + r-rlang + r-rsamtools + r-rtracklayer + r-s4vectors + r-soggi + r-summarizedexperiment + r-tidyr + r-tiff + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.hsapiens.ucsc.hg38.knowngene + r-txdb.mmusculus.ucsc.mm10.knowngene + r-txdb.mmusculus.ucsc.mm9.knowngene +) +optdepends=( + r-biocstyle + r-knitr + r-png + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-profileplyr/lilac.py b/prepare/r-profileplyr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-profileplyr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-profileplyr/lilac.yaml b/prepare/r-profileplyr/lilac.yaml new file mode 100644 index 0000000000..294ec26161 --- /dev/null +++ b/prepare/r-profileplyr/lilac.yaml @@ -0,0 +1,41 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-cairo +- r-chipseeker +- r-circlize +- r-complexheatmap +- r-dplyr +- r-enrichedheatmap +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-magrittr +- r-org.hs.eg.db +- r-org.mm.eg.db +- r-pheatmap +- r-r.utils +- r-rgreat +- r-rjson +- r-rlang +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-soggi +- r-summarizedexperiment +- r-tidyr +- r-tiff +- r-txdb.hsapiens.ucsc.hg19.knowngene +- r-txdb.hsapiens.ucsc.hg38.knowngene +- r-txdb.mmusculus.ucsc.mm10.knowngene +- r-txdb.mmusculus.ucsc.mm9.knowngene +update_on: +- regex: profileplyr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/profileplyr diff --git a/prepare/r-profilescoredist/PKGBUILD b/prepare/r-profilescoredist/PKGBUILD new file mode 100644 index 0000000000..4cfb175ceb --- /dev/null +++ b/prepare/r-profilescoredist/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=profileScoreDist +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Profile score distributions' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-rcpp +) +optdepends=( + r-biocstyle + r-knitr + r-motifdb +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-profilescoredist/lilac.py b/prepare/r-profilescoredist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-profilescoredist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-profilescoredist/lilac.yaml b/prepare/r-profilescoredist/lilac.yaml new file mode 100644 index 0000000000..be9674ace1 --- /dev/null +++ b/prepare/r-profilescoredist/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-rcpp +update_on: +- regex: profileScoreDist_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/profileScoreDist diff --git a/prepare/r-proftools/PKGBUILD b/prepare/r-proftools/PKGBUILD new file mode 100644 index 0000000000..b601f43392 --- /dev/null +++ b/prepare/r-proftools/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=proftools +_pkgver=0.99-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Profile Output Processing Tools for R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-boot + r-graph + r-knitr + r-rgraphviz +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-proftools/lilac.py b/prepare/r-proftools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-proftools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-proftools/lilac.yaml b/prepare/r-proftools/lilac.yaml new file mode 100644 index 0000000000..b625dd65b5 --- /dev/null +++ b/prepare/r-proftools/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: proftools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=proftools diff --git a/prepare/r-progeny/PKGBUILD b/prepare/r-progeny/PKGBUILD new file mode 100644 index 0000000000..b703e36fc9 --- /dev/null +++ b/prepare/r-progeny/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=progeny +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pathway RespOnsive GENes for activity inference from gene expression' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Apache') +depends=( + r + r-biobase + r-dplyr + r-ggplot2 + r-ggrepel + r-gridextra + r-tidyr +) +optdepends=( + r-airway + r-biocfilecache + r-biocstyle + r-biomart + r-broom + r-deseq2 + r-knitr + r-pheatmap + r-readr + r-readxl + r-rmarkdown + r-seurat + r-singlecellexperiment + r-testthat + r-tibble +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-progeny/lilac.py b/prepare/r-progeny/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-progeny/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-progeny/lilac.yaml b/prepare/r-progeny/lilac.yaml new file mode 100644 index 0000000000..028477a098 --- /dev/null +++ b/prepare/r-progeny/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-dplyr +- r-ggplot2 +- r-ggrepel +- r-gridextra +- r-tidyr +update_on: +- regex: progeny_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/progeny diff --git a/prepare/r-progressr/PKGBUILD b/prepare/r-progressr/PKGBUILD new file mode 100644 index 0000000000..9aa4604586 --- /dev/null +++ b/prepare/r-progressr/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=progressr +_pkgver=0.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Inclusive, Unifying API for Progress Updates' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-digest +) +optdepends=( + r-base64enc + r-beepr + r-commonmark + r-crayon + r-dofuture + r-foreach + r-furrr + r-future + r-future.apply + r-graphics + r-pbmcapply + r-plyr + r-progress + r-purrr + r-rstudioapi + r-shiny + r-tcltk + r-tools +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-progressr/lilac.py b/prepare/r-progressr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-progressr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-progressr/lilac.yaml b/prepare/r-progressr/lilac.yaml new file mode 100644 index 0000000000..8a92041040 --- /dev/null +++ b/prepare/r-progressr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +update_on: +- regex: progressr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=progressr diff --git a/prepare/r-proj4/PKGBUILD b/prepare/r-proj4/PKGBUILD new file mode 100644 index 0000000000..e0c01b443f --- /dev/null +++ b/prepare/r-proj4/PKGBUILD @@ -0,0 +1,27 @@ +# system requirements: proj 4.4.6 or higher (http://proj.maptools.org/) +# Maintainer: Guoyi Zhang + +_pkgname=proj4 +_pkgver=1.0-10.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A simple interface to the PROJ.4 cartographic projections library' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-proj4/lilac.py b/prepare/r-proj4/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-proj4/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-proj4/lilac.yaml b/prepare/r-proj4/lilac.yaml new file mode 100644 index 0000000000..d2d8ca59bc --- /dev/null +++ b/prepare/r-proj4/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: proj4_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=proj4 diff --git a/prepare/r-projectr/PKGBUILD b/prepare/r-projectr/PKGBUILD new file mode 100644 index 0000000000..81342b53c6 --- /dev/null +++ b/prepare/r-projectr/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=projectR +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cogaps + r-dplyr + r-ggalluvial + r-ggplot2 + r-limma + r-nmf + r-rcolorbrewer + r-reshape2 + r-rocr + r-scales + r-viridis +) +optdepends=( + r-biocstyle + r-complexheatmap + r-devtools + r-grid + r-gridextra + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-projectr/lilac.py b/prepare/r-projectr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-projectr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-projectr/lilac.yaml b/prepare/r-projectr/lilac.yaml new file mode 100644 index 0000000000..9a91bd743a --- /dev/null +++ b/prepare/r-projectr/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cogaps +- r-dplyr +- r-ggalluvial +- r-ggplot2 +- r-limma +- r-nmf +- r-rcolorbrewer +- r-reshape2 +- r-rocr +- r-scales +- r-viridis +update_on: +- regex: projectR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/projectR diff --git a/prepare/r-proloc/PKGBUILD b/prepare/r-proloc/PKGBUILD new file mode 100644 index 0000000000..4bc31378d4 --- /dev/null +++ b/prepare/r-proloc/PKGBUILD @@ -0,0 +1,74 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pRoloc +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A unifying bioinformatics framework for spatial proteomics' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-biomart + r-caret + r-coda + r-dendextend + r-e1071 + r-fnn + r-ggplot2 + r-gtools + r-hexbin + r-kernlab + r-knitr + r-laplacesdemon + r-mclust + r-mixtools + r-mlinterfaces + r-msnbase + r-mvtnorm + r-plyr + r-proxy + r-randomforest + r-rcolorbrewer + r-rcpp + r-rcpparmadillo + r-sampling + r-scales +) +optdepends=( + r-akima + r-annotationdbi + r-biocstyle + r-dplyr + r-fields + r-go.db + r-hpar + r-magick + r-nipals + r-prolocdata + r-reshape + r-rgl + r-rmarkdown + r-roxygen2 + r-rtsne + r-testthat + r-vegan + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-proloc/lilac.py b/prepare/r-proloc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-proloc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-proloc/lilac.yaml b/prepare/r-proloc/lilac.yaml new file mode 100644 index 0000000000..48a4bba8d5 --- /dev/null +++ b/prepare/r-proloc/lilac.yaml @@ -0,0 +1,37 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-biomart +- r-caret +- r-coda +- r-dendextend +- r-e1071 +- r-fnn +- r-ggplot2 +- r-gtools +- r-hexbin +- r-kernlab +- r-knitr +- r-laplacesdemon +- r-mclust +- r-mixtools +- r-mlinterfaces +- r-msnbase +- r-mvtnorm +- r-plyr +- r-proxy +- r-randomforest +- r-rcolorbrewer +- r-rcpp +- r-rcpparmadillo +- r-sampling +- r-scales +update_on: +- regex: pRoloc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pRoloc diff --git a/prepare/r-prolocgui/PKGBUILD b/prepare/r-prolocgui/PKGBUILD new file mode 100644 index 0000000000..8d6153ab70 --- /dev/null +++ b/prepare/r-prolocgui/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pRolocGUI +_pkgver=2.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive visualisation of spatial proteomics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-colorspace + r-colourpicker + r-dplyr + r-dt + r-ggplot2 + r-msnbase + r-proloc + r-scales + r-shiny + r-shinydashboard + r-shinydashboardplus + r-shinyhelper + r-shinyjs + r-shinywidgets +) +optdepends=( + r-biocstyle + r-knitr + r-prolocdata + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-prolocgui/lilac.py b/prepare/r-prolocgui/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-prolocgui/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-prolocgui/lilac.yaml b/prepare/r-prolocgui/lilac.yaml new file mode 100644 index 0000000000..9d3f6e8aa1 --- /dev/null +++ b/prepare/r-prolocgui/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-colorspace +- r-colourpicker +- r-dplyr +- r-dt +- r-ggplot2 +- r-msnbase +- r-proloc +- r-scales +- r-shiny +- r-shinydashboard +- r-shinydashboardplus +- r-shinyhelper +- r-shinyjs +- r-shinywidgets +update_on: +- regex: pRolocGUI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pRolocGUI diff --git a/prepare/r-promise/PKGBUILD b/prepare/r-promise/PKGBUILD new file mode 100644 index 0000000000..1033f8b11e --- /dev/null +++ b/prepare/r-promise/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PROMISE +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PRojection Onto the Most Interesting Statistical Evidence' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-gseabase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-promise/lilac.py b/prepare/r-promise/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-promise/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-promise/lilac.yaml b/prepare/r-promise/lilac.yaml new file mode 100644 index 0000000000..15c7e34e5e --- /dev/null +++ b/prepare/r-promise/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-gseabase +update_on: +- regex: PROMISE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PROMISE diff --git a/prepare/r-promises/PKGBUILD b/prepare/r-promises/PKGBUILD new file mode 100644 index 0000000000..2c97ab1d80 --- /dev/null +++ b/prepare/r-promises/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=promises +_pkgver=1.2.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Abstractions for Promise-Based Asynchronous Programming' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-later + r-magrittr + r-r6 + r-rcpp + r-rlang +) +optdepends=( + r-fastmap + r-future + r-knitr + r-purrr + r-rmarkdown + r-spelling + r-testthat + r-vembedr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-promises/lilac.py b/prepare/r-promises/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-promises/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-promises/lilac.yaml b/prepare/r-promises/lilac.yaml new file mode 100644 index 0000000000..4a9ca9b3b1 --- /dev/null +++ b/prepare/r-promises/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-later +- r-magrittr +- r-r6 +- r-rcpp +- r-rlang +update_on: +- regex: promises_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=promises diff --git a/prepare/r-proper/PKGBUILD b/prepare/r-proper/PKGBUILD new file mode 100644 index 0000000000..79c012fbb5 --- /dev/null +++ b/prepare/r-proper/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PROPER +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PROspective Power Evaluation for RNAseq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-edger +) +optdepends=( + r-biocstyle + r-deseq2 + r-dss + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-proper/lilac.py b/prepare/r-proper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-proper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-proper/lilac.yaml b/prepare/r-proper/lilac.yaml new file mode 100644 index 0000000000..c3382870a1 --- /dev/null +++ b/prepare/r-proper/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-edger +update_on: +- regex: PROPER_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PROPER diff --git a/prepare/r-propr/PKGBUILD b/prepare/r-propr/PKGBUILD new file mode 100644 index 0000000000..22c9c4317d --- /dev/null +++ b/prepare/r-propr/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=propr +_pkgver=4.2.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Calculating Proportionality Between Vectors of Compositional Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-fastcluster + r-ggplot2 + r-igraph + r-rcpp +) +optdepends=( + r-aldex2 + r-biobase + r-cccrm + r-compositions + r-data.table + r-datasets + r-ggdendro + r-grid + r-knitr + r-limma + r-parallel + r-plotly + r-reshape2 + r-rgl + r-rmarkdown + r-sdmtools + r-testthat + r-vegan +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-propr/lilac.py b/prepare/r-propr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-propr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-propr/lilac.yaml b/prepare/r-propr/lilac.yaml new file mode 100644 index 0000000000..fe31a0ac56 --- /dev/null +++ b/prepare/r-propr/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fastcluster +- r-ggplot2 +- r-igraph +- r-rcpp +update_on: +- regex: propr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=propr diff --git a/prepare/r-props/PKGBUILD b/prepare/r-props/PKGBUILD new file mode 100644 index 0000000000..e2d304f4ed --- /dev/null +++ b/prepare/r-props/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PROPS +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PRObabilistic Pathway Score (PROPS)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-bnlearn + r-reshape2 + r-sva +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-props/lilac.py b/prepare/r-props/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-props/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-props/lilac.yaml b/prepare/r-props/lilac.yaml new file mode 100644 index 0000000000..8fe3618aef --- /dev/null +++ b/prepare/r-props/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-bnlearn +- r-reshape2 +- r-sva +update_on: +- regex: PROPS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PROPS diff --git a/prepare/r-prostar/PKGBUILD b/prepare/r-prostar/PKGBUILD new file mode 100644 index 0000000000..8532a1c0a3 --- /dev/null +++ b/prepare/r-prostar/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Prostar +_pkgver=1.26.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Provides a GUI for DAPAR' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocmanager + r-colourpicker + r-dapar + r-dapardata + r-data.table + r-dt + r-future + r-highcharter + r-htmlwidgets + r-later + r-promises + r-r.utils + r-rclipboard + r-rhandsontable + r-sass + r-shiny + r-shinyace + r-shinybs + r-shinycssloaders + r-shinyjqui + r-shinyjs + r-shinythemes + r-shinytree + r-shinywidgets + r-tibble + r-webshot + r-xml +) +optdepends=( + r-biocstyle + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-prostar/lilac.py b/prepare/r-prostar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-prostar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-prostar/lilac.yaml b/prepare/r-prostar/lilac.yaml new file mode 100644 index 0000000000..93fc75b59d --- /dev/null +++ b/prepare/r-prostar/lilac.yaml @@ -0,0 +1,36 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocmanager +- r-colourpicker +- r-dapar +- r-dapardata +- r-data.table +- r-dt +- r-future +- r-highcharter +- r-htmlwidgets +- r-later +- r-promises +- r-r.utils +- r-rclipboard +- r-rhandsontable +- r-sass +- r-shiny +- r-shinyace +- r-shinybs +- r-shinycssloaders +- r-shinyjqui +- r-shinyjs +- r-shinythemes +- r-shinytree +- r-shinywidgets +- r-tibble +- r-webshot +- r-xml +update_on: +- regex: Prostar_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Prostar diff --git a/prepare/r-proteinprofiles/PKGBUILD b/prepare/r-proteinprofiles/PKGBUILD new file mode 100644 index 0000000000..e199685653 --- /dev/null +++ b/prepare/r-proteinprofiles/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=proteinProfiles +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Protein Profiling' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-proteinprofiles/lilac.py b/prepare/r-proteinprofiles/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-proteinprofiles/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-proteinprofiles/lilac.yaml b/prepare/r-proteinprofiles/lilac.yaml new file mode 100644 index 0000000000..95349a3c3d --- /dev/null +++ b/prepare/r-proteinprofiles/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: proteinProfiles_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/proteinProfiles diff --git a/prepare/r-proteodisco/PKGBUILD b/prepare/r-proteodisco/PKGBUILD new file mode 100644 index 0000000000..ecd5437add --- /dev/null +++ b/prepare/r-proteodisco/PKGBUILD @@ -0,0 +1,68 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ProteoDisco +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-checkmate + r-cleaver + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-parallellogger + r-plyr + r-rlang + r-s4vectors + r-tibble + r-tidyr + r-variantannotation + r-xvector +) +optdepends=( + r-annotationdbi + r-biocstyle + r-bsgenome + r-bsgenome.hsapiens.ucsc.hg19 + r-delayedarray + r-devtools + r-ggplot2 + r-knitr + r-markdown + r-matrixstats + r-org.hs.eg.db + r-purrr + r-rcurl + r-readr + r-reshape2 + r-rmarkdown + r-rtracklayer + r-scales + r-seqinr + r-stringr + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-proteodisco/lilac.py b/prepare/r-proteodisco/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-proteodisco/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-proteodisco/lilac.yaml b/prepare/r-proteodisco/lilac.yaml new file mode 100644 index 0000000000..8155baefe5 --- /dev/null +++ b/prepare/r-proteodisco/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-checkmate +- r-cleaver +- r-dplyr +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-parallellogger +- r-plyr +- r-rlang +- r-s4vectors +- r-tibble +- r-tidyr +- r-variantannotation +- r-xvector +update_on: +- regex: ProteoDisco_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ProteoDisco diff --git a/prepare/r-proteomicsannotationhubdata/PKGBUILD b/prepare/r-proteomicsannotationhubdata/PKGBUILD new file mode 100644 index 0000000000..ff9d403660 --- /dev/null +++ b/prepare/r-proteomicsannotationhubdata/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ProteomicsAnnotationHubData +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Transform public proteomics data resources into Bioconductor Data Structures' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationhub + r-annotationhubdata + r-biobase + r-biocmanager + r-biostrings + r-genomeinfodb + r-msnbase + r-mzr + r-rcurl +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-proteomicsannotationhubdata/lilac.py b/prepare/r-proteomicsannotationhubdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-proteomicsannotationhubdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-proteomicsannotationhubdata/lilac.yaml b/prepare/r-proteomicsannotationhubdata/lilac.yaml new file mode 100644 index 0000000000..ec81762e7a --- /dev/null +++ b/prepare/r-proteomicsannotationhubdata/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-annotationhubdata +- r-biobase +- r-biocmanager +- r-biostrings +- r-genomeinfodb +- r-msnbase +- r-mzr +- r-rcurl +update_on: +- regex: ProteomicsAnnotationHubData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ProteomicsAnnotationHubData diff --git a/prepare/r-proteomm/PKGBUILD b/prepare/r-proteomm/PKGBUILD new file mode 100644 index 0000000000..ab7bd455bf --- /dev/null +++ b/prepare/r-proteomm/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ProteoMM +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biomart + r-gdata + r-ggplot2 + r-ggrepel + r-gtools + r-matrixstats +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-proteomm/lilac.py b/prepare/r-proteomm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-proteomm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-proteomm/lilac.yaml b/prepare/r-proteomm/lilac.yaml new file mode 100644 index 0000000000..420d43f820 --- /dev/null +++ b/prepare/r-proteomm/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-gdata +- r-ggplot2 +- r-ggrepel +- r-gtools +- r-matrixstats +update_on: +- regex: ProteoMM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ProteoMM diff --git a/prepare/r-protgenerics/PKGBUILD b/prepare/r-protgenerics/PKGBUILD new file mode 100644 index 0000000000..0d8d7bee2f --- /dev/null +++ b/prepare/r-protgenerics/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ProtGenerics +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generic infrastructure for Bioconductor mass spectrometry packages' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-protgenerics/lilac.py b/prepare/r-protgenerics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-protgenerics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-protgenerics/lilac.yaml b/prepare/r-protgenerics/lilac.yaml new file mode 100644 index 0000000000..747c59940f --- /dev/null +++ b/prepare/r-protgenerics/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ProtGenerics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ProtGenerics diff --git a/prepare/r-proto/PKGBUILD b/prepare/r-proto/PKGBUILD new file mode 100644 index 0000000000..8384444684 --- /dev/null +++ b/prepare/r-proto/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=proto +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Prototype Object-Based Programming' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-proto/lilac.py b/prepare/r-proto/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-proto/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-proto/lilac.yaml b/prepare/r-proto/lilac.yaml new file mode 100644 index 0000000000..4a2db7f40c --- /dev/null +++ b/prepare/r-proto/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: proto_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=proto diff --git a/prepare/r-protolite/PKGBUILD b/prepare/r-protolite/PKGBUILD new file mode 100644 index 0000000000..9a27d0878a --- /dev/null +++ b/prepare/r-protolite/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: libprotobuf and protobuf-compiler +# Maintainer: Guoyi Zhang + +_pkgname=protolite +_pkgver=2.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Highly Optimized Protocol Buffer Serializers' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-jsonlite + r-rcpp +) +optdepends=( + r-curl + r-rprotobuf + r-sf + r-spelling + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-protolite/lilac.py b/prepare/r-protolite/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-protolite/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-protolite/lilac.yaml b/prepare/r-protolite/lilac.yaml new file mode 100644 index 0000000000..d2d9823047 --- /dev/null +++ b/prepare/r-protolite/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-jsonlite +- r-rcpp +update_on: +- regex: protolite_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=protolite diff --git a/prepare/r-protr/PKGBUILD b/prepare/r-protr/PKGBUILD new file mode 100644 index 0000000000..7d788a6ab8 --- /dev/null +++ b/prepare/r-protr/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: ncbi-blast+ (see) +# Maintainer: Guoyi Zhang + +_pkgname=protr +_pkgver=1.6-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generating Various Numerical Representation Schemes for Protein Sequences' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +optdepends=( + r-biostrings + r-doparallel + r-foreach + r-gosemsim + r-knitr + r-org.hs.eg.db + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-protr/lilac.py b/prepare/r-protr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-protr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-protr/lilac.yaml b/prepare/r-protr/lilac.yaml new file mode 100644 index 0000000000..5d9ddc832c --- /dev/null +++ b/prepare/r-protr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: protr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=protr diff --git a/prepare/r-protviz/PKGBUILD b/prepare/r-protviz/PKGBUILD new file mode 100644 index 0000000000..f840076c4c --- /dev/null +++ b/prepare/r-protviz/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=protViz +_pkgver=0.7.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-lattice + r-testthat + r-xtable +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-protviz/lilac.py b/prepare/r-protviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-protviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-protviz/lilac.yaml b/prepare/r-protviz/lilac.yaml new file mode 100644 index 0000000000..24c198e2aa --- /dev/null +++ b/prepare/r-protviz/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: protViz_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=protViz diff --git a/prepare/r-proxy/PKGBUILD b/prepare/r-proxy/PKGBUILD new file mode 100644 index 0000000000..f4d1496abc --- /dev/null +++ b/prepare/r-proxy/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=proxy +_pkgver=0.4-26 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Distance and Similarity Measures' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-cba +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-proxy/lilac.py b/prepare/r-proxy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-proxy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-proxy/lilac.yaml b/prepare/r-proxy/lilac.yaml new file mode 100644 index 0000000000..ea0ddfb1cd --- /dev/null +++ b/prepare/r-proxy/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: proxy_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=proxy diff --git a/prepare/r-proxyc/PKGBUILD b/prepare/r-proxyc/PKGBUILD new file mode 100644 index 0000000000..fec3456446 --- /dev/null +++ b/prepare/r-proxyc/PKGBUILD @@ -0,0 +1,35 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=proxyC +_pkgver=0.2.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Computes Proximity in Large Sparse Matrices' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcpparmadillo + r-rcppparallel +) +optdepends=( + r-entropy + r-proxy + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-proxyc/lilac.py b/prepare/r-proxyc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-proxyc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-proxyc/lilac.yaml b/prepare/r-proxyc/lilac.yaml new file mode 100644 index 0000000000..744df5ba2f --- /dev/null +++ b/prepare/r-proxyc/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcpparmadillo +- r-rcppparallel +update_on: +- regex: proxyC_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=proxyC diff --git a/prepare/r-prroc/PKGBUILD b/prepare/r-prroc/PKGBUILD new file mode 100644 index 0000000000..12faa31752 --- /dev/null +++ b/prepare/r-prroc/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PRROC +_pkgver=1.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Precision-Recall and ROC Curves for Weighted and Unweighted Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-ggplot2 + r-rocr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-prroc/lilac.py b/prepare/r-prroc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-prroc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-prroc/lilac.yaml b/prepare/r-prroc/lilac.yaml new file mode 100644 index 0000000000..bf323fbd1e --- /dev/null +++ b/prepare/r-prroc/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: PRROC_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=PRROC diff --git a/prepare/r-pryr/PKGBUILD b/prepare/r-pryr/PKGBUILD new file mode 100644 index 0000000000..05cd657ef1 --- /dev/null +++ b/prepare/r-pryr/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pryr +_pkgver=0.1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Computing on the Language' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-lobstr + r-rcpp + r-stringr +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pryr/lilac.py b/prepare/r-pryr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pryr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pryr/lilac.yaml b/prepare/r-pryr/lilac.yaml new file mode 100644 index 0000000000..862fea0105 --- /dev/null +++ b/prepare/r-pryr/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lobstr +- r-rcpp +- r-stringr +update_on: +- regex: pryr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pryr diff --git a/prepare/r-ps/PKGBUILD b/prepare/r-ps/PKGBUILD new file mode 100644 index 0000000000..244e9109b1 --- /dev/null +++ b/prepare/r-ps/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ps +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='List, Query, Manipulate System Processes' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-callr + r-covr + r-curl + r-pingr + r-processx + r-r6 + r-rlang + r-testthat + r-tibble +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ps/lilac.py b/prepare/r-ps/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ps/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ps/lilac.yaml b/prepare/r-ps/lilac.yaml new file mode 100644 index 0000000000..23905732ee --- /dev/null +++ b/prepare/r-ps/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ps_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ps diff --git a/prepare/r-pscbs/PKGBUILD b/prepare/r-pscbs/PKGBUILD new file mode 100644 index 0000000000..96dc7d5fd7 --- /dev/null +++ b/prepare/r-pscbs/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PSCBS +_pkgver=0.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Parent-Specific DNA Copy Numbers' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-aroma.light + r-dnacopy + r-future + r-listenv + r-matrixstats + r-r.cache + r-r.methodss3 + r-r.oo + r-r.utils +) +optdepends=( + r-ggplot2 + r-hmisc + r-r.devices + r-r.rsp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pscbs/lilac.py b/prepare/r-pscbs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pscbs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pscbs/lilac.yaml b/prepare/r-pscbs/lilac.yaml new file mode 100644 index 0000000000..c0ae106491 --- /dev/null +++ b/prepare/r-pscbs/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aroma.light +- r-dnacopy +- r-future +- r-listenv +- r-matrixstats +- r-r.cache +- r-r.methodss3 +- r-r.oo +- r-r.utils +update_on: +- regex: PSCBS_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=PSCBS diff --git a/prepare/r-pscl/PKGBUILD b/prepare/r-pscl/PKGBUILD new file mode 100644 index 0000000000..a1b053a021 --- /dev/null +++ b/prepare/r-pscl/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pscl +_pkgver=1.5.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Political Science Computational Laboratory' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-car + r-coda + r-lattice + r-lmtest + r-mcmcpack + r-mgcv + r-mvtnorm + r-sandwich + r-vcd + r-zoo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pscl/lilac.py b/prepare/r-pscl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pscl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pscl/lilac.yaml b/prepare/r-pscl/lilac.yaml new file mode 100644 index 0000000000..bd79adf9d2 --- /dev/null +++ b/prepare/r-pscl/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pscl_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pscl diff --git a/prepare/r-psea/PKGBUILD b/prepare/r-psea/PKGBUILD new file mode 100644 index 0000000000..772f97c31e --- /dev/null +++ b/prepare/r-psea/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PSEA +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Population-Specific Expression Analysis.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-psea/lilac.py b/prepare/r-psea/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-psea/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-psea/lilac.yaml b/prepare/r-psea/lilac.yaml new file mode 100644 index 0000000000..41b1d430de --- /dev/null +++ b/prepare/r-psea/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: PSEA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PSEA diff --git a/prepare/r-psichomics/PKGBUILD b/prepare/r-psichomics/PKGBUILD new file mode 100644 index 0000000000..14138ee8d4 --- /dev/null +++ b/prepare/r-psichomics/PKGBUILD @@ -0,0 +1,72 @@ +# Maintainer: Guoyi Zhang + +_pkgname=psichomics +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-annotationhub + r-biocfilecache + r-colourpicker + r-data.table + r-digest + r-dplyr + r-dt + r-edger + r-fastica + r-fastmatch + r-ggplot2 + r-ggrepel + r-highcharter + r-htmltools + r-httr + r-jsonlite + r-limma + r-pairsd3 + r-plyr + r-purrr + r-r.utils + r-rcpp + r-recount + r-reshape2 + r-rfast + r-shiny + r-shinybs + r-shinyjs + r-stringr + r-summarizedexperiment + r-xml + r-xtable +) +optdepends=( + r-car + r-covr + r-devtools + r-gplots + r-knitr + r-parallel + r-rmarkdown + r-rstudioapi + r-spelling + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-psichomics/lilac.py b/prepare/r-psichomics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-psichomics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-psichomics/lilac.yaml b/prepare/r-psichomics/lilac.yaml new file mode 100644 index 0000000000..d2c7632a3b --- /dev/null +++ b/prepare/r-psichomics/lilac.yaml @@ -0,0 +1,42 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-biocfilecache +- r-colourpicker +- r-data.table +- r-digest +- r-dplyr +- r-dt +- r-edger +- r-fastica +- r-fastmatch +- r-ggplot2 +- r-ggrepel +- r-highcharter +- r-htmltools +- r-httr +- r-jsonlite +- r-limma +- r-pairsd3 +- r-plyr +- r-purrr +- r-r.utils +- r-rcpp +- r-recount +- r-reshape2 +- r-rfast +- r-shiny +- r-shinybs +- r-shinyjs +- r-stringr +- r-summarizedexperiment +- r-xml +- r-xtable +update_on: +- regex: psichomics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/psichomics diff --git a/prepare/r-psicquic/PKGBUILD b/prepare/r-psicquic/PKGBUILD new file mode 100644 index 0000000000..5c596f1adc --- /dev/null +++ b/prepare/r-psicquic/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PSICQUIC +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Proteomics Standard Initiative Common QUery InterfaCe' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Apache') +depends=( + r + r-biocgenerics + r-biomart + r-httr + r-iranges + r-plyr + r-rcurl +) +optdepends=( + r-org.hs.eg.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-psicquic/lilac.py b/prepare/r-psicquic/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-psicquic/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-psicquic/lilac.yaml b/prepare/r-psicquic/lilac.yaml new file mode 100644 index 0000000000..0037335e2c --- /dev/null +++ b/prepare/r-psicquic/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biomart +- r-httr +- r-iranges +- r-plyr +- r-rcurl +update_on: +- regex: PSICQUIC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PSICQUIC diff --git a/prepare/r-pspline/PKGBUILD b/prepare/r-pspline/PKGBUILD new file mode 100644 index 0000000000..3b9177f128 --- /dev/null +++ b/prepare/r-pspline/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pspline +_pkgver=1.0-18 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Penalized Smoothing Splines' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Unlimited') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pspline/lilac.py b/prepare/r-pspline/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pspline/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pspline/lilac.yaml b/prepare/r-pspline/lilac.yaml new file mode 100644 index 0000000000..31641d8be9 --- /dev/null +++ b/prepare/r-pspline/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pspline_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pspline diff --git a/prepare/r-psych/PKGBUILD b/prepare/r-psych/PKGBUILD new file mode 100644 index 0000000000..782a07e7a9 --- /dev/null +++ b/prepare/r-psych/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=psych +_pkgver=2.1.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Procedures for Psychological, Psychometric, and Personality Research' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mnormt +) +optdepends=( + r-gparotation + r-graph + r-knitr + r-lavaan + r-lme4 + r-psychtools + r-rcsdp + r-rgraphviz +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-psych/lilac.py b/prepare/r-psych/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-psych/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-psych/lilac.yaml b/prepare/r-psych/lilac.yaml new file mode 100644 index 0000000000..eee0a1a2c4 --- /dev/null +++ b/prepare/r-psych/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mnormt +update_on: +- regex: psych_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=psych diff --git a/prepare/r-psygenet2r/PKGBUILD b/prepare/r-psygenet2r/PKGBUILD new file mode 100644 index 0000000000..4320b45f98 --- /dev/null +++ b/prepare/r-psygenet2r/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=psygenet2r +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-bgeedb + r-biobase + r-biomart + r-ggplot2 + r-go.db + r-igraph + r-labeling + r-rcurl + r-reshape2 + r-stringr + r-topgo +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-psygenet2r/lilac.py b/prepare/r-psygenet2r/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-psygenet2r/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-psygenet2r/lilac.yaml b/prepare/r-psygenet2r/lilac.yaml new file mode 100644 index 0000000000..4a4dfdf2fe --- /dev/null +++ b/prepare/r-psygenet2r/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bgeedb +- r-biobase +- r-biomart +- r-ggplot2 +- r-go.db +- r-igraph +- r-labeling +- r-rcurl +- r-reshape2 +- r-stringr +- r-topgo +update_on: +- regex: psygenet2r_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/psygenet2r diff --git a/prepare/r-ptairms/PKGBUILD b/prepare/r-ptairms/PKGBUILD new file mode 100644 index 0000000000..41252f8f65 --- /dev/null +++ b/prepare/r-ptairms/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ptairMS +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pre-processing PTR-TOF-MS Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-bit64 + r-chron + r-data.table + r-doparallel + r-dt + r-envipat + r-foreach + r-ggplot2 + r-ggpubr + r-gridextra + r-hmisc + r-minpack.lm + r-msnbase + r-plotly + r-rcpp + r-rhdf5 + r-rlang + r-scales + r-shiny + r-shinyscreenshot + r-signal +) +optdepends=( + r-biocstyle + r-knitr + r-ptairdata + r-rmarkdown + r-ropls + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ptairms/lilac.py b/prepare/r-ptairms/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ptairms/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ptairms/lilac.yaml b/prepare/r-ptairms/lilac.yaml new file mode 100644 index 0000000000..cfdefd655e --- /dev/null +++ b/prepare/r-ptairms/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-bit64 +- r-chron +- r-data.table +- r-doparallel +- r-dt +- r-envipat +- r-foreach +- r-ggplot2 +- r-ggpubr +- r-gridextra +- r-hmisc +- r-minpack.lm +- r-msnbase +- r-plotly +- r-rcpp +- r-rhdf5 +- r-rlang +- r-scales +- r-shiny +- r-shinyscreenshot +- r-signal +update_on: +- regex: ptairMS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ptairMS diff --git a/prepare/r-ptw/PKGBUILD b/prepare/r-ptw/PKGBUILD new file mode 100644 index 0000000000..7fb6d05878 --- /dev/null +++ b/prepare/r-ptw/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ptw +_pkgver=1.9-15 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Parametric Time Warping' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-nloptr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ptw/lilac.py b/prepare/r-ptw/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ptw/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ptw/lilac.yaml b/prepare/r-ptw/lilac.yaml new file mode 100644 index 0000000000..ebb92ead79 --- /dev/null +++ b/prepare/r-ptw/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-nloptr +update_on: +- regex: ptw_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ptw diff --git a/prepare/r-pubscore/PKGBUILD b/prepare/r-pubscore/PKGBUILD new file mode 100644 index 0000000000..def94db4e9 --- /dev/null +++ b/prepare/r-pubscore/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PubScore +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automatic calculation of literature relevance of genes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-ggplot2 + r-ggrepel + r-igraph + r-intergraph + r-network + r-progress + r-rentrez + r-sna +) +optdepends=( + r-biocmanager + r-biomart + r-fcbf + r-knitr + r-plotly + r-rmarkdown + r-singlecellexperiment + r-summarizedexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pubscore/lilac.py b/prepare/r-pubscore/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pubscore/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pubscore/lilac.yaml b/prepare/r-pubscore/lilac.yaml new file mode 100644 index 0000000000..579e1dd1ba --- /dev/null +++ b/prepare/r-pubscore/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-ggrepel +- r-igraph +- r-intergraph +- r-network +- r-progress +- r-rentrez +- r-sna +update_on: +- regex: PubScore_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PubScore diff --git a/prepare/r-pulsedsilac/PKGBUILD b/prepare/r-pulsedsilac/PKGBUILD new file mode 100644 index 0000000000..2080685538 --- /dev/null +++ b/prepare/r-pulsedsilac/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pulsedSilac +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of pulsed-SILAC quantitative proteomics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cowplot + r-ggplot2 + r-ggridges + r-mumin + r-r.utils + r-robustbase + r-s4vectors + r-summarizedexperiment + r-tarifx + r-upsetr +) +optdepends=( + r-gridextra + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pulsedsilac/lilac.py b/prepare/r-pulsedsilac/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pulsedsilac/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pulsedsilac/lilac.yaml b/prepare/r-pulsedsilac/lilac.yaml new file mode 100644 index 0000000000..17f6c77433 --- /dev/null +++ b/prepare/r-pulsedsilac/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cowplot +- r-ggplot2 +- r-ggridges +- r-mumin +- r-r.utils +- r-robustbase +- r-s4vectors +- r-summarizedexperiment +- r-tarifx +- r-upsetr +update_on: +- regex: pulsedSilac_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pulsedSilac diff --git a/prepare/r-puma/PKGBUILD b/prepare/r-puma/PKGBUILD new file mode 100644 index 0000000000..53e9e07d10 --- /dev/null +++ b/prepare/r-puma/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=puma +_pkgver=3.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)" +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-affy + r-affyio + r-biobase + r-mclust + r-oligo + r-oligoclasses +) +optdepends=( + r-affydata + r-annotate + r-limma + r-pumadata + r-rocr + r-snow +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-puma/lilac.py b/prepare/r-puma/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-puma/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-puma/lilac.yaml b/prepare/r-puma/lilac.yaml new file mode 100644 index 0000000000..a08902d9a8 --- /dev/null +++ b/prepare/r-puma/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-affyio +- r-biobase +- r-mclust +- r-oligo +- r-oligoclasses +update_on: +- regex: puma_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/puma diff --git a/prepare/r-purecn/PKGBUILD b/prepare/r-purecn/PKGBUILD new file mode 100644 index 0000000000..d4aa19e59f --- /dev/null +++ b/prepare/r-purecn/PKGBUILD @@ -0,0 +1,64 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PureCN +_pkgver=2.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Copy number calling and SNV classification using targeted short read sequencing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-biostrings + r-data.table + r-dnacopy + r-futile.logger + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-gridextra + r-iranges + r-mclust + r-rcolorbrewer + r-rhdf5 + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-variantannotation + r-vgam +) +optdepends=( + r-biocparallel + r-biocstyle + r-copynumber + r-covr + r-genomicsdb + r-jsonlite + r-knitr + r-markdown + r-optparse + r-org.hs.eg.db + r-pscbs + r-r.utils + r-rmarkdown + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-purecn/lilac.py b/prepare/r-purecn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-purecn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-purecn/lilac.yaml b/prepare/r-purecn/lilac.yaml new file mode 100644 index 0000000000..b030562a93 --- /dev/null +++ b/prepare/r-purecn/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biostrings +- r-data.table +- r-dnacopy +- r-futile.logger +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-gridextra +- r-iranges +- r-mclust +- r-rcolorbrewer +- r-rhdf5 +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +- r-variantannotation +- r-vgam +update_on: +- regex: PureCN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PureCN diff --git a/prepare/r-pvac/PKGBUILD b/prepare/r-pvac/PKGBUILD new file mode 100644 index 0000000000..72dd888a9b --- /dev/null +++ b/prepare/r-pvac/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pvac +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PCA-based gene filtering for Affymetrix arrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-affy + r-biobase +) +optdepends=( + r-affydata + r-allmll + r-genefilter + r-pbapply +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pvac/lilac.py b/prepare/r-pvac/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pvac/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pvac/lilac.yaml b/prepare/r-pvac/lilac.yaml new file mode 100644 index 0000000000..d7f2e14677 --- /dev/null +++ b/prepare/r-pvac/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +update_on: +- regex: pvac_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pvac diff --git a/prepare/r-pvca/PKGBUILD b/prepare/r-pvca/PKGBUILD new file mode 100644 index 0000000000..318357d685 --- /dev/null +++ b/prepare/r-pvca/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pvca +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Principal Variance Component Analysis (PVCA)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-lme4 + r-vsn +) +optdepends=( + r-golubesets +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pvca/lilac.py b/prepare/r-pvca/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pvca/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pvca/lilac.yaml b/prepare/r-pvca/lilac.yaml new file mode 100644 index 0000000000..c0a506c153 --- /dev/null +++ b/prepare/r-pvca/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-lme4 +- r-vsn +update_on: +- regex: pvca_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pvca diff --git a/prepare/r-pvclust/PKGBUILD b/prepare/r-pvclust/PKGBUILD new file mode 100644 index 0000000000..fdd78db85d --- /dev/null +++ b/prepare/r-pvclust/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pvclust +_pkgver=2.2-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-mass + r-parallel +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pvclust/lilac.py b/prepare/r-pvclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pvclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pvclust/lilac.yaml b/prepare/r-pvclust/lilac.yaml new file mode 100644 index 0000000000..1bda6f1839 --- /dev/null +++ b/prepare/r-pvclust/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pvclust_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pvclust diff --git a/prepare/r-pviz/PKGBUILD b/prepare/r-pviz/PKGBUILD new file mode 100644 index 0000000000..d39259116f --- /dev/null +++ b/prepare/r-pviz/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Pviz +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Peptide Annotation and Data Visualization using Gviz' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-biovizbase + r-data.table + r-genomicranges + r-gviz + r-iranges +) +optdepends=( + r-knitr + r-pepdat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pviz/lilac.py b/prepare/r-pviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pviz/lilac.yaml b/prepare/r-pviz/lilac.yaml new file mode 100644 index 0000000000..a3b34be959 --- /dev/null +++ b/prepare/r-pviz/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-biovizbase +- r-data.table +- r-genomicranges +- r-gviz +- r-iranges +update_on: +- regex: Pviz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Pviz diff --git a/prepare/r-pwmenrich/PKGBUILD b/prepare/r-pwmenrich/PKGBUILD new file mode 100644 index 0000000000..8540fc2306 --- /dev/null +++ b/prepare/r-pwmenrich/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=PWMEnrich +_pkgver=4.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PWM enrichment analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biocgenerics + r-biostrings + r-evd + r-gdata + r-s4vectors + r-seqlogo +) +optdepends=( + r-biocstyle + r-bsgenome + r-bsgenome.dmelanogaster.ucsc.dm3 + r-gtools + r-knitr + r-motifdb + r-parallel + r-pwmenrich.dmelanogaster.background + r-pwmenrich.hsapiens.background + r-pwmenrich.mmusculus.background + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pwmenrich/lilac.py b/prepare/r-pwmenrich/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pwmenrich/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pwmenrich/lilac.yaml b/prepare/r-pwmenrich/lilac.yaml new file mode 100644 index 0000000000..b990cdbfee --- /dev/null +++ b/prepare/r-pwmenrich/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-evd +- r-gdata +- r-s4vectors +- r-seqlogo +update_on: +- regex: PWMEnrich_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/PWMEnrich diff --git a/prepare/r-pwomics/PKGBUILD b/prepare/r-pwomics/PKGBUILD new file mode 100644 index 0000000000..1ea4596fbe --- /dev/null +++ b/prepare/r-pwomics/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pwOmics +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pathway-based data integration of omics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-annotationhub + r-biobase + r-biocgenerics + r-biomart + r-data.table + r-genomicranges + r-gplots + r-graph + r-igraph + r-rbiopaxparser + r-stringdb +) +optdepends=( + r-ebdbnet + r-longitudinal + r-mfuzz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pwomics/lilac.py b/prepare/r-pwomics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pwomics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pwomics/lilac.yaml b/prepare/r-pwomics/lilac.yaml new file mode 100644 index 0000000000..5c33aa5594 --- /dev/null +++ b/prepare/r-pwomics/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-biobase +- r-biocgenerics +- r-biomart +- r-data.table +- r-genomicranges +- r-gplots +- r-graph +- r-igraph +- r-rbiopaxparser +- r-stringdb +update_on: +- regex: pwOmics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pwOmics diff --git a/prepare/r-pwr/PKGBUILD b/prepare/r-pwr/PKGBUILD new file mode 100644 index 0000000000..f9e0eab077 --- /dev/null +++ b/prepare/r-pwr/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pwr +_pkgver=1.3-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Basic Functions for Power Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-ggplot2 + r-knitr + r-rmarkdown + r-scales +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pwr/lilac.py b/prepare/r-pwr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pwr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pwr/lilac.yaml b/prepare/r-pwr/lilac.yaml new file mode 100644 index 0000000000..c42ae8089e --- /dev/null +++ b/prepare/r-pwr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: pwr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=pwr diff --git a/prepare/r-pwrewas.data/PKGBUILD b/prepare/r-pwrewas.data/PKGBUILD new file mode 100644 index 0000000000..0947512765 --- /dev/null +++ b/prepare/r-pwrewas.data/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pwrEWAS.data +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='pwrEWAS.data: Reference data accompanying pwrEWAS' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-experimenthub +) +optdepends=( + r-biocgenerics + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pwrewas.data/lilac.py b/prepare/r-pwrewas.data/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pwrewas.data/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pwrewas.data/lilac.yaml b/prepare/r-pwrewas.data/lilac.yaml new file mode 100644 index 0000000000..73972d3d58 --- /dev/null +++ b/prepare/r-pwrewas.data/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-experimenthub +update_on: +- regex: pwrEWAS.data_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pwrEWAS.data diff --git a/prepare/r-pwrewas/PKGBUILD b/prepare/r-pwrewas/PKGBUILD new file mode 100644 index 0000000000..3d5d276678 --- /dev/null +++ b/prepare/r-pwrewas/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=pwrEWAS +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-abind + r-biocmanager + r-cpgassoc + r-doparallel + r-dosnow + r-foreach + r-genefilter + r-ggplot2 + r-limma + r-pwrewas.data + r-shiny + r-shinybs + r-shinywidgets + r-truncnorm +) +optdepends=( + r-biocgenerics + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-pwrewas/lilac.py b/prepare/r-pwrewas/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-pwrewas/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-pwrewas/lilac.yaml b/prepare/r-pwrewas/lilac.yaml new file mode 100644 index 0000000000..81867d4e36 --- /dev/null +++ b/prepare/r-pwrewas/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-biocmanager +- r-cpgassoc +- r-doparallel +- r-dosnow +- r-foreach +- r-genefilter +- r-ggplot2 +- r-limma +- r-pwrewas.data +- r-shiny +- r-shinybs +- r-shinywidgets +- r-truncnorm +update_on: +- regex: pwrEWAS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/pwrEWAS diff --git a/prepare/r-qap/PKGBUILD b/prepare/r-qap/PKGBUILD new file mode 100644 index 0000000000..2ed5b5b185 --- /dev/null +++ b/prepare/r-qap/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qap +_pkgver=0.1-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Heuristics for the Quadratic Assignment Problem (QAP)' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-testthat +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qap/lilac.py b/prepare/r-qap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qap/lilac.yaml b/prepare/r-qap/lilac.yaml new file mode 100644 index 0000000000..8876c82027 --- /dev/null +++ b/prepare/r-qap/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: qap_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=qap diff --git a/prepare/r-qckitfastq/PKGBUILD b/prepare/r-qckitfastq/PKGBUILD new file mode 100644 index 0000000000..cb503a0031 --- /dev/null +++ b/prepare/r-qckitfastq/PKGBUILD @@ -0,0 +1,43 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=qckitfastq +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='FASTQ Quality Control' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-data.table + r-dplyr + r-ggplot2 + r-magrittr + r-rcpp + r-reshape2 + r-rlang + r-rseqan + r-seqtools + r-zlibbioc +) +optdepends=( + r-kableextra + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qckitfastq/lilac.py b/prepare/r-qckitfastq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qckitfastq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qckitfastq/lilac.yaml b/prepare/r-qckitfastq/lilac.yaml new file mode 100644 index 0000000000..07988bda14 --- /dev/null +++ b/prepare/r-qckitfastq/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-dplyr +- r-ggplot2 +- r-magrittr +- r-rcpp +- r-reshape2 +- r-rlang +- r-rseqan +- r-seqtools +- r-zlibbioc +update_on: +- regex: qckitfastq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/qckitfastq diff --git a/prepare/r-qcmetrics/PKGBUILD b/prepare/r-qcmetrics/PKGBUILD new file mode 100644 index 0000000000..8cff31f490 --- /dev/null +++ b/prepare/r-qcmetrics/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qcmetrics +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Framework for Quality Control' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-knitr + r-pander + r-s4vectors + r-xtable +) +optdepends=( + r-affy + r-biocstyle + r-ggplot2 + r-lattice + r-msnbase + r-mzr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qcmetrics/lilac.py b/prepare/r-qcmetrics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qcmetrics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qcmetrics/lilac.yaml b/prepare/r-qcmetrics/lilac.yaml new file mode 100644 index 0000000000..8b04fff33d --- /dev/null +++ b/prepare/r-qcmetrics/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-knitr +- r-pander +- r-s4vectors +- r-xtable +update_on: +- regex: qcmetrics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/qcmetrics diff --git a/prepare/r-qdapregex/PKGBUILD b/prepare/r-qdapregex/PKGBUILD new file mode 100644 index 0000000000..0377a8e565 --- /dev/null +++ b/prepare/r-qdapregex/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qdapRegex +_pkgver=0.7.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Regular Expression Removal, Extraction, and Replacement Tools' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-stringi +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qdapregex/lilac.py b/prepare/r-qdapregex/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qdapregex/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qdapregex/lilac.yaml b/prepare/r-qdapregex/lilac.yaml new file mode 100644 index 0000000000..5add62183e --- /dev/null +++ b/prepare/r-qdapregex/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-stringi +update_on: +- regex: qdapRegex_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=qdapRegex diff --git a/prepare/r-qdaptools/PKGBUILD b/prepare/r-qdaptools/PKGBUILD new file mode 100644 index 0000000000..d435f6d8af --- /dev/null +++ b/prepare/r-qdaptools/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qdapTools +_pkgver=1.3.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Tools for the 'qdap' Package" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-chron + r-data.table + r-rcurl + r-xml +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qdaptools/lilac.py b/prepare/r-qdaptools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qdaptools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qdaptools/lilac.yaml b/prepare/r-qdaptools/lilac.yaml new file mode 100644 index 0000000000..d56fcd20eb --- /dev/null +++ b/prepare/r-qdaptools/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-chron +- r-data.table +- r-rcurl +- r-xml +update_on: +- regex: qdapTools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=qdapTools diff --git a/prepare/r-qdnaseq/PKGBUILD b/prepare/r-qdnaseq/PKGBUILD new file mode 100644 index 0000000000..fcf2022173 --- /dev/null +++ b/prepare/r-qdnaseq/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=QDNAseq +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quantitative DNA Sequencing for Chromosomal Aberrations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-cghbase + r-cghcall + r-dnacopy + r-future.apply + r-genomicranges + r-iranges + r-matrixstats + r-r.utils + r-rsamtools +) +optdepends=( + r-biocstyle + r-bsgenome + r-digest + r-future + r-genomeinfodb + r-parallelly + r-qdnaseq.hg19 + r-qdnaseq.mm10 + r-r.cache +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qdnaseq/lilac.py b/prepare/r-qdnaseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qdnaseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qdnaseq/lilac.yaml b/prepare/r-qdnaseq/lilac.yaml new file mode 100644 index 0000000000..5e5d1b0967 --- /dev/null +++ b/prepare/r-qdnaseq/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-cghbase +- r-cghcall +- r-dnacopy +- r-future.apply +- r-genomicranges +- r-iranges +- r-matrixstats +- r-r.utils +- r-rsamtools +update_on: +- regex: QDNAseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/QDNAseq diff --git a/prepare/r-qfeatures/PKGBUILD b/prepare/r-qfeatures/PKGBUILD new file mode 100644 index 0000000000..c48b01bab9 --- /dev/null +++ b/prepare/r-qfeatures/PKGBUILD @@ -0,0 +1,63 @@ +# Maintainer: Guoyi Zhang + +_pkgname=QFeatures +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quantitative features for mass spectrometry data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationfilter + r-biobase + r-biocgenerics + r-igraph + r-iranges + r-lazyeval + r-mscoreutils + r-multiassayexperiment + r-plotly + r-protgenerics + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-complexheatmap + r-dplyr + r-dt + r-ggplot2 + r-gplots + r-hdf5array + r-impute + r-imputelcmd + r-knitr + r-limma + r-magrittr + r-matrixstats + r-msdata + r-norm + r-pcamethods + r-preprocesscore + r-rmarkdown + r-shiny + r-shinydashboard + r-singlecellexperiment + r-testthat + r-vsn +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qfeatures/lilac.py b/prepare/r-qfeatures/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qfeatures/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qfeatures/lilac.yaml b/prepare/r-qfeatures/lilac.yaml new file mode 100644 index 0000000000..c0b3f9fea8 --- /dev/null +++ b/prepare/r-qfeatures/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationfilter +- r-biobase +- r-biocgenerics +- r-igraph +- r-iranges +- r-lazyeval +- r-mscoreutils +- r-multiassayexperiment +- r-plotly +- r-protgenerics +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: QFeatures_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/QFeatures diff --git a/prepare/r-qlcmatrix/PKGBUILD b/prepare/r-qlcmatrix/PKGBUILD new file mode 100644 index 0000000000..ff6b6d111c --- /dev/null +++ b/prepare/r-qlcmatrix/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qlcMatrix +_pkgver=0.9.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utility Sparse Matrix Functions for Quantitative Language Comparison' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-docopt + r-slam + r-sparsesvd +) +optdepends=( + r-knitr + r-mass +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qlcmatrix/lilac.py b/prepare/r-qlcmatrix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qlcmatrix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qlcmatrix/lilac.yaml b/prepare/r-qlcmatrix/lilac.yaml new file mode 100644 index 0000000000..77c8ff33ea --- /dev/null +++ b/prepare/r-qlcmatrix/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-docopt +- r-slam +- r-sparsesvd +update_on: +- regex: qlcMatrix_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=qlcMatrix diff --git a/prepare/r-qpcr/PKGBUILD b/prepare/r-qpcr/PKGBUILD new file mode 100644 index 0000000000..dc8818c835 --- /dev/null +++ b/prepare/r-qpcr/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qpcR +_pkgver=1.4-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Modelling and Analysis of Real-Time PCR Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-minpack.lm + r-rgl + r-robustbase +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qpcr/lilac.py b/prepare/r-qpcr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qpcr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qpcr/lilac.yaml b/prepare/r-qpcr/lilac.yaml new file mode 100644 index 0000000000..8d7639164d --- /dev/null +++ b/prepare/r-qpcr/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-minpack.lm +- r-rgl +- r-robustbase +update_on: +- regex: qpcR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=qpcR diff --git a/prepare/r-qpcrnorm/PKGBUILD b/prepare/r-qpcrnorm/PKGBUILD new file mode 100644 index 0000000000..04ee3830c5 --- /dev/null +++ b/prepare/r-qpcrnorm/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qpcrNorm +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data-driven normalization strategies for high-throughput qPCR data.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-affy + r-biobase + r-limma +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qpcrnorm/lilac.py b/prepare/r-qpcrnorm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qpcrnorm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qpcrnorm/lilac.yaml b/prepare/r-qpcrnorm/lilac.yaml new file mode 100644 index 0000000000..04484187df --- /dev/null +++ b/prepare/r-qpcrnorm/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +- r-limma +update_on: +- regex: qpcrNorm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/qpcrNorm diff --git a/prepare/r-qpdf/PKGBUILD b/prepare/r-qpdf/PKGBUILD new file mode 100644 index 0000000000..2f7a4b0265 --- /dev/null +++ b/prepare/r-qpdf/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qpdf +_pkgver=1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Split, Combine and Compress PDF Files' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-askpass + r-curl + r-rcpp +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qpdf/lilac.py b/prepare/r-qpdf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qpdf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qpdf/lilac.yaml b/prepare/r-qpdf/lilac.yaml new file mode 100644 index 0000000000..adb34ed8be --- /dev/null +++ b/prepare/r-qpdf/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-askpass +- r-curl +- r-rcpp +update_on: +- regex: qpdf_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=qpdf diff --git a/prepare/r-qpgraph/PKGBUILD b/prepare/r-qpgraph/PKGBUILD new file mode 100644 index 0000000000..c2e3404a24 --- /dev/null +++ b/prepare/r-qpgraph/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qpgraph +_pkgver=2.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimation of genetic and molecular regulatory networks from high-throughput genomics data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotate + r-annotationdbi + r-biobase + r-biocparallel + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-mvtnorm + r-qtl + r-rgraphviz + r-s4vectors +) +optdepends=( + r-biocgenerics + r-biocstyle + r-category + r-genefilter + r-gostats + r-org.eck12.eg.db + r-rlecuyer + r-runit + r-snow +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qpgraph/lilac.py b/prepare/r-qpgraph/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qpgraph/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qpgraph/lilac.yaml b/prepare/r-qpgraph/lilac.yaml new file mode 100644 index 0000000000..25feec09d4 --- /dev/null +++ b/prepare/r-qpgraph/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-biobase +- r-biocparallel +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-graph +- r-iranges +- r-mvtnorm +- r-qtl +- r-rgraphviz +- r-s4vectors +update_on: +- regex: qpgraph_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/qpgraph diff --git a/prepare/r-qplexanalyzer/PKGBUILD b/prepare/r-qplexanalyzer/PKGBUILD new file mode 100644 index 0000000000..9aab95d06f --- /dev/null +++ b/prepare/r-qplexanalyzer/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qPLEXanalyzer +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for qPLEX-RIME data analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-biobase + r-biocgenerics + r-biostrings + r-dplyr + r-ggdendro + r-ggplot2 + r-iranges + r-limma + r-magrittr + r-msnbase + r-preprocesscore + r-purrr + r-rcolorbrewer + r-readr + r-rlang + r-scales + r-stringr + r-tibble + r-tidyr + r-tidyselect +) +optdepends=( + r-gridextra + r-knitr + r-qplexdata + r-rmarkdown + r-testthat + r-uniprot.ws + r-vdiffr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qplexanalyzer/lilac.py b/prepare/r-qplexanalyzer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qplexanalyzer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qplexanalyzer/lilac.yaml b/prepare/r-qplexanalyzer/lilac.yaml new file mode 100644 index 0000000000..e6d6114098 --- /dev/null +++ b/prepare/r-qplexanalyzer/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biobase +- r-biocgenerics +- r-biostrings +- r-dplyr +- r-ggdendro +- r-ggplot2 +- r-iranges +- r-limma +- r-magrittr +- r-msnbase +- r-preprocesscore +- r-purrr +- r-rcolorbrewer +- r-readr +- r-rlang +- r-scales +- r-stringr +- r-tibble +- r-tidyr +- r-tidyselect +update_on: +- regex: qPLEXanalyzer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/qPLEXanalyzer diff --git a/prepare/r-qqman/PKGBUILD b/prepare/r-qqman/PKGBUILD new file mode 100644 index 0000000000..ea88839fdc --- /dev/null +++ b/prepare/r-qqman/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qqman +_pkgver=0.1.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Q-Q and Manhattan Plots for GWAS Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-calibrate +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qqman/lilac.py b/prepare/r-qqman/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qqman/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qqman/lilac.yaml b/prepare/r-qqman/lilac.yaml new file mode 100644 index 0000000000..f6c35e9f8c --- /dev/null +++ b/prepare/r-qqman/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-calibrate +update_on: +- regex: qqman_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=qqman diff --git a/prepare/r-qrqc/PKGBUILD b/prepare/r-qrqc/PKGBUILD new file mode 100644 index 0000000000..cee773d287 --- /dev/null +++ b/prepare/r-qrqc/PKGBUILD @@ -0,0 +1,36 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=qrqc +_pkgver=1.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quick Read Quality Control' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-biovizbase + r-brew + r-ggplot2 + r-plyr + r-reshape + r-rhtslib + r-testthat + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qrqc/lilac.py b/prepare/r-qrqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qrqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qrqc/lilac.yaml b/prepare/r-qrqc/lilac.yaml new file mode 100644 index 0000000000..1526a41b89 --- /dev/null +++ b/prepare/r-qrqc/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-biovizbase +- r-brew +- r-ggplot2 +- r-plyr +- r-reshape +- r-rhtslib +- r-testthat +- r-xtable +update_on: +- regex: qrqc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/qrqc diff --git a/prepare/r-qs/PKGBUILD b/prepare/r-qs/PKGBUILD new file mode 100644 index 0000000000..af96320247 --- /dev/null +++ b/prepare/r-qs/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=qs +_pkgver=0.25.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quick Serialization of R Objects' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rapiserialize + r-rcpp + r-stringfish +) +optdepends=( + r-data.table + r-dplyr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qs/lilac.py b/prepare/r-qs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qs/lilac.yaml b/prepare/r-qs/lilac.yaml new file mode 100644 index 0000000000..10e4074726 --- /dev/null +++ b/prepare/r-qs/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rapiserialize +- r-rcpp +- r-stringfish +update_on: +- regex: qs_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=qs diff --git a/prepare/r-qsea/PKGBUILD b/prepare/r-qsea/PKGBUILD new file mode 100644 index 0000000000..8c47497afa --- /dev/null +++ b/prepare/r-qsea/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qsea +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='IP-seq data analysis and vizualization' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-gtools + r-hmmcopy + r-iranges + r-limma + r-rsamtools + r-rtracklayer + r-zoo +) +optdepends=( + r-biocmanager + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-knitr + r-mass + r-medipsdata + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qsea/lilac.py b/prepare/r-qsea/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qsea/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qsea/lilac.yaml b/prepare/r-qsea/lilac.yaml new file mode 100644 index 0000000000..192a018207 --- /dev/null +++ b/prepare/r-qsea/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-genomeinfodb +- r-genomicranges +- r-gtools +- r-hmmcopy +- r-iranges +- r-limma +- r-rsamtools +- r-rtracklayer +- r-zoo +update_on: +- regex: qsea_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/qsea diff --git a/prepare/r-qsmooth/PKGBUILD b/prepare/r-qsmooth/PKGBUILD new file mode 100644 index 0000000000..4a494064df --- /dev/null +++ b/prepare/r-qsmooth/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qsmooth +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Smooth quantile normalization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CCPL:by-nc-sa') +depends=( + r + r-hmisc + r-summarizedexperiment + r-sva +) +optdepends=( + r-biocstyle + r-bodymaprat + r-knitr + r-quantro + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qsmooth/lilac.py b/prepare/r-qsmooth/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qsmooth/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qsmooth/lilac.yaml b/prepare/r-qsmooth/lilac.yaml new file mode 100644 index 0000000000..e8d66650cd --- /dev/null +++ b/prepare/r-qsmooth/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-hmisc +- r-summarizedexperiment +- r-sva +update_on: +- regex: qsmooth_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/qsmooth diff --git a/prepare/r-qsutils/PKGBUILD b/prepare/r-qsutils/PKGBUILD new file mode 100644 index 0000000000..a44d694292 --- /dev/null +++ b/prepare/r-qsutils/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=QSutils +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quasispecies Diversity' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-ape + r-biocgenerics + r-biostrings + r-psych +) +optdepends=( + r-biocstyle + r-ggplot2 + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qsutils/lilac.py b/prepare/r-qsutils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qsutils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qsutils/lilac.yaml b/prepare/r-qsutils/lilac.yaml new file mode 100644 index 0000000000..47e75a6964 --- /dev/null +++ b/prepare/r-qsutils/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-biocgenerics +- r-biostrings +- r-psych +update_on: +- regex: QSutils_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/QSutils diff --git a/prepare/r-qtl/PKGBUILD b/prepare/r-qtl/PKGBUILD new file mode 100644 index 0000000000..28b610f1b5 --- /dev/null +++ b/prepare/r-qtl/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qtl +_pkgver=1.50 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Analyzing QTL Experiments' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qtl/lilac.py b/prepare/r-qtl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qtl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qtl/lilac.yaml b/prepare/r-qtl/lilac.yaml new file mode 100644 index 0000000000..b031e88822 --- /dev/null +++ b/prepare/r-qtl/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: qtl_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=qtl diff --git a/prepare/r-qtlizer/PKGBUILD b/prepare/r-qtlizer/PKGBUILD new file mode 100644 index 0000000000..1709655dd3 --- /dev/null +++ b/prepare/r-qtlizer/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Qtlizer +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Comprehensive QTL annotation of GWAS results' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-curl + r-genomicranges + r-httr + r-stringi +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qtlizer/lilac.py b/prepare/r-qtlizer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qtlizer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qtlizer/lilac.yaml b/prepare/r-qtlizer/lilac.yaml new file mode 100644 index 0000000000..2f243f8fcc --- /dev/null +++ b/prepare/r-qtlizer/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-genomicranges +- r-httr +- r-stringi +update_on: +- regex: Qtlizer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Qtlizer diff --git a/prepare/r-quadprog/PKGBUILD b/prepare/r-quadprog/PKGBUILD new file mode 100644 index 0000000000..7f9f441376 --- /dev/null +++ b/prepare/r-quadprog/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=quadprog +_pkgver=1.5-8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions to Solve Quadratic Programming Problems' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-quadprog/lilac.py b/prepare/r-quadprog/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-quadprog/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-quadprog/lilac.yaml b/prepare/r-quadprog/lilac.yaml new file mode 100644 index 0000000000..95c6e3304c --- /dev/null +++ b/prepare/r-quadprog/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: quadprog_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=quadprog diff --git a/prepare/r-qualv/PKGBUILD b/prepare/r-qualv/PKGBUILD new file mode 100644 index 0000000000..96bdeb1b43 --- /dev/null +++ b/prepare/r-qualv/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qualV +_pkgver=0.3-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Qualitative Validation Methods' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qualv/lilac.py b/prepare/r-qualv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qualv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qualv/lilac.yaml b/prepare/r-qualv/lilac.yaml new file mode 100644 index 0000000000..5435ad216c --- /dev/null +++ b/prepare/r-qualv/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: qualV_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=qualV diff --git a/prepare/r-quanteda/PKGBUILD b/prepare/r-quanteda/PKGBUILD new file mode 100644 index 0000000000..ebab5e6453 --- /dev/null +++ b/prepare/r-quanteda/PKGBUILD @@ -0,0 +1,65 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=quanteda +_pkgver=3.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quantitative Analysis of Textual Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-fastmatch + r-magrittr + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-snowballc + r-stopwords + r-stringi + r-xml2 + r-yaml +) +optdepends=( + r-dplyr + r-formatr + r-ggplot2 + r-jsonlite + r-knitr + r-lda + r-lsa + r-purrr + r-quanteda + r-quanteda.textmodels + r-quanteda.textplots + r-quanteda.textstats + r-rcolorbrewer + r-rmarkdown + r-slam + r-spacyr + r-spelling + r-stm + r-testthat + r-text2vec + r-tibble + r-tidytext + r-tm + r-tokenizers + r-topicmodels + r-xtable +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-quanteda/lilac.py b/prepare/r-quanteda/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-quanteda/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-quanteda/lilac.yaml b/prepare/r-quanteda/lilac.yaml new file mode 100644 index 0000000000..2127dc4ac4 --- /dev/null +++ b/prepare/r-quanteda/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fastmatch +- r-magrittr +- r-rcpp +- r-rcpparmadillo +- r-rcppparallel +- r-snowballc +- r-stopwords +- r-stringi +- r-xml2 +- r-yaml +update_on: +- regex: quanteda_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=quanteda diff --git a/prepare/r-quantiseqr/PKGBUILD b/prepare/r-quantiseqr/PKGBUILD new file mode 100644 index 0000000000..2aa88767d6 --- /dev/null +++ b/prepare/r-quantiseqr/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=quantiseqr +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quantification of the Tumor Immune contexture from RNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-ggplot2 + r-limsolve + r-preprocesscore + r-rlang + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-annotationdbi + r-biocstyle + r-dplyr + r-experimenthub + r-geoquery + r-knitr + r-macrophage + r-org.hs.eg.db + r-reshape2 + r-rmarkdown + r-testthat + r-tibble +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-quantiseqr/lilac.py b/prepare/r-quantiseqr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-quantiseqr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-quantiseqr/lilac.yaml b/prepare/r-quantiseqr/lilac.yaml new file mode 100644 index 0000000000..e729962fb9 --- /dev/null +++ b/prepare/r-quantiseqr/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-ggplot2 +- r-limsolve +- r-preprocesscore +- r-rlang +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: quantiseqr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/quantiseqr diff --git a/prepare/r-quantmod/PKGBUILD b/prepare/r-quantmod/PKGBUILD new file mode 100644 index 0000000000..7504841cd9 --- /dev/null +++ b/prepare/r-quantmod/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=quantmod +_pkgver=0.4.18 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quantitative Financial Modelling Framework' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-curl + r-ttr + r-xts + r-zoo +) +optdepends=( + r-dbi + r-downloader + r-jsonlite + r-rmysql + r-rsqlite + r-timeseries + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-quantmod/lilac.py b/prepare/r-quantmod/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-quantmod/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-quantmod/lilac.yaml b/prepare/r-quantmod/lilac.yaml new file mode 100644 index 0000000000..c5409229a7 --- /dev/null +++ b/prepare/r-quantmod/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-ttr +- r-xts +- r-zoo +update_on: +- regex: quantmod_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=quantmod diff --git a/prepare/r-quantreg/PKGBUILD b/prepare/r-quantreg/PKGBUILD new file mode 100644 index 0000000000..f4271dfeb7 --- /dev/null +++ b/prepare/r-quantreg/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=quantreg +_pkgver=5.86 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quantile Regression' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-conquer + r-matrixmodels + r-sparsem +) +optdepends=( + r-akima + r-formula + r-logspline + r-mass + r-nor1mix + r-r.rsp + r-rgl + r-survival + r-tripack + r-zoo +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-quantreg/lilac.py b/prepare/r-quantreg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-quantreg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-quantreg/lilac.yaml b/prepare/r-quantreg/lilac.yaml new file mode 100644 index 0000000000..7a60a17a2e --- /dev/null +++ b/prepare/r-quantreg/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-conquer +- r-matrixmodels +- r-sparsem +update_on: +- regex: quantreg_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=quantreg diff --git a/prepare/r-quantro/PKGBUILD b/prepare/r-quantro/PKGBUILD new file mode 100644 index 0000000000..fbbf47c71d --- /dev/null +++ b/prepare/r-quantro/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=quantro +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A test for when to use quantile normalization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-doparallel + r-foreach + r-ggplot2 + r-iterators + r-minfi + r-rcolorbrewer +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-quantro/lilac.py b/prepare/r-quantro/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-quantro/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-quantro/lilac.yaml b/prepare/r-quantro/lilac.yaml new file mode 100644 index 0000000000..2c265578b7 --- /dev/null +++ b/prepare/r-quantro/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-doparallel +- r-foreach +- r-ggplot2 +- r-iterators +- r-minfi +- r-rcolorbrewer +update_on: +- regex: quantro_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/quantro diff --git a/prepare/r-quantsmooth/PKGBUILD b/prepare/r-quantsmooth/PKGBUILD new file mode 100644 index 0000000000..16487f21ac --- /dev/null +++ b/prepare/r-quantsmooth/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=quantsmooth +_pkgver=1.60.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quantile smoothing and genomic visualization of array data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-quantreg +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-quantsmooth/lilac.py b/prepare/r-quantsmooth/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-quantsmooth/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-quantsmooth/lilac.yaml b/prepare/r-quantsmooth/lilac.yaml new file mode 100644 index 0000000000..1d0df393df --- /dev/null +++ b/prepare/r-quantsmooth/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-quantreg +update_on: +- regex: quantsmooth_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/quantsmooth diff --git a/prepare/r-quartpac/PKGBUILD b/prepare/r-quartpac/PKGBUILD new file mode 100644 index 0000000000..b4ffb0d1e4 --- /dev/null +++ b/prepare/r-quartpac/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=QuartPAC +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identification of mutational clusters in protein quaternary structures.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-graphpac + r-ipac + r-spacepac +) +optdepends=( + r-biocgenerics + r-rgl + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-quartpac/lilac.py b/prepare/r-quartpac/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-quartpac/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-quartpac/lilac.yaml b/prepare/r-quartpac/lilac.yaml new file mode 100644 index 0000000000..0f89268230 --- /dev/null +++ b/prepare/r-quartpac/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-graphpac +- r-ipac +- r-spacepac +update_on: +- regex: QuartPAC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/QuartPAC diff --git a/prepare/r-quasr/PKGBUILD b/prepare/r-quasr/PKGBUILD new file mode 100644 index 0000000000..ecddc67be8 --- /dev/null +++ b/prepare/r-quasr/PKGBUILD @@ -0,0 +1,54 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=QuasR +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quantify and Annotate Short Reads in R' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicfeatures + r-genomicfiles + r-genomicranges + r-iranges + r-rbowtie + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-shortread +) +optdepends=( + r-biocstyle + r-covr + r-genomicalignments + r-gviz + r-knitr + r-rhisat2 + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-quasr/lilac.py b/prepare/r-quasr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-quasr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-quasr/lilac.yaml b/prepare/r-quasr/lilac.yaml new file mode 100644 index 0000000000..a302311a42 --- /dev/null +++ b/prepare/r-quasr/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-genomeinfodb +- r-genomicfeatures +- r-genomicfiles +- r-genomicranges +- r-iranges +- r-rbowtie +- r-rhtslib +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-shortread +update_on: +- regex: QuasR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/QuasR diff --git a/prepare/r-quaternaryprod/PKGBUILD b/prepare/r-quaternaryprod/PKGBUILD new file mode 100644 index 0000000000..e3c1220756 --- /dev/null +++ b/prepare/r-quaternaryprod/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=QuaternaryProd +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-rcpp + r-yaml +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-quaternaryprod/lilac.py b/prepare/r-quaternaryprod/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-quaternaryprod/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-quaternaryprod/lilac.yaml b/prepare/r-quaternaryprod/lilac.yaml new file mode 100644 index 0000000000..4f3e6d80d3 --- /dev/null +++ b/prepare/r-quaternaryprod/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-rcpp +- r-yaml +update_on: +- regex: QuaternaryProd_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/QuaternaryProd diff --git a/prepare/r-qubic/PKGBUILD b/prepare/r-qubic/PKGBUILD new file mode 100644 index 0000000000..2ea919eef9 --- /dev/null +++ b/prepare/r-qubic/PKGBUILD @@ -0,0 +1,38 @@ +# system requirements: C++11, Rtools (>= 3.1) +# Maintainer: Guoyi Zhang + +_pkgname=QUBIC +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package for qualitative biclustering in support of gene co-expression analyses' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CCPL:by-nc-sa') +depends=( + r + r-biclust + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-fields + r-knitr + r-qgraph + r-qubicdata + r-rcolorbrewer + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qubic/lilac.py b/prepare/r-qubic/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qubic/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qubic/lilac.yaml b/prepare/r-qubic/lilac.yaml new file mode 100644 index 0000000000..61417d14e9 --- /dev/null +++ b/prepare/r-qubic/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biclust +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: QUBIC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/QUBIC diff --git a/prepare/r-questionr/PKGBUILD b/prepare/r-questionr/PKGBUILD new file mode 100644 index 0000000000..eb47c81ac7 --- /dev/null +++ b/prepare/r-questionr/PKGBUILD @@ -0,0 +1,48 @@ +# system requirements: xclip (Linux) +# Maintainer: Guoyi Zhang + +_pkgname=questionr +_pkgver=0.7.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions to Make Surveys Processing Easier' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-classint + r-highr + r-htmltools + r-labelled + r-miniui + r-rstudioapi + r-shiny + r-styler +) +optdepends=( + r-dplyr + r-forcats + r-ggplot2 + r-hmisc + r-janitor + r-knitr + r-rmarkdown + r-roxygen2 + r-survey + r-testthat + r-tidyr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-questionr/lilac.py b/prepare/r-questionr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-questionr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-questionr/lilac.yaml b/prepare/r-questionr/lilac.yaml new file mode 100644 index 0000000000..793ebd3f29 --- /dev/null +++ b/prepare/r-questionr/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-classint +- r-highr +- r-htmltools +- r-labelled +- r-miniui +- r-rstudioapi +- r-shiny +- r-styler +update_on: +- regex: questionr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=questionr diff --git a/prepare/r-qusage/PKGBUILD b/prepare/r-qusage/PKGBUILD new file mode 100644 index 0000000000..be2e660f8d --- /dev/null +++ b/prepare/r-qusage/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qusage +_pkgver=2.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='qusage: Quantitative Set Analysis for Gene Expression' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-emmeans + r-fftw + r-limma +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qusage/lilac.py b/prepare/r-qusage/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qusage/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qusage/lilac.yaml b/prepare/r-qusage/lilac.yaml new file mode 100644 index 0000000000..b130eb8eb2 --- /dev/null +++ b/prepare/r-qusage/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-emmeans +- r-fftw +- r-limma +update_on: +- regex: qusage_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/qusage diff --git a/prepare/r-qvalue/PKGBUILD b/prepare/r-qvalue/PKGBUILD new file mode 100644 index 0000000000..b4e70753bb --- /dev/null +++ b/prepare/r-qvalue/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qvalue +_pkgver=2.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Q-value estimation for false discovery rate control' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-ggplot2 + r-reshape2 +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qvalue/lilac.py b/prepare/r-qvalue/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qvalue/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qvalue/lilac.yaml b/prepare/r-qvalue/lilac.yaml new file mode 100644 index 0000000000..51039574c4 --- /dev/null +++ b/prepare/r-qvalue/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-reshape2 +update_on: +- regex: qvalue_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/qvalue diff --git a/prepare/r-qvcalc/PKGBUILD b/prepare/r-qvcalc/PKGBUILD new file mode 100644 index 0000000000..4ae39e62e9 --- /dev/null +++ b/prepare/r-qvcalc/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=qvcalc +_pkgver=1.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quasi Variances for Factor Effects in Statistical Models' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-mass + r-psychotools + r-relimp + r-survival +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-qvcalc/lilac.py b/prepare/r-qvcalc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-qvcalc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-qvcalc/lilac.yaml b/prepare/r-qvcalc/lilac.yaml new file mode 100644 index 0000000000..2a90286cf1 --- /dev/null +++ b/prepare/r-qvcalc/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: qvcalc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=qvcalc diff --git a/prepare/r-r.cache/PKGBUILD b/prepare/r-r.cache/PKGBUILD new file mode 100644 index 0000000000..ea78e090f7 --- /dev/null +++ b/prepare/r-r.cache/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=R.cache +_pkgver=0.15.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast and Light-Weight Caching (Memoization) of Objects and Results to Speed Up Computations' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-digest + r-r.methodss3 + r-r.oo + r-r.utils +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-r.cache/lilac.py b/prepare/r-r.cache/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-r.cache/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-r.cache/lilac.yaml b/prepare/r-r.cache/lilac.yaml new file mode 100644 index 0000000000..ea6aa287c5 --- /dev/null +++ b/prepare/r-r.cache/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-r.methodss3 +- r-r.oo +- r-r.utils +update_on: +- regex: R.cache_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=R.cache diff --git a/prepare/r-r.devices/PKGBUILD b/prepare/r-r.devices/PKGBUILD new file mode 100644 index 0000000000..15f91e8a40 --- /dev/null +++ b/prepare/r-r.devices/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=R.devices +_pkgver=2.17.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Unified Handling of Graphics Devices' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-base64enc + r-r.methodss3 + r-r.oo + r-r.utils +) +optdepends=( + r-cairo + r-digest + r-r.rsp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-r.devices/lilac.py b/prepare/r-r.devices/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-r.devices/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-r.devices/lilac.yaml b/prepare/r-r.devices/lilac.yaml new file mode 100644 index 0000000000..948762c01f --- /dev/null +++ b/prepare/r-r.devices/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-r.methodss3 +- r-r.oo +- r-r.utils +update_on: +- regex: R.devices_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=R.devices diff --git a/prepare/r-r.filesets/PKGBUILD b/prepare/r-r.filesets/PKGBUILD new file mode 100644 index 0000000000..beb426fcb1 --- /dev/null +++ b/prepare/r-r.filesets/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=R.filesets +_pkgver=2.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Easy Handling of and Access to Files Organized in Structured Directories' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-digest + r-r.cache + r-r.methodss3 + r-r.oo + r-r.utils +) +optdepends=( + r-gtools +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-r.filesets/lilac.py b/prepare/r-r.filesets/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-r.filesets/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-r.filesets/lilac.yaml b/prepare/r-r.filesets/lilac.yaml new file mode 100644 index 0000000000..9f5111bcbc --- /dev/null +++ b/prepare/r-r.filesets/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-r.cache +- r-r.methodss3 +- r-r.oo +- r-r.utils +update_on: +- regex: R.filesets_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=R.filesets diff --git a/prepare/r-r.huge/PKGBUILD b/prepare/r-r.huge/PKGBUILD new file mode 100644 index 0000000000..afaa211101 --- /dev/null +++ b/prepare/r-r.huge/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=R.huge +_pkgver=0.9.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methods for Accessing Huge Amounts of Data [deprecated]' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-r.methodss3 + r-r.oo + r-r.utils +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-r.huge/lilac.py b/prepare/r-r.huge/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-r.huge/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-r.huge/lilac.yaml b/prepare/r-r.huge/lilac.yaml new file mode 100644 index 0000000000..6c55e98be1 --- /dev/null +++ b/prepare/r-r.huge/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-r.methodss3 +- r-r.oo +- r-r.utils +update_on: +- regex: R.huge_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=R.huge diff --git a/prepare/r-r.matlab/PKGBUILD b/prepare/r-r.matlab/PKGBUILD new file mode 100644 index 0000000000..199c98a7da --- /dev/null +++ b/prepare/r-r.matlab/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=R.matlab +_pkgver=3.6.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Read and Write MAT Files and Call MATLAB from Within R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-r.methodss3 + r-r.oo + r-r.utils +) +optdepends=( + r-matrix + r-sparsem +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-r.matlab/lilac.py b/prepare/r-r.matlab/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-r.matlab/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-r.matlab/lilac.yaml b/prepare/r-r.matlab/lilac.yaml new file mode 100644 index 0000000000..2d0ae01374 --- /dev/null +++ b/prepare/r-r.matlab/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-r.methodss3 +- r-r.oo +- r-r.utils +update_on: +- regex: R.matlab_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=R.matlab diff --git a/prepare/r-r.methodss3/PKGBUILD b/prepare/r-r.methodss3/PKGBUILD new file mode 100644 index 0000000000..080eb357c9 --- /dev/null +++ b/prepare/r-r.methodss3/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=R.methodsS3 +_pkgver=1.8.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='S3 Methods Simplified' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +optdepends=( + r-codetools +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-r.methodss3/lilac.py b/prepare/r-r.methodss3/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-r.methodss3/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-r.methodss3/lilac.yaml b/prepare/r-r.methodss3/lilac.yaml new file mode 100644 index 0000000000..ca6fbf63c2 --- /dev/null +++ b/prepare/r-r.methodss3/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: R.methodsS3_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=R.methodsS3 diff --git a/prepare/r-r.oo/PKGBUILD b/prepare/r-r.oo/PKGBUILD new file mode 100644 index 0000000000..2867ff1d89 --- /dev/null +++ b/prepare/r-r.oo/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=R.oo +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Object-Oriented Programming with or without References' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-r.methodss3 +) +optdepends=( + r-tools +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-r.oo/lilac.py b/prepare/r-r.oo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-r.oo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-r.oo/lilac.yaml b/prepare/r-r.oo/lilac.yaml new file mode 100644 index 0000000000..6253b15639 --- /dev/null +++ b/prepare/r-r.oo/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-r.methodss3 +update_on: +- regex: R.oo_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=R.oo diff --git a/prepare/r-r.rsp/PKGBUILD b/prepare/r-r.rsp/PKGBUILD new file mode 100644 index 0000000000..22ee17e154 --- /dev/null +++ b/prepare/r-r.rsp/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=R.rsp +_pkgver=0.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dynamic Generation of Scientific Reports' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-digest + r-r.cache + r-r.methodss3 + r-r.oo + r-r.utils +) +optdepends=( + r-base64enc + r-knitr + r-markdown + r-r.devices + r-tcltk +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-r.rsp/lilac.py b/prepare/r-r.rsp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-r.rsp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-r.rsp/lilac.yaml b/prepare/r-r.rsp/lilac.yaml new file mode 100644 index 0000000000..0e310fe725 --- /dev/null +++ b/prepare/r-r.rsp/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-r.cache +- r-r.methodss3 +- r-r.oo +- r-r.utils +update_on: +- regex: R.rsp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=R.rsp diff --git a/prepare/r-r.utils/PKGBUILD b/prepare/r-r.utils/PKGBUILD new file mode 100644 index 0000000000..d5256831f0 --- /dev/null +++ b/prepare/r-r.utils/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=R.utils +_pkgver=2.11.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Various Programming Utilities' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-r.methodss3 + r-r.oo +) +optdepends=( + r-digest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-r.utils/lilac.py b/prepare/r-r.utils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-r.utils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-r.utils/lilac.yaml b/prepare/r-r.utils/lilac.yaml new file mode 100644 index 0000000000..98f87e9290 --- /dev/null +++ b/prepare/r-r.utils/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-r.methodss3 +- r-r.oo +update_on: +- regex: R.utils_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=R.utils diff --git a/prepare/r-r2html/PKGBUILD b/prepare/r-r2html/PKGBUILD new file mode 100644 index 0000000000..fc0bdd9ad5 --- /dev/null +++ b/prepare/r-r2html/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=R2HTML +_pkgver=2.3.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='HTML Exportation for R Objects' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-boot + r-cluster + r-nlme + r-nnet + r-rpart + r-splines + r-survival +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-r2html/lilac.py b/prepare/r-r2html/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-r2html/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-r2html/lilac.yaml b/prepare/r-r2html/lilac.yaml new file mode 100644 index 0000000000..45dfc762c9 --- /dev/null +++ b/prepare/r-r2html/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: R2HTML_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=R2HTML diff --git a/prepare/r-r2jags/PKGBUILD b/prepare/r-r2jags/PKGBUILD new file mode 100644 index 0000000000..72a440524a --- /dev/null +++ b/prepare/r-r2jags/PKGBUILD @@ -0,0 +1,34 @@ +# system requirements: JAGS (http://mcmc-jags.sourceforge.net) +# Maintainer: Guoyi Zhang + +_pkgname=R2jags +_pkgver=0.7-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Using R to Run 'JAGS'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-coda + r-r2winbugs + r-rjags +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-r2jags/lilac.py b/prepare/r-r2jags/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-r2jags/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-r2jags/lilac.yaml b/prepare/r-r2jags/lilac.yaml new file mode 100644 index 0000000000..1ae5d5d683 --- /dev/null +++ b/prepare/r-r2jags/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-coda +- r-r2winbugs +- r-rjags +update_on: +- regex: R2jags_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=R2jags diff --git a/prepare/r-r2winbugs/PKGBUILD b/prepare/r-r2winbugs/PKGBUILD new file mode 100644 index 0000000000..298762fe73 --- /dev/null +++ b/prepare/r-r2winbugs/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: OpenBugs for functions bugs() and openbugs() orWinBUGS 1.4 for function bugs() +# Maintainer: Guoyi Zhang + +_pkgname=R2WinBUGS +_pkgver=2.1-21 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Running 'WinBUGS' and 'OpenBUGS' from 'R' / 'S-PLUS'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-coda +) +optdepends=( + r-brugs +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-r2winbugs/lilac.py b/prepare/r-r2winbugs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-r2winbugs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-r2winbugs/lilac.yaml b/prepare/r-r2winbugs/lilac.yaml new file mode 100644 index 0000000000..b7e981620d --- /dev/null +++ b/prepare/r-r2winbugs/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-coda +update_on: +- regex: R2WinBUGS_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=R2WinBUGS diff --git a/prepare/r-r3cpet/PKGBUILD b/prepare/r-r3cpet/PKGBUILD new file mode 100644 index 0000000000..f4e77964b2 --- /dev/null +++ b/prepare/r-r3cpet/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=R3CPET +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-clvalid + r-data.table + r-genomeinfodb + r-genomicranges + r-ggbio + r-ggplot2 + r-hmisc + r-igraph + r-iranges + r-pheatmap + r-rcpp + r-rcurl + r-reshape2 + r-s4vectors +) +optdepends=( + r-annotationdbi + r-biocstyle + r-biomart + r-biovizbase + r-chippeakanno + r-knitr + r-org.hs.eg.db + r-shiny + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-r3cpet/lilac.py b/prepare/r-r3cpet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-r3cpet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-r3cpet/lilac.yaml b/prepare/r-r3cpet/lilac.yaml new file mode 100644 index 0000000000..1b973863c7 --- /dev/null +++ b/prepare/r-r3cpet/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-clvalid +- r-data.table +- r-genomeinfodb +- r-genomicranges +- r-ggbio +- r-ggplot2 +- r-hmisc +- r-igraph +- r-iranges +- r-pheatmap +- r-rcpp +- r-rcurl +- r-reshape2 +- r-s4vectors +update_on: +- regex: R3CPET_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/R3CPET diff --git a/prepare/r-r3cseq/PKGBUILD b/prepare/r-r3cseq/PKGBUILD new file mode 100644 index 0000000000..81c2979c17 --- /dev/null +++ b/prepare/r-r3cseq/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=r3Cseq +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-data.table + r-genomeinfodb + r-genomicranges + r-iranges + r-qvalue + r-rcolorbrewer + r-rsamtools + r-rtracklayer + r-sqldf + r-vgam +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg18.masked + r-bsgenome.hsapiens.ucsc.hg19.masked + r-bsgenome.mmusculus.ucsc.mm10.masked + r-bsgenome.mmusculus.ucsc.mm9.masked + r-bsgenome.rnorvegicus.ucsc.rn5.masked +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-r3cseq/lilac.py b/prepare/r-r3cseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-r3cseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-r3cseq/lilac.yaml b/prepare/r-r3cseq/lilac.yaml new file mode 100644 index 0000000000..31ecb2caf6 --- /dev/null +++ b/prepare/r-r3cseq/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-data.table +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-qvalue +- r-rcolorbrewer +- r-rsamtools +- r-rtracklayer +- r-sqldf +- r-vgam +update_on: +- regex: r3Cseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/r3Cseq diff --git a/prepare/r-r453plus1toolbox/PKGBUILD b/prepare/r-r453plus1toolbox/PKGBUILD new file mode 100644 index 0000000000..9cadbf8e17 --- /dev/null +++ b/prepare/r-r453plus1toolbox/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=R453Plus1Toolbox +_pkgver=1.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="A package for importing and analyzing data from Roche's Genome Sequencer System" +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-biocgenerics + r-biomart + r-biostrings + r-bsgenome + r-genomicranges + r-iranges + r-r2html + r-rsamtools + r-s4vectors + r-shortread + r-summarizedexperiment + r-teachingdemos + r-variantannotation + r-xtable + r-xvector +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.scerevisiae.ucsc.saccer2 + r-rtracklayer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-r453plus1toolbox/lilac.py b/prepare/r-r453plus1toolbox/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-r453plus1toolbox/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-r453plus1toolbox/lilac.yaml b/prepare/r-r453plus1toolbox/lilac.yaml new file mode 100644 index 0000000000..fd4dcab708 --- /dev/null +++ b/prepare/r-r453plus1toolbox/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biomart +- r-biostrings +- r-bsgenome +- r-genomicranges +- r-iranges +- r-r2html +- r-rsamtools +- r-s4vectors +- r-shortread +- r-summarizedexperiment +- r-teachingdemos +- r-variantannotation +- r-xtable +- r-xvector +update_on: +- regex: R453Plus1Toolbox_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/R453Plus1Toolbox diff --git a/prepare/r-r4rna/PKGBUILD b/prepare/r-r4rna/PKGBUILD new file mode 100644 index 0000000000..f9f4aeb723 --- /dev/null +++ b/prepare/r-r4rna/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=R4RNA +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package for RNA visualization and analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-r4rna/lilac.py b/prepare/r-r4rna/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-r4rna/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-r4rna/lilac.yaml b/prepare/r-r4rna/lilac.yaml new file mode 100644 index 0000000000..0ece87284e --- /dev/null +++ b/prepare/r-r4rna/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +update_on: +- regex: R4RNA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/R4RNA diff --git a/prepare/r-radiant.data/PKGBUILD b/prepare/r-radiant.data/PKGBUILD new file mode 100644 index 0000000000..75d14a59cd --- /dev/null +++ b/prepare/r-radiant.data/PKGBUILD @@ -0,0 +1,67 @@ +# Maintainer: Guoyi Zhang + +_pkgname=radiant.data +_pkgver=1.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data Menu for Radiant: Business Analytics using R and Shiny' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('AGPL') +depends=( + r + r-base64enc + r-broom + r-car + r-curl + r-dplyr + r-dt + r-ggplot2 + r-glue + r-import + r-jsonlite + r-knitr + r-lubridate + r-magrittr + r-markdown + r-patchwork + r-plotly + r-psych + r-randomizr + r-readr + r-readxl + r-rlang + r-rmarkdown + r-rstudioapi + r-scales + r-shiny + r-shinyace + r-shinyfiles + r-stringi + r-tibble + r-tidyr + r-writexl +) +optdepends=( + r-dbi + r-odbc + r-pkgdown + r-rpostgresql + r-rsqlite + r-svglite + r-testthat + r-webshot +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-radiant.data/lilac.py b/prepare/r-radiant.data/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-radiant.data/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-radiant.data/lilac.yaml b/prepare/r-radiant.data/lilac.yaml new file mode 100644 index 0000000000..c701a9d2e2 --- /dev/null +++ b/prepare/r-radiant.data/lilac.yaml @@ -0,0 +1,40 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-broom +- r-car +- r-curl +- r-dplyr +- r-dt +- r-ggplot2 +- r-glue +- r-import +- r-jsonlite +- r-knitr +- r-lubridate +- r-magrittr +- r-markdown +- r-patchwork +- r-plotly +- r-psych +- r-randomizr +- r-readr +- r-readxl +- r-rlang +- r-rmarkdown +- r-rstudioapi +- r-scales +- r-shiny +- r-shinyace +- r-shinyfiles +- r-stringi +- r-tibble +- r-tidyr +- r-writexl +update_on: +- regex: radiant.data_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=radiant.data diff --git a/prepare/r-radiogx/PKGBUILD b/prepare/r-radiogx/PKGBUILD new file mode 100644 index 0000000000..b43900f189 --- /dev/null +++ b/prepare/r-radiogx/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RadioGx +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Large-Scale Radio-Genomic Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-biobase + r-biocparallel + r-catools + r-coregx + r-downloader + r-magicaxis + r-matrixstats + r-rcolorbrewer + r-reshape2 + r-s4vectors + r-scales + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-markdown + r-pander + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-radiogx/lilac.py b/prepare/r-radiogx/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-radiogx/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-radiogx/lilac.yaml b/prepare/r-radiogx/lilac.yaml new file mode 100644 index 0000000000..f8b93f29ae --- /dev/null +++ b/prepare/r-radiogx/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biobase +- r-biocparallel +- r-catools +- r-coregx +- r-downloader +- r-magicaxis +- r-matrixstats +- r-rcolorbrewer +- r-reshape2 +- r-s4vectors +- r-scales +- r-summarizedexperiment +update_on: +- regex: RadioGx_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RadioGx diff --git a/prepare/r-rafalib/PKGBUILD b/prepare/r-rafalib/PKGBUILD new file mode 100644 index 0000000000..4075c9e91c --- /dev/null +++ b/prepare/r-rafalib/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rafalib +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Convenience Functions for Routine Data Exploration' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-rcolorbrewer +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rafalib/lilac.py b/prepare/r-rafalib/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rafalib/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rafalib/lilac.yaml b/prepare/r-rafalib/lilac.yaml new file mode 100644 index 0000000000..e44a3699a5 --- /dev/null +++ b/prepare/r-rafalib/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcolorbrewer +update_on: +- regex: rafalib_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rafalib diff --git a/prepare/r-ragg/PKGBUILD b/prepare/r-ragg/PKGBUILD new file mode 100644 index 0000000000..43be671a14 --- /dev/null +++ b/prepare/r-ragg/PKGBUILD @@ -0,0 +1,36 @@ +# system requirements: C++11, freetype2, libpng, libtiff, libjpeg +# Maintainer: Guoyi Zhang + +_pkgname=ragg +_pkgver=1.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Graphic Devices Based on AGG' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-systemfonts + r-textshaping +) +optdepends=( + r-covr + r-graphics + r-grid + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ragg/lilac.py b/prepare/r-ragg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ragg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ragg/lilac.yaml b/prepare/r-ragg/lilac.yaml new file mode 100644 index 0000000000..65c16df68d --- /dev/null +++ b/prepare/r-ragg/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-systemfonts +- r-textshaping +update_on: +- regex: ragg_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ragg diff --git a/prepare/r-raggedexperiment/PKGBUILD b/prepare/r-raggedexperiment/PKGBUILD new file mode 100644 index 0000000000..a3e8d96767 --- /dev/null +++ b/prepare/r-raggedexperiment/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RaggedExperiment +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Representation of Sparse Experiments and Assays Across Samples' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-genomeinfodb + r-genomicranges + r-iranges + r-matrixgenerics + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-multiassayexperiment + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-raggedexperiment/lilac.py b/prepare/r-raggedexperiment/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-raggedexperiment/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-raggedexperiment/lilac.yaml b/prepare/r-raggedexperiment/lilac.yaml new file mode 100644 index 0000000000..081b3ff71a --- /dev/null +++ b/prepare/r-raggedexperiment/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-matrixgenerics +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: RaggedExperiment_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RaggedExperiment diff --git a/prepare/r-rain/PKGBUILD b/prepare/r-rain/PKGBUILD new file mode 100644 index 0000000000..bc1fd8f6d4 --- /dev/null +++ b/prepare/r-rain/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rain +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Rhythmicity Analysis Incorporating Non-parametric Methods' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-gmp + r-multtest +) +optdepends=( + r-biocstyle + r-lattice +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rain/lilac.py b/prepare/r-rain/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rain/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rain/lilac.yaml b/prepare/r-rain/lilac.yaml new file mode 100644 index 0000000000..24d5cfaa6e --- /dev/null +++ b/prepare/r-rain/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gmp +- r-multtest +update_on: +- regex: rain_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rain diff --git a/prepare/r-rainbow/PKGBUILD b/prepare/r-rainbow/PKGBUILD new file mode 100644 index 0000000000..8c0ed94557 --- /dev/null +++ b/prepare/r-rainbow/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rainbow +_pkgver=3.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bagplots, Boxplots and Rainbow Plots for Functional Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-colorspace + r-hdrcde + r-ks + r-pcapp +) +optdepends=( + r-forecast +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rainbow/lilac.py b/prepare/r-rainbow/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rainbow/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rainbow/lilac.yaml b/prepare/r-rainbow/lilac.yaml new file mode 100644 index 0000000000..3e17f725d9 --- /dev/null +++ b/prepare/r-rainbow/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colorspace +- r-hdrcde +- r-ks +- r-pcapp +update_on: +- regex: rainbow_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rainbow diff --git a/prepare/r-rama/PKGBUILD b/prepare/r-rama/PKGBUILD new file mode 100644 index 0000000000..8fcad03dbe --- /dev/null +++ b/prepare/r-rama/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rama +_pkgver=1.68.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Robust Analysis of MicroArrays' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rama/lilac.py b/prepare/r-rama/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rama/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rama/lilac.yaml b/prepare/r-rama/lilac.yaml new file mode 100644 index 0000000000..1040510ab3 --- /dev/null +++ b/prepare/r-rama/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: rama_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rama diff --git a/prepare/r-ramr/PKGBUILD b/prepare/r-ramr/PKGBUILD new file mode 100644 index 0000000000..5e96c610f3 --- /dev/null +++ b/prepare/r-ramr/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ramr +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detection of Rare Aberrantly Methylated Regions in Array and NGS Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-doparallel + r-dorng + r-envstats + r-extdist + r-foreach + r-genomicranges + r-ggplot2 + r-iranges + r-matrixstats + r-reshape2 + r-s4vectors +) +optdepends=( + r-annotatr + r-gridextra + r-knitr + r-lola + r-org.hs.eg.db + r-rmarkdown + r-runit + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ramr/lilac.py b/prepare/r-ramr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ramr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ramr/lilac.yaml b/prepare/r-ramr/lilac.yaml new file mode 100644 index 0000000000..cf4009d606 --- /dev/null +++ b/prepare/r-ramr/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-doparallel +- r-dorng +- r-envstats +- r-extdist +- r-foreach +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-matrixstats +- r-reshape2 +- r-s4vectors +update_on: +- regex: ramr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ramr diff --git a/prepare/r-ramwas/PKGBUILD b/prepare/r-ramwas/PKGBUILD new file mode 100644 index 0000000000..61ba82a54d --- /dev/null +++ b/prepare/r-ramwas/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ramwas +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biocgenerics + r-biomart + r-biostrings + r-digest + r-filematrix + r-genomicalignments + r-glmnet + r-rsamtools +) +optdepends=( + r-biocstyle + r-bsgenome.ecoli.ncbi.20080805 + r-knitr + r-pander + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ramwas/lilac.py b/prepare/r-ramwas/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ramwas/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ramwas/lilac.yaml b/prepare/r-ramwas/lilac.yaml new file mode 100644 index 0000000000..4182c871c6 --- /dev/null +++ b/prepare/r-ramwas/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biomart +- r-biostrings +- r-digest +- r-filematrix +- r-genomicalignments +- r-glmnet +- r-rsamtools +update_on: +- regex: ramwas_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ramwas diff --git a/prepare/r-randomcolor/PKGBUILD b/prepare/r-randomcolor/PKGBUILD new file mode 100644 index 0000000000..54206c2a8e --- /dev/null +++ b/prepare/r-randomcolor/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=randomcoloR +_pkgver=1.1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generate Attractive Random Colors' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('CC0') +depends=( + r + r-colorspace + r-rtsne + r-scales + r-stringr + r-v8 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-randomcolor/lilac.py b/prepare/r-randomcolor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-randomcolor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-randomcolor/lilac.yaml b/prepare/r-randomcolor/lilac.yaml new file mode 100644 index 0000000000..75bae4565e --- /dev/null +++ b/prepare/r-randomcolor/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colorspace +- r-rtsne +- r-scales +- r-stringr +- r-v8 +update_on: +- regex: randomcoloR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=randomcoloR diff --git a/prepare/r-randomforest/PKGBUILD b/prepare/r-randomforest/PKGBUILD new file mode 100644 index 0000000000..5f0ea07f43 --- /dev/null +++ b/prepare/r-randomforest/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=randomForest +_pkgver=4.6-14 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Breiman and Cutler's Random Forests for Classification and Regression" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-mass + r-rcolorbrewer +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-randomforest/lilac.py b/prepare/r-randomforest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-randomforest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-randomforest/lilac.yaml b/prepare/r-randomforest/lilac.yaml new file mode 100644 index 0000000000..2a0e35e2cf --- /dev/null +++ b/prepare/r-randomforest/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: randomForest_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=randomForest diff --git a/prepare/r-randomizr/PKGBUILD b/prepare/r-randomizr/PKGBUILD new file mode 100644 index 0000000000..5ef52526d2 --- /dev/null +++ b/prepare/r-randomizr/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=randomizr +_pkgver=0.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Easy-to-Use Tools for Common Forms of Random Assignment and Sampling' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-blocktools + r-dplyr + r-knitr + r-ri + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-randomizr/lilac.py b/prepare/r-randomizr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-randomizr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-randomizr/lilac.yaml b/prepare/r-randomizr/lilac.yaml new file mode 100644 index 0000000000..554e1a7a1d --- /dev/null +++ b/prepare/r-randomizr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: randomizr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=randomizr diff --git a/prepare/r-randomwalkrestartmh/PKGBUILD b/prepare/r-randomwalkrestartmh/PKGBUILD new file mode 100644 index 0000000000..3c639a8a7d --- /dev/null +++ b/prepare/r-randomwalkrestartmh/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RandomWalkRestartMH +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Random walk with restart on multiplex and heterogeneous Networks' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dnet + r-igraph +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-randomwalkrestartmh/lilac.py b/prepare/r-randomwalkrestartmh/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-randomwalkrestartmh/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-randomwalkrestartmh/lilac.yaml b/prepare/r-randomwalkrestartmh/lilac.yaml new file mode 100644 index 0000000000..35c861da90 --- /dev/null +++ b/prepare/r-randomwalkrestartmh/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dnet +- r-igraph +update_on: +- regex: RandomWalkRestartMH_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RandomWalkRestartMH diff --git a/prepare/r-randpack/PKGBUILD b/prepare/r-randpack/PKGBUILD new file mode 100644 index 0000000000..22c42c26b2 --- /dev/null +++ b/prepare/r-randpack/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=randPack +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Randomization routines for Clinical Trials' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-randpack/lilac.py b/prepare/r-randpack/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-randpack/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-randpack/lilac.yaml b/prepare/r-randpack/lilac.yaml new file mode 100644 index 0000000000..11ae1d5083 --- /dev/null +++ b/prepare/r-randpack/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: randPack_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/randPack diff --git a/prepare/r-randrotation/PKGBUILD b/prepare/r-randrotation/PKGBUILD new file mode 100644 index 0000000000..aaeb2a2386 --- /dev/null +++ b/prepare/r-randrotation/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=randRotation +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Random Rotation Methods for High Dimensional Data with Batch Structure' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rdpack +) +optdepends=( + r-biocparallel + r-biocstyle + r-knitr + r-limma + r-lme4 + r-nlme + r-rmarkdown + r-sva + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-randrotation/lilac.py b/prepare/r-randrotation/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-randrotation/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-randrotation/lilac.yaml b/prepare/r-randrotation/lilac.yaml new file mode 100644 index 0000000000..8fb2c2a8b0 --- /dev/null +++ b/prepare/r-randrotation/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rdpack +update_on: +- regex: randRotation_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/randRotation diff --git a/prepare/r-randtests/PKGBUILD b/prepare/r-randtests/PKGBUILD new file mode 100644 index 0000000000..c6ea593491 --- /dev/null +++ b/prepare/r-randtests/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=randtests +_pkgver=1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Testing randomness in R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-randtests/lilac.py b/prepare/r-randtests/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-randtests/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-randtests/lilac.yaml b/prepare/r-randtests/lilac.yaml new file mode 100644 index 0000000000..d92bd2261c --- /dev/null +++ b/prepare/r-randtests/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: randtests_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=randtests diff --git a/prepare/r-ranger/PKGBUILD b/prepare/r-ranger/PKGBUILD new file mode 100644 index 0000000000..beb8d833ee --- /dev/null +++ b/prepare/r-ranger/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ranger +_pkgver=0.13.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Fast Implementation of Random Forests' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcppeigen +) +optdepends=( + r-covr + r-survival + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ranger/lilac.py b/prepare/r-ranger/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ranger/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ranger/lilac.yaml b/prepare/r-ranger/lilac.yaml new file mode 100644 index 0000000000..8d7892817a --- /dev/null +++ b/prepare/r-ranger/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcppeigen +update_on: +- regex: ranger_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ranger diff --git a/prepare/r-rankprod/PKGBUILD b/prepare/r-rankprod/PKGBUILD new file mode 100644 index 0000000000..aafaceb6c5 --- /dev/null +++ b/prepare/r-rankprod/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RankProd +_pkgver=3.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Rank Product method for identifying differentially expressed genes with application in meta-analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-gmp + r-rmpfr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rankprod/lilac.py b/prepare/r-rankprod/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rankprod/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rankprod/lilac.yaml b/prepare/r-rankprod/lilac.yaml new file mode 100644 index 0000000000..bb5d8b1bb8 --- /dev/null +++ b/prepare/r-rankprod/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gmp +- r-rmpfr +update_on: +- regex: RankProd_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RankProd diff --git a/prepare/r-rann/PKGBUILD b/prepare/r-rann/PKGBUILD new file mode 100644 index 0000000000..23c49d8010 --- /dev/null +++ b/prepare/r-rann/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RANN +_pkgver=2.6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rann/lilac.py b/prepare/r-rann/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rann/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rann/lilac.yaml b/prepare/r-rann/lilac.yaml new file mode 100644 index 0000000000..1e3dd27e0c --- /dev/null +++ b/prepare/r-rann/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RANN_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RANN diff --git a/prepare/r-rapiclient/PKGBUILD b/prepare/r-rapiclient/PKGBUILD new file mode 100644 index 0000000000..7d677f529d --- /dev/null +++ b/prepare/r-rapiclient/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rapiclient +_pkgver=0.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dynamic OpenAPI/Swagger Client' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-httr + r-jsonlite + r-yaml +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rapiclient/lilac.py b/prepare/r-rapiclient/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rapiclient/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rapiclient/lilac.yaml b/prepare/r-rapiclient/lilac.yaml new file mode 100644 index 0000000000..1e3933aa24 --- /dev/null +++ b/prepare/r-rapiclient/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-httr +- r-jsonlite +- r-yaml +update_on: +- regex: rapiclient_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rapiclient diff --git a/prepare/r-rapidjsonr/PKGBUILD b/prepare/r-rapidjsonr/PKGBUILD new file mode 100644 index 0000000000..ab69014514 --- /dev/null +++ b/prepare/r-rapidjsonr/PKGBUILD @@ -0,0 +1,28 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=rapidjsonr +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'Rapidjson' C++ Header Files" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rapidjsonr/lilac.py b/prepare/r-rapidjsonr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rapidjsonr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rapidjsonr/lilac.yaml b/prepare/r-rapidjsonr/lilac.yaml new file mode 100644 index 0000000000..9ddad0fe71 --- /dev/null +++ b/prepare/r-rapidjsonr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: rapidjsonr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rapidjsonr diff --git a/prepare/r-rapiserialize/PKGBUILD b/prepare/r-rapiserialize/PKGBUILD new file mode 100644 index 0000000000..f451385481 --- /dev/null +++ b/prepare/r-rapiserialize/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RApiSerialize +_pkgver=0.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R API Serialization' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rapiserialize/lilac.py b/prepare/r-rapiserialize/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rapiserialize/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rapiserialize/lilac.yaml b/prepare/r-rapiserialize/lilac.yaml new file mode 100644 index 0000000000..164a039820 --- /dev/null +++ b/prepare/r-rapiserialize/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RApiSerialize_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RApiSerialize diff --git a/prepare/r-rapportools/PKGBUILD b/prepare/r-rapportools/PKGBUILD new file mode 100644 index 0000000000..459a452055 --- /dev/null +++ b/prepare/r-rapportools/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rapportools +_pkgver=1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Miscellaneous (stats) helper functions with sane defaults for reporting' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('AGPL') +depends=( + r + r-pander + r-plyr + r-reshape +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rapportools/lilac.py b/prepare/r-rapportools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rapportools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rapportools/lilac.yaml b/prepare/r-rapportools/lilac.yaml new file mode 100644 index 0000000000..6d6f989cd0 --- /dev/null +++ b/prepare/r-rapportools/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-pander +- r-plyr +- r-reshape +update_on: +- regex: rapportools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rapportools diff --git a/prepare/r-rarevariantvis/PKGBUILD b/prepare/r-rarevariantvis/PKGBUILD new file mode 100644 index 0000000000..8e800679c5 --- /dev/null +++ b/prepare/r-rarevariantvis/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RareVariantVis +_pkgver=2.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A suite for analysis of rare genomic variants in whole genome sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-bsgenome + r-bsgenome.hsapiens.ucsc.hg19 + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-genomicscores + r-googlevis + r-gtools + r-iranges + r-phastcons100way.ucsc.hg19 + r-s4vectors + r-summarizedexperiment + r-txdb.hsapiens.ucsc.hg19.knowngene + r-variantannotation +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rarevariantvis/lilac.py b/prepare/r-rarevariantvis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rarevariantvis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rarevariantvis/lilac.yaml b/prepare/r-rarevariantvis/lilac.yaml new file mode 100644 index 0000000000..cfc46769b3 --- /dev/null +++ b/prepare/r-rarevariantvis/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-bsgenome +- r-bsgenome.hsapiens.ucsc.hg19 +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-genomicscores +- r-googlevis +- r-gtools +- r-iranges +- r-phastcons100way.ucsc.hg19 +- r-s4vectors +- r-summarizedexperiment +- r-txdb.hsapiens.ucsc.hg19.knowngene +- r-variantannotation +update_on: +- regex: RareVariantVis_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RareVariantVis diff --git a/prepare/r-rarpack/PKGBUILD b/prepare/r-rarpack/PKGBUILD new file mode 100644 index 0000000000..d5fdfc73e5 --- /dev/null +++ b/prepare/r-rarpack/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rARPACK +_pkgver=0.11-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Solvers for Large Scale Eigenvalue and SVD Problems' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-rspectra +) +optdepends=( + r-matrix +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rarpack/lilac.py b/prepare/r-rarpack/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rarpack/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rarpack/lilac.yaml b/prepare/r-rarpack/lilac.yaml new file mode 100644 index 0000000000..390695fe47 --- /dev/null +++ b/prepare/r-rarpack/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rspectra +update_on: +- regex: rARPACK_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rARPACK diff --git a/prepare/r-raster/PKGBUILD b/prepare/r-raster/PKGBUILD new file mode 100644 index 0000000000..038363db71 --- /dev/null +++ b/prepare/r-raster/PKGBUILD @@ -0,0 +1,45 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=raster +_pkgver=3.5-11 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Geographic Data Analysis and Modeling' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-sp + r-terra +) +optdepends=( + r-exactextractr + r-fields + r-gstat + r-igraph + r-mass + r-ncdf4 + r-parallel + r-rastervis + r-rgdal + r-rgeos + r-sf + r-tcltk + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-raster/lilac.py b/prepare/r-raster/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-raster/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-raster/lilac.yaml b/prepare/r-raster/lilac.yaml new file mode 100644 index 0000000000..d9eb2db96c --- /dev/null +++ b/prepare/r-raster/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-sp +- r-terra +update_on: +- regex: raster_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=raster diff --git a/prepare/r-rastervis/PKGBUILD b/prepare/r-rastervis/PKGBUILD new file mode 100644 index 0000000000..4baab193c2 --- /dev/null +++ b/prepare/r-rastervis/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rasterVis +_pkgver=0.51.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization Methods for Raster Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-hexbin + r-latticeextra + r-raster + r-rcolorbrewer + r-sp + r-terra + r-viridislite + r-zoo +) +optdepends=( + r-colorspace + r-dichromat + r-ggplot2 + r-rgl + r-sf +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rastervis/lilac.py b/prepare/r-rastervis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rastervis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rastervis/lilac.yaml b/prepare/r-rastervis/lilac.yaml new file mode 100644 index 0000000000..d2829e909d --- /dev/null +++ b/prepare/r-rastervis/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-hexbin +- r-latticeextra +- r-raster +- r-rcolorbrewer +- r-sp +- r-terra +- r-viridislite +- r-zoo +update_on: +- regex: rasterVis_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rasterVis diff --git a/prepare/r-rawrr/PKGBUILD b/prepare/r-rawrr/PKGBUILD new file mode 100644 index 0000000000..f3cc41b19a --- /dev/null +++ b/prepare/r-rawrr/PKGBUILD @@ -0,0 +1,36 @@ +# system requirements: mono-runtime 4.x or higher (including System.Datalibrary) on Linux/macOS, .Net Framework (>= 4.5.1) on MicrosoftWindows. +# Maintainer: Guoyi Zhang + +_pkgname=rawrr +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Direct Access to Orbitrap Data and Beyond' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biocstyle + r-experimenthub + r-knitr + r-protviz + r-rmarkdown + r-tartare + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rawrr/lilac.py b/prepare/r-rawrr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rawrr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rawrr/lilac.yaml b/prepare/r-rawrr/lilac.yaml new file mode 100644 index 0000000000..831c76a483 --- /dev/null +++ b/prepare/r-rawrr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: rawrr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rawrr diff --git a/prepare/r-rbcbook1/PKGBUILD b/prepare/r-rbcbook1/PKGBUILD new file mode 100644 index 0000000000..5ca1d54d72 --- /dev/null +++ b/prepare/r-rbcbook1/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RbcBook1 +_pkgver=1.62.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Support for Springer monograph on Bioconductor' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-graph +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rbcbook1/lilac.py b/prepare/r-rbcbook1/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rbcbook1/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rbcbook1/lilac.yaml b/prepare/r-rbcbook1/lilac.yaml new file mode 100644 index 0000000000..d73400b327 --- /dev/null +++ b/prepare/r-rbcbook1/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-graph +update_on: +- regex: RbcBook1_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RbcBook1 diff --git a/prepare/r-rbec/PKGBUILD b/prepare/r-rbec/PKGBUILD new file mode 100644 index 0000000000..cd3f89abdc --- /dev/null +++ b/prepare/r-rbec/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rbec +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-dada2 + r-doparallel + r-foreach + r-ggplot2 + r-rcpp + r-readr +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rbec/lilac.py b/prepare/r-rbec/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rbec/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rbec/lilac.yaml b/prepare/r-rbec/lilac.yaml new file mode 100644 index 0000000000..28af37ad58 --- /dev/null +++ b/prepare/r-rbec/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dada2 +- r-doparallel +- r-foreach +- r-ggplot2 +- r-rcpp +- r-readr +update_on: +- regex: Rbec_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rbec diff --git a/prepare/r-rbgl/PKGBUILD b/prepare/r-rbgl/PKGBUILD new file mode 100644 index 0000000000..6a65a6e844 --- /dev/null +++ b/prepare/r-rbgl/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RBGL +_pkgver=1.70.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An interface to the BOOST graph library' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bh + r-graph +) +optdepends=( + r-biocgenerics + r-rgraphviz + r-runit + r-xml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rbgl/lilac.py b/prepare/r-rbgl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rbgl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rbgl/lilac.yaml b/prepare/r-rbgl/lilac.yaml new file mode 100644 index 0000000000..b4c9c2d500 --- /dev/null +++ b/prepare/r-rbgl/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-graph +update_on: +- regex: RBGL_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RBGL diff --git a/prepare/r-rbibutils/PKGBUILD b/prepare/r-rbibutils/PKGBUILD new file mode 100644 index 0000000000..5d9f4b2375 --- /dev/null +++ b/prepare/r-rbibutils/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rbibutils +_pkgver=2.2.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Read 'Bibtex' Files and Convert Between Bibliography Formats" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rbibutils/lilac.py b/prepare/r-rbibutils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rbibutils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rbibutils/lilac.yaml b/prepare/r-rbibutils/lilac.yaml new file mode 100644 index 0000000000..03be651e57 --- /dev/null +++ b/prepare/r-rbibutils/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: rbibutils_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rbibutils diff --git a/prepare/r-rbioinf/PKGBUILD b/prepare/r-rbioinf/PKGBUILD new file mode 100644 index 0000000000..164a620eac --- /dev/null +++ b/prepare/r-rbioinf/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RBioinf +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RBioinf' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-graph +) +optdepends=( + r-rgraphviz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rbioinf/lilac.py b/prepare/r-rbioinf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rbioinf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rbioinf/lilac.yaml b/prepare/r-rbioinf/lilac.yaml new file mode 100644 index 0000000000..4f9c403a86 --- /dev/null +++ b/prepare/r-rbioinf/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +update_on: +- regex: RBioinf_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RBioinf diff --git a/prepare/r-rbiopaxparser/PKGBUILD b/prepare/r-rbiopaxparser/PKGBUILD new file mode 100644 index 0000000000..0c6ec66b12 --- /dev/null +++ b/prepare/r-rbiopaxparser/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rBiopaxParser +_pkgver=2.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Parses BioPax files and represents them in R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-xml +) +optdepends=( + r-biocgenerics + r-graph + r-igraph + r-rbgl + r-rcurl + r-rgraphviz + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rbiopaxparser/lilac.py b/prepare/r-rbiopaxparser/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rbiopaxparser/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rbiopaxparser/lilac.yaml b/prepare/r-rbiopaxparser/lilac.yaml new file mode 100644 index 0000000000..85d4c408bd --- /dev/null +++ b/prepare/r-rbiopaxparser/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-xml +update_on: +- regex: rBiopaxParser_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rBiopaxParser diff --git a/prepare/r-rbm/PKGBUILD b/prepare/r-rbm/PKGBUILD new file mode 100644 index 0000000000..d97f74578b --- /dev/null +++ b/prepare/r-rbm/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RBM +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RBM: a R package for microarray and RNA-Seq data analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-limma + r-marray +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rbm/lilac.py b/prepare/r-rbm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rbm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rbm/lilac.yaml b/prepare/r-rbm/lilac.yaml new file mode 100644 index 0000000000..c22792fe69 --- /dev/null +++ b/prepare/r-rbm/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-limma +- r-marray +update_on: +- regex: RBM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RBM diff --git a/prepare/r-rbokeh/PKGBUILD b/prepare/r-rbokeh/PKGBUILD new file mode 100644 index 0000000000..78875934ee --- /dev/null +++ b/prepare/r-rbokeh/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rbokeh +_pkgver=0.5.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Interface for Bokeh' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-digest + r-gistr + r-hexbin + r-htmlwidgets + r-jsonlite + r-lazyeval + r-magrittr + r-maps + r-pryr + r-scales +) +optdepends=( + r-data.table + r-knitr + r-lattice + r-latticeextra + r-lintr + r-markdown + r-rmarkdown + r-roxygen2 + r-shiny + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rbokeh/lilac.py b/prepare/r-rbokeh/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rbokeh/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rbokeh/lilac.yaml b/prepare/r-rbokeh/lilac.yaml new file mode 100644 index 0000000000..8acb51c097 --- /dev/null +++ b/prepare/r-rbokeh/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-gistr +- r-hexbin +- r-htmlwidgets +- r-jsonlite +- r-lazyeval +- r-magrittr +- r-maps +- r-pryr +- r-scales +update_on: +- regex: rbokeh_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rbokeh diff --git a/prepare/r-rbowtie/PKGBUILD b/prepare/r-rbowtie/PKGBUILD new file mode 100644 index 0000000000..9fe2879a41 --- /dev/null +++ b/prepare/r-rbowtie/PKGBUILD @@ -0,0 +1,34 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=Rbowtie +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R bowtie wrapper' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-biocstyle + r-knitr + r-parallel + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rbowtie/lilac.py b/prepare/r-rbowtie/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rbowtie/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rbowtie/lilac.yaml b/prepare/r-rbowtie/lilac.yaml new file mode 100644 index 0000000000..ad30888e11 --- /dev/null +++ b/prepare/r-rbowtie/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Rbowtie_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rbowtie diff --git a/prepare/r-rbowtie2/PKGBUILD b/prepare/r-rbowtie2/PKGBUILD new file mode 100644 index 0000000000..36cb8c727e --- /dev/null +++ b/prepare/r-rbowtie2/PKGBUILD @@ -0,0 +1,34 @@ +# system requirements: C++11, GNU make, samtools +# Maintainer: Guoyi Zhang + +_pkgname=Rbowtie2 +_pkgver=2.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R Wrapper for Bowtie2 and AdapterRemoval' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-magrittr + r-rsamtools +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rbowtie2/lilac.py b/prepare/r-rbowtie2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rbowtie2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rbowtie2/lilac.yaml b/prepare/r-rbowtie2/lilac.yaml new file mode 100644 index 0000000000..cd83fa3b41 --- /dev/null +++ b/prepare/r-rbowtie2/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-magrittr +- r-rsamtools +update_on: +- regex: Rbowtie2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rbowtie2 diff --git a/prepare/r-rbsurv/PKGBUILD b/prepare/r-rbsurv/PKGBUILD new file mode 100644 index 0000000000..acdca8801d --- /dev/null +++ b/prepare/r-rbsurv/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rbsurv +_pkgver=2.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Robust likelihood-based survival modeling with microarray data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rbsurv/lilac.py b/prepare/r-rbsurv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rbsurv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rbsurv/lilac.yaml b/prepare/r-rbsurv/lilac.yaml new file mode 100644 index 0000000000..eadec51475 --- /dev/null +++ b/prepare/r-rbsurv/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: rbsurv_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rbsurv diff --git a/prepare/r-rcade/PKGBUILD b/prepare/r-rcade/PKGBUILD new file mode 100644 index 0000000000..135e775cba --- /dev/null +++ b/prepare/r-rcade/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rcade +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bayseq + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-plotrix + r-rgl + r-rsamtools + r-s4vectors +) +optdepends=( + r-biocgenerics + r-biocstyle + r-biomart + r-limma + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcade/lilac.py b/prepare/r-rcade/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcade/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcade/lilac.yaml b/prepare/r-rcade/lilac.yaml new file mode 100644 index 0000000000..1424306558 --- /dev/null +++ b/prepare/r-rcade/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bayseq +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-plotrix +- r-rgl +- r-rsamtools +- r-s4vectors +update_on: +- regex: Rcade_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rcade diff --git a/prepare/r-rcapture/PKGBUILD b/prepare/r-rcapture/PKGBUILD new file mode 100644 index 0000000000..25ba7877db --- /dev/null +++ b/prepare/r-rcapture/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rcapture +_pkgver=1.4-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Loglinear Models for Capture-Recapture Experiments' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcapture/lilac.py b/prepare/r-rcapture/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcapture/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcapture/lilac.yaml b/prepare/r-rcapture/lilac.yaml new file mode 100644 index 0000000000..98ed659cdb --- /dev/null +++ b/prepare/r-rcapture/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Rcapture_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rcapture diff --git a/prepare/r-rcas/PKGBUILD b/prepare/r-rcas/PKGBUILD new file mode 100644 index 0000000000..abbfc5e0b2 --- /dev/null +++ b/prepare/r-rcas/PKGBUILD @@ -0,0 +1,57 @@ +# system requirements: pandoc (>= 1.12.3) +# Maintainer: Guoyi Zhang + +_pkgname=RCAS +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RNA Centric Annotation System' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biostrings + r-bsgenome + r-bsgenome.hsapiens.ucsc.hg19 + r-cowplot + r-data.table + r-dt + r-genomation + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggseqlogo + r-gprofiler2 + r-iranges + r-knitr + r-pbapply + r-pheatmap + r-plotly + r-plotrix + r-proxy + r-ranger + r-rmarkdown + r-rsqlite + r-rtracklayer + r-s4vectors +) +optdepends=( + r-covr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcas/lilac.py b/prepare/r-rcas/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcas/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcas/lilac.yaml b/prepare/r-rcas/lilac.yaml new file mode 100644 index 0000000000..555d6838af --- /dev/null +++ b/prepare/r-rcas/lilac.yaml @@ -0,0 +1,35 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-bsgenome.hsapiens.ucsc.hg19 +- r-cowplot +- r-data.table +- r-dt +- r-genomation +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-ggseqlogo +- r-gprofiler2 +- r-iranges +- r-knitr +- r-pbapply +- r-pheatmap +- r-plotly +- r-plotrix +- r-proxy +- r-ranger +- r-rmarkdown +- r-rsqlite +- r-rtracklayer +- r-s4vectors +update_on: +- regex: RCAS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RCAS diff --git a/prepare/r-rcaspar/PKGBUILD b/prepare/r-rcaspar/PKGBUILD new file mode 100644 index 0000000000..2b0c10af37 --- /dev/null +++ b/prepare/r-rcaspar/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RCASPAR +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A package for survival time prediction based on a piecewise baseline hazard Cox regression model.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcaspar/lilac.py b/prepare/r-rcaspar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcaspar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcaspar/lilac.yaml b/prepare/r-rcaspar/lilac.yaml new file mode 100644 index 0000000000..c9dbbda662 --- /dev/null +++ b/prepare/r-rcaspar/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RCASPAR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RCASPAR diff --git a/prepare/r-rcdk/PKGBUILD b/prepare/r-rcdk/PKGBUILD new file mode 100644 index 0000000000..c02a54d6d2 --- /dev/null +++ b/prepare/r-rcdk/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: Java JDK 8 or higher +# Maintainer: Guoyi Zhang + +_pkgname=rcdk +_pkgver=3.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Interface to the 'CDK' Libraries" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-fingerprint + r-iterators + r-itertools + r-png + r-rcdklibs + r-rjava +) +optdepends=( + r-devtools + r-knitr + r-rmarkdown + r-runit + r-xtable +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcdk/lilac.py b/prepare/r-rcdk/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcdk/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcdk/lilac.yaml b/prepare/r-rcdk/lilac.yaml new file mode 100644 index 0000000000..ad4b5692a0 --- /dev/null +++ b/prepare/r-rcdk/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fingerprint +- r-iterators +- r-itertools +- r-png +- r-rcdklibs +- r-rjava +update_on: +- regex: rcdk_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rcdk diff --git a/prepare/r-rcdklibs/PKGBUILD b/prepare/r-rcdklibs/PKGBUILD new file mode 100644 index 0000000000..592870f402 --- /dev/null +++ b/prepare/r-rcdklibs/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rcdklibs +_pkgver=2.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The CDK Libraries Packaged for R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-rjava +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcdklibs/lilac.py b/prepare/r-rcdklibs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcdklibs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcdklibs/lilac.yaml b/prepare/r-rcdklibs/lilac.yaml new file mode 100644 index 0000000000..d8687754a2 --- /dev/null +++ b/prepare/r-rcdklibs/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rjava +update_on: +- regex: rcdklibs_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rcdklibs diff --git a/prepare/r-rcellminer/PKGBUILD b/prepare/r-rcellminer/PKGBUILD new file mode 100644 index 0000000000..bad98fd19f --- /dev/null +++ b/prepare/r-rcellminer/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rcellminer +_pkgver=2.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-ggplot2 + r-gplots + r-rcellminerdata + r-shiny + r-stringr +) +optdepends=( + r-biocgenerics + r-biocstyle + r-dosnow + r-foreach + r-glmnet + r-heatmaply + r-jsonlite + r-knitr + r-parallel + r-rcolorbrewer + r-rmarkdown + r-sqldf + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcellminer/lilac.py b/prepare/r-rcellminer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcellminer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcellminer/lilac.yaml b/prepare/r-rcellminer/lilac.yaml new file mode 100644 index 0000000000..50e5faeac2 --- /dev/null +++ b/prepare/r-rcellminer/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-ggplot2 +- r-gplots +- r-rcellminerdata +- r-shiny +- r-stringr +update_on: +- regex: rcellminer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rcellminer diff --git a/prepare/r-rcellminerdata/PKGBUILD b/prepare/r-rcellminerdata/PKGBUILD new file mode 100644 index 0000000000..98c54b7efc --- /dev/null +++ b/prepare/r-rcellminerdata/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rcellminerData +_pkgver=2.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='rcellminerData: Molecular Profiles and Drug Response for the NCI-60 Cell Lines' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase +) +optdepends=( + r-biocstyle + r-knitr + r-rcellminer + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcellminerdata/lilac.py b/prepare/r-rcellminerdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcellminerdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcellminerdata/lilac.yaml b/prepare/r-rcellminerdata/lilac.yaml new file mode 100644 index 0000000000..c8cf0b1506 --- /dev/null +++ b/prepare/r-rcellminerdata/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: rcellminerData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rcellminerData diff --git a/prepare/r-rcgh/PKGBUILD b/prepare/r-rcgh/PKGBUILD new file mode 100644 index 0000000000..e634a1cd04 --- /dev/null +++ b/prepare/r-rcgh/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rCGH +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-acgh + r-affy + r-annotationdbi + r-dnacopy + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-limma + r-mclust + r-org.hs.eg.db + r-plyr + r-shiny + r-txdb.hsapiens.ucsc.hg18.knowngene + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.hsapiens.ucsc.hg38.knowngene +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcgh/lilac.py b/prepare/r-rcgh/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcgh/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcgh/lilac.yaml b/prepare/r-rcgh/lilac.yaml new file mode 100644 index 0000000000..61d9913df5 --- /dev/null +++ b/prepare/r-rcgh/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-acgh +- r-affy +- r-annotationdbi +- r-dnacopy +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-limma +- r-mclust +- r-org.hs.eg.db +- r-plyr +- r-shiny +- r-txdb.hsapiens.ucsc.hg18.knowngene +- r-txdb.hsapiens.ucsc.hg19.knowngene +- r-txdb.hsapiens.ucsc.hg38.knowngene +update_on: +- regex: rCGH_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rCGH diff --git a/prepare/r-rcgmin/PKGBUILD b/prepare/r-rcgmin/PKGBUILD new file mode 100644 index 0000000000..b3e5ea8ea4 --- /dev/null +++ b/prepare/r-rcgmin/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rcgmin +_pkgver=2013-2.21 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Conjugate Gradient Minimization of Nonlinear Functions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-numderiv +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcgmin/lilac.py b/prepare/r-rcgmin/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcgmin/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcgmin/lilac.yaml b/prepare/r-rcgmin/lilac.yaml new file mode 100644 index 0000000000..dff3b5a84d --- /dev/null +++ b/prepare/r-rcgmin/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-numderiv +update_on: +- regex: Rcgmin_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rcgmin diff --git a/prepare/r-rcircos/PKGBUILD b/prepare/r-rcircos/PKGBUILD new file mode 100644 index 0000000000..bbc80522b6 --- /dev/null +++ b/prepare/r-rcircos/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RCircos +_pkgver=1.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Circos 2D Track Plot' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcircos/lilac.py b/prepare/r-rcircos/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcircos/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcircos/lilac.yaml b/prepare/r-rcircos/lilac.yaml new file mode 100644 index 0000000000..88b73f282a --- /dev/null +++ b/prepare/r-rcircos/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RCircos_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RCircos diff --git a/prepare/r-rcistarget/PKGBUILD b/prepare/r-rcistarget/PKGBUILD new file mode 100644 index 0000000000..74986dd006 --- /dev/null +++ b/prepare/r-rcistarget/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RcisTarget +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-arrow + r-aucell + r-biocgenerics + r-data.table + r-dplyr + r-feather + r-genomeinfodb + r-genomicranges + r-gseabase + r-r.utils + r-summarizedexperiment + r-tibble +) +optdepends=( + r-biobase + r-biocparallel + r-biocstyle + r-domc + r-doparallel + r-dorng + r-dt + r-foreach + r-gplots + r-igraph + r-knitr + r-rcistarget.hg19.motifdbs.cisbponly.500bp + r-rmarkdown + r-rtracklayer + r-testthat + r-visnetwork + r-zoo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcistarget/lilac.py b/prepare/r-rcistarget/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcistarget/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcistarget/lilac.yaml b/prepare/r-rcistarget/lilac.yaml new file mode 100644 index 0000000000..653f4cfa4b --- /dev/null +++ b/prepare/r-rcistarget/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-arrow +- r-aucell +- r-biocgenerics +- r-data.table +- r-dplyr +- r-feather +- r-genomeinfodb +- r-genomicranges +- r-gseabase +- r-r.utils +- r-summarizedexperiment +- r-tibble +update_on: +- regex: RcisTarget_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RcisTarget diff --git a/prepare/r-rclipboard/PKGBUILD b/prepare/r-rclipboard/PKGBUILD new file mode 100644 index 0000000000..239a3cab36 --- /dev/null +++ b/prepare/r-rclipboard/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rclipboard +_pkgver=0.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Shiny/R Wrapper for 'clipboard.js'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-shiny +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rclipboard/lilac.py b/prepare/r-rclipboard/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rclipboard/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rclipboard/lilac.yaml b/prepare/r-rclipboard/lilac.yaml new file mode 100644 index 0000000000..25a47d3798 --- /dev/null +++ b/prepare/r-rclipboard/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-shiny +update_on: +- regex: rclipboard_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rclipboard diff --git a/prepare/r-rcm/PKGBUILD b/prepare/r-rcm/PKGBUILD new file mode 100644 index 0000000000..9b8c73cdb5 --- /dev/null +++ b/prepare/r-rcm/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RCM +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fit row-column association models with the negative binomial distribution for the microbiome' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-alabama + r-edger + r-ggplot2 + r-nleqslv + r-phyloseq + r-rcolorbrewer + r-reshape2 + r-tensor + r-tseries + r-vgam +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcm/lilac.py b/prepare/r-rcm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcm/lilac.yaml b/prepare/r-rcm/lilac.yaml new file mode 100644 index 0000000000..f1b53b002a --- /dev/null +++ b/prepare/r-rcm/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-alabama +- r-edger +- r-ggplot2 +- r-nleqslv +- r-phyloseq +- r-rcolorbrewer +- r-reshape2 +- r-tensor +- r-tseries +- r-vgam +update_on: +- regex: RCM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RCM diff --git a/prepare/r-rcmdcheck/PKGBUILD b/prepare/r-rcmdcheck/PKGBUILD new file mode 100644 index 0000000000..7fac3ff1f5 --- /dev/null +++ b/prepare/r-rcmdcheck/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rcmdcheck +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Run 'R CMD check' from 'R' and Capture Results" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-callr + r-cli + r-curl + r-desc + r-digest + r-pkgbuild + r-prettyunits + r-r6 + r-rprojroot + r-sessioninfo + r-withr + r-xopen +) +optdepends=( + r-covr + r-knitr + r-mockery + r-processx + r-ps + r-rmarkdown + r-svglite + r-testthat + r-webfakes +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcmdcheck/lilac.py b/prepare/r-rcmdcheck/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcmdcheck/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcmdcheck/lilac.yaml b/prepare/r-rcmdcheck/lilac.yaml new file mode 100644 index 0000000000..71e07f5234 --- /dev/null +++ b/prepare/r-rcmdcheck/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-callr +- r-cli +- r-curl +- r-desc +- r-digest +- r-pkgbuild +- r-prettyunits +- r-r6 +- r-rprojroot +- r-sessioninfo +- r-withr +- r-xopen +update_on: +- regex: rcmdcheck_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rcmdcheck diff --git a/prepare/r-rcmdrmisc/PKGBUILD b/prepare/r-rcmdrmisc/PKGBUILD new file mode 100644 index 0000000000..d521ead93d --- /dev/null +++ b/prepare/r-rcmdrmisc/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RcmdrMisc +_pkgver=2.7-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Commander Miscellaneous Functions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-car + r-colorspace + r-e1071 + r-haven + r-hmisc + r-nortest + r-readstata13 + r-readxl + r-sandwich +) +optdepends=( + r-boot + r-cardata + r-datasets +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcmdrmisc/lilac.py b/prepare/r-rcmdrmisc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcmdrmisc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcmdrmisc/lilac.yaml b/prepare/r-rcmdrmisc/lilac.yaml new file mode 100644 index 0000000000..0399c5f711 --- /dev/null +++ b/prepare/r-rcmdrmisc/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-car +- r-colorspace +- r-e1071 +- r-haven +- r-hmisc +- r-nortest +- r-readstata13 +- r-readxl +- r-sandwich +update_on: +- regex: RcmdrMisc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RcmdrMisc diff --git a/prepare/r-rcolorbrewer/PKGBUILD b/prepare/r-rcolorbrewer/PKGBUILD new file mode 100644 index 0000000000..e27c752a78 --- /dev/null +++ b/prepare/r-rcolorbrewer/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RColorBrewer +_pkgver=1.1-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ColorBrewer Palettes' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcolorbrewer/lilac.py b/prepare/r-rcolorbrewer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcolorbrewer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcolorbrewer/lilac.yaml b/prepare/r-rcolorbrewer/lilac.yaml new file mode 100644 index 0000000000..1f79d10b9e --- /dev/null +++ b/prepare/r-rcolorbrewer/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RColorBrewer_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RColorBrewer diff --git a/prepare/r-rcpi/PKGBUILD b/prepare/r-rcpi/PKGBUILD new file mode 100644 index 0000000000..fe4875d8ba --- /dev/null +++ b/prepare/r-rcpi/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rcpi +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-chemminer + r-doparallel + r-fmcsr + r-foreach + r-gosemsim + r-rcdk + r-rcurl + r-rjson +) +optdepends=( + r-biocgenerics + r-chemmineob + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcpi/lilac.py b/prepare/r-rcpi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcpi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcpi/lilac.yaml b/prepare/r-rcpi/lilac.yaml new file mode 100644 index 0000000000..c3338b4a71 --- /dev/null +++ b/prepare/r-rcpi/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-chemminer +- r-doparallel +- r-fmcsr +- r-foreach +- r-gosemsim +- r-rcdk +- r-rcurl +- r-rjson +update_on: +- regex: Rcpi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rcpi diff --git a/prepare/r-rcpp/PKGBUILD b/prepare/r-rcpp/PKGBUILD new file mode 100644 index 0000000000..c1d3251990 --- /dev/null +++ b/prepare/r-rcpp/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rcpp +_pkgver=1.0.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Seamless R and C++ Integration' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-inline + r-pkgkitten + r-rbenchmark + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcpp/lilac.py b/prepare/r-rcpp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcpp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcpp/lilac.yaml b/prepare/r-rcpp/lilac.yaml new file mode 100644 index 0000000000..32bdd7496d --- /dev/null +++ b/prepare/r-rcpp/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Rcpp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rcpp diff --git a/prepare/r-rcppalgos/PKGBUILD b/prepare/r-rcppalgos/PKGBUILD new file mode 100644 index 0000000000..78e6d4bda3 --- /dev/null +++ b/prepare/r-rcppalgos/PKGBUILD @@ -0,0 +1,38 @@ +# system requirements: C++11, gmp (>= 4.2.3) +# Maintainer: Guoyi Zhang + +_pkgname=RcppAlgos +_pkgver=2.4.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='High Performance Tools for Combinatorics and Computational Mathematics' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-gmp + r-rcpp + r-rcppthread +) +optdepends=( + r-knitr + r-microbenchmark + r-numbers + r-rcppbigintalgos + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcppalgos/lilac.py b/prepare/r-rcppalgos/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcppalgos/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcppalgos/lilac.yaml b/prepare/r-rcppalgos/lilac.yaml new file mode 100644 index 0000000000..0c466f23b9 --- /dev/null +++ b/prepare/r-rcppalgos/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gmp +- r-rcpp +- r-rcppthread +update_on: +- regex: RcppAlgos_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RcppAlgos diff --git a/prepare/r-rcppannoy/PKGBUILD b/prepare/r-rcppannoy/PKGBUILD new file mode 100644 index 0000000000..054a3c50ec --- /dev/null +++ b/prepare/r-rcppannoy/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RcppAnnoy +_pkgver=0.0.19 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest Neighbors" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcppannoy/lilac.py b/prepare/r-rcppannoy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcppannoy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcppannoy/lilac.yaml b/prepare/r-rcppannoy/lilac.yaml new file mode 100644 index 0000000000..c511eb6645 --- /dev/null +++ b/prepare/r-rcppannoy/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: RcppAnnoy_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RcppAnnoy diff --git a/prepare/r-rcpparmadillo/PKGBUILD b/prepare/r-rcpparmadillo/PKGBUILD new file mode 100644 index 0000000000..9f9d0c89c0 --- /dev/null +++ b/prepare/r-rcpparmadillo/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RcppArmadillo +_pkgver=0.10.7.5.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-matrix + r-pkgkitten + r-reticulate + r-slam + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcpparmadillo/lilac.py b/prepare/r-rcpparmadillo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcpparmadillo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcpparmadillo/lilac.yaml b/prepare/r-rcpparmadillo/lilac.yaml new file mode 100644 index 0000000000..f3095549e6 --- /dev/null +++ b/prepare/r-rcpparmadillo/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: RcppArmadillo_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RcppArmadillo diff --git a/prepare/r-rcppcctz/PKGBUILD b/prepare/r-rcppcctz/PKGBUILD new file mode 100644 index 0000000000..7e4c914e88 --- /dev/null +++ b/prepare/r-rcppcctz/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: A 64-bit POSIX OS such as Linux or OS X with IANAtime zone data in /usr/share/zoneinfo as well as arecent-enough C++11 compiler (such as g++-4.9 or later which ispreferred, g++-4.8 works too). On Windows the zoneinfo includedwith R is used; and time parsing support is enabled via abackport of std::get_time from the LLVM libc++ library. +# Maintainer: Guoyi Zhang + +_pkgname=RcppCCTZ +_pkgver=0.2.10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'Rcpp' Bindings for the 'CCTZ' Library" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcppcctz/lilac.py b/prepare/r-rcppcctz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcppcctz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcppcctz/lilac.yaml b/prepare/r-rcppcctz/lilac.yaml new file mode 100644 index 0000000000..d6a0f56e3e --- /dev/null +++ b/prepare/r-rcppcctz/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: RcppCCTZ_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RcppCCTZ diff --git a/prepare/r-rcppdate/PKGBUILD b/prepare/r-rcppdate/PKGBUILD new file mode 100644 index 0000000000..bfbe6616a9 --- /dev/null +++ b/prepare/r-rcppdate/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RcppDate +_pkgver=0.0.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'date' C++ Header Library for Date and Time Functionality" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-rcpp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcppdate/lilac.py b/prepare/r-rcppdate/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcppdate/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcppdate/lilac.yaml b/prepare/r-rcppdate/lilac.yaml new file mode 100644 index 0000000000..fdec5ec815 --- /dev/null +++ b/prepare/r-rcppdate/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RcppDate_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RcppDate diff --git a/prepare/r-rcppdist/PKGBUILD b/prepare/r-rcppdist/PKGBUILD new file mode 100644 index 0000000000..1b9cfdefcc --- /dev/null +++ b/prepare/r-rcppdist/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RcppDist +_pkgver=0.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'Rcpp' Integration of Additional Probability Distributions" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcppdist/lilac.py b/prepare/r-rcppdist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcppdist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcppdist/lilac.yaml b/prepare/r-rcppdist/lilac.yaml new file mode 100644 index 0000000000..34985ad34b --- /dev/null +++ b/prepare/r-rcppdist/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: RcppDist_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RcppDist diff --git a/prepare/r-rcppeigen/PKGBUILD b/prepare/r-rcppeigen/PKGBUILD new file mode 100644 index 0000000000..7c19321cd1 --- /dev/null +++ b/prepare/r-rcppeigen/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RcppEigen +_pkgver=0.3.3.9.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-inline + r-microbenchmark + r-pkgkitten + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcppeigen/lilac.py b/prepare/r-rcppeigen/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcppeigen/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcppeigen/lilac.yaml b/prepare/r-rcppeigen/lilac.yaml new file mode 100644 index 0000000000..56a9e99cfa --- /dev/null +++ b/prepare/r-rcppeigen/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: RcppEigen_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RcppEigen diff --git a/prepare/r-rcppgsl/PKGBUILD b/prepare/r-rcppgsl/PKGBUILD new file mode 100644 index 0000000000..9cb3457bc8 --- /dev/null +++ b/prepare/r-rcppgsl/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: GNU GSL +# Maintainer: Guoyi Zhang + +_pkgname=RcppGSL +_pkgver=0.3.10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'Rcpp' Integration for 'GNU GSL' Vectors and Matrices" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcppgsl/lilac.py b/prepare/r-rcppgsl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcppgsl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcppgsl/lilac.yaml b/prepare/r-rcppgsl/lilac.yaml new file mode 100644 index 0000000000..160291426a --- /dev/null +++ b/prepare/r-rcppgsl/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: RcppGSL_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RcppGSL diff --git a/prepare/r-rcpphnsw/PKGBUILD b/prepare/r-rcpphnsw/PKGBUILD new file mode 100644 index 0000000000..da1c690854 --- /dev/null +++ b/prepare/r-rcpphnsw/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RcppHNSW +_pkgver=0.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'Rcpp' Bindings for 'hnswlib', a Library for Approximate Nearest Neighbors" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcpphnsw/lilac.py b/prepare/r-rcpphnsw/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcpphnsw/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcpphnsw/lilac.yaml b/prepare/r-rcpphnsw/lilac.yaml new file mode 100644 index 0000000000..9acdb258f1 --- /dev/null +++ b/prepare/r-rcpphnsw/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: RcppHNSW_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RcppHNSW diff --git a/prepare/r-rcppnumerical/PKGBUILD b/prepare/r-rcppnumerical/PKGBUILD new file mode 100644 index 0000000000..1bddff999c --- /dev/null +++ b/prepare/r-rcppnumerical/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RcppNumerical +_pkgver=0.4-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'Rcpp' Integration for Numerical Computing Libraries" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcppeigen +) +optdepends=( + r-knitr + r-mvtnorm + r-prettydoc + r-rcppeigen + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcppnumerical/lilac.py b/prepare/r-rcppnumerical/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcppnumerical/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcppnumerical/lilac.yaml b/prepare/r-rcppnumerical/lilac.yaml new file mode 100644 index 0000000000..a5e06865d7 --- /dev/null +++ b/prepare/r-rcppnumerical/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcppeigen +update_on: +- regex: RcppNumerical_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RcppNumerical diff --git a/prepare/r-rcppparallel/PKGBUILD b/prepare/r-rcppparallel/PKGBUILD new file mode 100644 index 0000000000..3e83e27731 --- /dev/null +++ b/prepare/r-rcppparallel/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: GNU make, Intel TBB, Windows: cmd.exe andcscript.exe, Solaris: g++ is required +# Maintainer: Guoyi Zhang + +_pkgname=RcppParallel +_pkgver=5.1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Parallel Programming Tools for 'Rcpp'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rcpp + r-rmarkdown + r-runit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcppparallel/lilac.py b/prepare/r-rcppparallel/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcppparallel/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcppparallel/lilac.yaml b/prepare/r-rcppparallel/lilac.yaml new file mode 100644 index 0000000000..3224072975 --- /dev/null +++ b/prepare/r-rcppparallel/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RcppParallel_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RcppParallel diff --git a/prepare/r-rcppprogress/PKGBUILD b/prepare/r-rcppprogress/PKGBUILD new file mode 100644 index 0000000000..7f2e7ddbb4 --- /dev/null +++ b/prepare/r-rcppprogress/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RcppProgress +_pkgver=0.4.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Interruptible Progress Bar with OpenMP Support for C++ in R Packages' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-devtools + r-rcpparmadillo + r-roxygen2 + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcppprogress/lilac.py b/prepare/r-rcppprogress/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcppprogress/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcppprogress/lilac.yaml b/prepare/r-rcppprogress/lilac.yaml new file mode 100644 index 0000000000..f6f6ac454f --- /dev/null +++ b/prepare/r-rcppprogress/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RcppProgress_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RcppProgress diff --git a/prepare/r-rcpproll/PKGBUILD b/prepare/r-rcpproll/PKGBUILD new file mode 100644 index 0000000000..d28af535f3 --- /dev/null +++ b/prepare/r-rcpproll/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RcppRoll +_pkgver=0.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Efficient Rolling / Windowed Operations' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-testthat + r-zoo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcpproll/lilac.py b/prepare/r-rcpproll/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcpproll/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcpproll/lilac.yaml b/prepare/r-rcpproll/lilac.yaml new file mode 100644 index 0000000000..89efbb28d0 --- /dev/null +++ b/prepare/r-rcpproll/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: RcppRoll_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RcppRoll diff --git a/prepare/r-rcppthread/PKGBUILD b/prepare/r-rcppthread/PKGBUILD new file mode 100644 index 0000000000..976a273665 --- /dev/null +++ b/prepare/r-rcppthread/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=RcppThread +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R-Friendly Threading in C++' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-r.rsp + r-rcpp + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcppthread/lilac.py b/prepare/r-rcppthread/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcppthread/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcppthread/lilac.yaml b/prepare/r-rcppthread/lilac.yaml new file mode 100644 index 0000000000..2723f7b57d --- /dev/null +++ b/prepare/r-rcppthread/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RcppThread_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RcppThread diff --git a/prepare/r-rcppziggurat/PKGBUILD b/prepare/r-rcppziggurat/PKGBUILD new file mode 100644 index 0000000000..fe17e7a491 --- /dev/null +++ b/prepare/r-rcppziggurat/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RcppZiggurat +_pkgver=0.1.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'Rcpp' Integration of Different "Ziggurat" Normal RNG Implementations" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcppgsl +) +optdepends=( + r-knitr + r-lattice + r-microbenchmark + r-pinp + r-rbenchmark + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcppziggurat/lilac.py b/prepare/r-rcppziggurat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcppziggurat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcppziggurat/lilac.yaml b/prepare/r-rcppziggurat/lilac.yaml new file mode 100644 index 0000000000..45127d04d0 --- /dev/null +++ b/prepare/r-rcppziggurat/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcppgsl +update_on: +- regex: RcppZiggurat_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RcppZiggurat diff --git a/prepare/r-rcsl/PKGBUILD b/prepare/r-rcsl/PKGBUILD new file mode 100644 index 0000000000..9677658cd2 --- /dev/null +++ b/prepare/r-rcsl/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RCSL +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Rank Constrained Similarity Learning for single cell RNA sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-igraph + r-nbclust + r-pracma + r-rcppannoy + r-rtsne + r-umap +) +optdepends=( + r-knitr + r-mclust + r-rcppannoy + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcsl/lilac.py b/prepare/r-rcsl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcsl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcsl/lilac.yaml b/prepare/r-rcsl/lilac.yaml new file mode 100644 index 0000000000..bbdc184ea7 --- /dev/null +++ b/prepare/r-rcsl/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-igraph +- r-nbclust +- r-pracma +- r-rcppannoy +- r-rtsne +- r-umap +update_on: +- regex: RCSL_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RCSL diff --git a/prepare/r-rcwl/PKGBUILD b/prepare/r-rcwl/PKGBUILD new file mode 100644 index 0000000000..b0790ecfdb --- /dev/null +++ b/prepare/r-rcwl/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rcwl +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R interface to the Common Workflow Language' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-basilisk + r-batchtools + r-biocparallel + r-diagrammer + r-r.utils + r-s4vectors + r-shiny + r-yaml +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcwl/lilac.py b/prepare/r-rcwl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcwl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcwl/lilac.yaml b/prepare/r-rcwl/lilac.yaml new file mode 100644 index 0000000000..7f207b9277 --- /dev/null +++ b/prepare/r-rcwl/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-basilisk +- r-batchtools +- r-biocparallel +- r-diagrammer +- r-r.utils +- r-s4vectors +- r-shiny +- r-yaml +update_on: +- regex: Rcwl_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rcwl diff --git a/prepare/r-rcwlpipelines/PKGBUILD b/prepare/r-rcwlpipelines/PKGBUILD new file mode 100644 index 0000000000..f53e41900b --- /dev/null +++ b/prepare/r-rcwlpipelines/PKGBUILD @@ -0,0 +1,39 @@ +# system requirements: nodejs +# Maintainer: Guoyi Zhang + +_pkgname=RcwlPipelines +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bioinformatics pipelines based on Rcwl' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocfilecache + r-git2r + r-httr + r-rappdirs + r-rcwl + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcwlpipelines/lilac.py b/prepare/r-rcwlpipelines/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcwlpipelines/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcwlpipelines/lilac.yaml b/prepare/r-rcwlpipelines/lilac.yaml new file mode 100644 index 0000000000..a903a5c843 --- /dev/null +++ b/prepare/r-rcwlpipelines/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-git2r +- r-httr +- r-rappdirs +- r-rcwl +- r-s4vectors +update_on: +- regex: RcwlPipelines_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RcwlPipelines diff --git a/prepare/r-rcy3/PKGBUILD b/prepare/r-rcy3/PKGBUILD new file mode 100644 index 0000000000..117af950af --- /dev/null +++ b/prepare/r-rcy3/PKGBUILD @@ -0,0 +1,50 @@ +# system requirements: Cytoscape (>= 3.7.1), CyREST (>= 3.8.0) +# Maintainer: Guoyi Zhang + +_pkgname=RCy3 +_pkgver=2.14.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions to Access and Control Cytoscape' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-base64enc + r-base64url + r-biocgenerics + r-fs + r-glue + r-graph + r-httr + r-irdisplay + r-irkernel + r-rcolorbrewer + r-rcurl + r-rjsonio + r-uchardet + r-uuid + r-xml +) +optdepends=( + r-biocstyle + r-grdevices + r-igraph + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcy3/lilac.py b/prepare/r-rcy3/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcy3/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcy3/lilac.yaml b/prepare/r-rcy3/lilac.yaml new file mode 100644 index 0000000000..90f03a8367 --- /dev/null +++ b/prepare/r-rcy3/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-base64url +- r-biocgenerics +- r-fs +- r-glue +- r-graph +- r-httr +- r-irdisplay +- r-irkernel +- r-rcolorbrewer +- r-rcurl +- r-rjsonio +- r-uchardet +- r-uuid +- r-xml +update_on: +- regex: RCy3_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RCy3 diff --git a/prepare/r-rcyjs/PKGBUILD b/prepare/r-rcyjs/PKGBUILD new file mode 100644 index 0000000000..04a3d24c35 --- /dev/null +++ b/prepare/r-rcyjs/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RCyjs +_pkgver=2.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Display and manipulate graphs in cytoscape.js' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-base64enc + r-biocgenerics + r-browserviz + r-graph + r-httpuv +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rcyjs/lilac.py b/prepare/r-rcyjs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rcyjs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rcyjs/lilac.yaml b/prepare/r-rcyjs/lilac.yaml new file mode 100644 index 0000000000..6c399c7d09 --- /dev/null +++ b/prepare/r-rcyjs/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-biocgenerics +- r-browserviz +- r-graph +- r-httpuv +update_on: +- regex: RCyjs_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RCyjs diff --git a/prepare/r-rdgidb/PKGBUILD b/prepare/r-rdgidb/PKGBUILD new file mode 100644 index 0000000000..4f78be0f5e --- /dev/null +++ b/prepare/r-rdgidb/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rDGIdb +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Wrapper for DGIdb' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-httr + r-jsonlite +) +optdepends=( + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rdgidb/lilac.py b/prepare/r-rdgidb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rdgidb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rdgidb/lilac.yaml b/prepare/r-rdgidb/lilac.yaml new file mode 100644 index 0000000000..07504dc425 --- /dev/null +++ b/prepare/r-rdgidb/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-httr +- r-jsonlite +update_on: +- regex: rDGIdb_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rDGIdb diff --git a/prepare/r-rdisop/PKGBUILD b/prepare/r-rdisop/PKGBUILD new file mode 100644 index 0000000000..bfaa8fa5e3 --- /dev/null +++ b/prepare/r-rdisop/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: None +# Maintainer: Guoyi Zhang + +_pkgname=Rdisop +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Decomposition of Isotopic Patterns' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rdisop/lilac.py b/prepare/r-rdisop/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rdisop/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rdisop/lilac.yaml b/prepare/r-rdisop/lilac.yaml new file mode 100644 index 0000000000..49e16bb89d --- /dev/null +++ b/prepare/r-rdisop/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: Rdisop_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rdisop diff --git a/prepare/r-rdpack/PKGBUILD b/prepare/r-rdpack/PKGBUILD new file mode 100644 index 0000000000..e27a2610ca --- /dev/null +++ b/prepare/r-rdpack/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rdpack +_pkgver=2.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Update and Manipulate Rd Documentation Objects' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rbibutils +) +optdepends=( + r-gbrd + r-grdevices + r-rprojroot + r-rstudioapi + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rdpack/lilac.py b/prepare/r-rdpack/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rdpack/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rdpack/lilac.yaml b/prepare/r-rdpack/lilac.yaml new file mode 100644 index 0000000000..5dce165132 --- /dev/null +++ b/prepare/r-rdpack/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rbibutils +update_on: +- regex: Rdpack_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rdpack diff --git a/prepare/r-rdrtoolbox/PKGBUILD b/prepare/r-rdrtoolbox/PKGBUILD new file mode 100644 index 0000000000..36aef2692f --- /dev/null +++ b/prepare/r-rdrtoolbox/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RDRToolbox +_pkgver=1.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A package for nonlinear dimension reduction with Isomap and LLE.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rgl +) +optdepends=( + r-golubesets +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rdrtoolbox/lilac.py b/prepare/r-rdrtoolbox/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rdrtoolbox/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rdrtoolbox/lilac.yaml b/prepare/r-rdrtoolbox/lilac.yaml new file mode 100644 index 0000000000..7c62d2d16d --- /dev/null +++ b/prepare/r-rdrtoolbox/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rgl +update_on: +- regex: RDRToolbox_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RDRToolbox diff --git a/prepare/r-reactable/PKGBUILD b/prepare/r-reactable/PKGBUILD new file mode 100644 index 0000000000..066e1fc728 --- /dev/null +++ b/prepare/r-reactable/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=reactable +_pkgver=0.2.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Interactive Data Tables Based on 'React Table'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-digest + r-htmltools + r-htmlwidgets + r-jsonlite + r-reactr +) +optdepends=( + r-covr + r-crosstalk + r-dplyr + r-leaflet + r-mass + r-rmarkdown + r-shiny + r-sparkline + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reactable/lilac.py b/prepare/r-reactable/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reactable/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reactable/lilac.yaml b/prepare/r-reactable/lilac.yaml new file mode 100644 index 0000000000..3ce02c3410 --- /dev/null +++ b/prepare/r-reactable/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-htmltools +- r-htmlwidgets +- r-jsonlite +- r-reactr +update_on: +- regex: reactable_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=reactable diff --git a/prepare/r-reactome.db/PKGBUILD b/prepare/r-reactome.db/PKGBUILD new file mode 100644 index 0000000000..91dd47e5bb --- /dev/null +++ b/prepare/r-reactome.db/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=reactome.db +_pkgver=1.77.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A set of annotation maps for reactome' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CCPL:by-nc-sa') +depends=( + r + r-annotationdbi +) +optdepends=( + r-rsqlite +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reactome.db/lilac.py b/prepare/r-reactome.db/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reactome.db/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reactome.db/lilac.yaml b/prepare/r-reactome.db/lilac.yaml new file mode 100644 index 0000000000..04dc81ba18 --- /dev/null +++ b/prepare/r-reactome.db/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +update_on: +- regex: reactome.db_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/reactome.db diff --git a/prepare/r-reactomecontentservice4r/PKGBUILD b/prepare/r-reactomecontentservice4r/PKGBUILD new file mode 100644 index 0000000000..d7f6d43588 --- /dev/null +++ b/prepare/r-reactomecontentservice4r/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ReactomeContentService4R +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interface for the Reactome Content Service' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Apache') +depends=( + r + r-data.table + r-doparallel + r-foreach + r-httr + r-jsonlite + r-magick +) +optdepends=( + r-knitr + r-pdftools + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reactomecontentservice4r/lilac.py b/prepare/r-reactomecontentservice4r/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reactomecontentservice4r/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reactomecontentservice4r/lilac.yaml b/prepare/r-reactomecontentservice4r/lilac.yaml new file mode 100644 index 0000000000..5d38bd7ffe --- /dev/null +++ b/prepare/r-reactomecontentservice4r/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-doparallel +- r-foreach +- r-httr +- r-jsonlite +- r-magick +update_on: +- regex: ReactomeContentService4R_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ReactomeContentService4R diff --git a/prepare/r-reactomegraph4r/PKGBUILD b/prepare/r-reactomegraph4r/PKGBUILD new file mode 100644 index 0000000000..e7fe0549cb --- /dev/null +++ b/prepare/r-reactomegraph4r/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ReactomeGraph4R +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interface for the Reactome Graph Database' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Apache') +depends=( + r + r-data.table + r-doparallel + r-foreach + r-getpass + r-jsonlite + r-magrittr + r-neo4r + r-purrr + r-reactomecontentservice4r + r-rlang +) +optdepends=( + r-knitr + r-networkd3 + r-rmarkdown + r-stringr + r-testthat + r-visnetwork + r-wesanderson +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reactomegraph4r/lilac.py b/prepare/r-reactomegraph4r/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reactomegraph4r/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reactomegraph4r/lilac.yaml b/prepare/r-reactomegraph4r/lilac.yaml new file mode 100644 index 0000000000..59aee12240 --- /dev/null +++ b/prepare/r-reactomegraph4r/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-doparallel +- r-foreach +- r-getpass +- r-jsonlite +- r-magrittr +- r-neo4r +- r-purrr +- r-reactomecontentservice4r +- r-rlang +update_on: +- regex: ReactomeGraph4R_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ReactomeGraph4R diff --git a/prepare/r-reactomegsa/PKGBUILD b/prepare/r-reactomegsa/PKGBUILD new file mode 100644 index 0000000000..9e5bb22ffd --- /dev/null +++ b/prepare/r-reactomegsa/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ReactomeGSA +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Client for the Reactome Analysis Service for comparative multi-omics gene set analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-ggplot2 + r-gplots + r-httr + r-jsonlite + r-progress + r-rcolorbrewer + r-tidyr +) +optdepends=( + r-biobase + r-devtools + r-edger + r-knitr + r-limma + r-reactomegsa.data + r-rmarkdown + r-scater + r-seurat + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reactomegsa/lilac.py b/prepare/r-reactomegsa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reactomegsa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reactomegsa/lilac.yaml b/prepare/r-reactomegsa/lilac.yaml new file mode 100644 index 0000000000..cc13cfaac0 --- /dev/null +++ b/prepare/r-reactomegsa/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-gplots +- r-httr +- r-jsonlite +- r-progress +- r-rcolorbrewer +- r-tidyr +update_on: +- regex: ReactomeGSA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ReactomeGSA diff --git a/prepare/r-reactomepa/PKGBUILD b/prepare/r-reactomepa/PKGBUILD new file mode 100644 index 0000000000..2be6173d99 --- /dev/null +++ b/prepare/r-reactomepa/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ReactomePA +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Reactome Pathway Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-dose + r-enrichplot + r-ggplot2 + r-ggraph + r-graphite + r-igraph + r-reactome.db +) +optdepends=( + r-biocstyle + r-clusterprofiler + r-knitr + r-org.hs.eg.db + r-prettydoc + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reactomepa/lilac.py b/prepare/r-reactomepa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reactomepa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reactomepa/lilac.yaml b/prepare/r-reactomepa/lilac.yaml new file mode 100644 index 0000000000..1e22df7b7a --- /dev/null +++ b/prepare/r-reactomepa/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-dose +- r-enrichplot +- r-ggplot2 +- r-ggraph +- r-graphite +- r-igraph +- r-reactome.db +update_on: +- regex: ReactomePA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ReactomePA diff --git a/prepare/r-reactr/PKGBUILD b/prepare/r-reactr/PKGBUILD new file mode 100644 index 0000000000..5333d1b936 --- /dev/null +++ b/prepare/r-reactr/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=reactR +_pkgver=0.4.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='React Helpers' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmltools +) +optdepends=( + r-htmlwidgets + r-jsonlite + r-knitr + r-rmarkdown + r-shiny + r-usethis + r-v8 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reactr/lilac.py b/prepare/r-reactr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reactr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reactr/lilac.yaml b/prepare/r-reactr/lilac.yaml new file mode 100644 index 0000000000..52f79bcab5 --- /dev/null +++ b/prepare/r-reactr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +update_on: +- regex: reactR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=reactR diff --git a/prepare/r-readbitmap/PKGBUILD b/prepare/r-readbitmap/PKGBUILD new file mode 100644 index 0000000000..cc97e0ceb0 --- /dev/null +++ b/prepare/r-readbitmap/PKGBUILD @@ -0,0 +1,35 @@ +# system requirements: libjpeg, libpng +# Maintainer: Guoyi Zhang + +_pkgname=readbitmap +_pkgver=0.1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Simple Unified Interface to Read Bitmap Images (BMP,JPEG,PNG,TIFF)' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bmp + r-jpeg + r-png + r-tiff +) +optdepends=( + r-pixmap + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-readbitmap/lilac.py b/prepare/r-readbitmap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-readbitmap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-readbitmap/lilac.yaml b/prepare/r-readbitmap/lilac.yaml new file mode 100644 index 0000000000..8213b4be45 --- /dev/null +++ b/prepare/r-readbitmap/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bmp +- r-jpeg +- r-png +- r-tiff +update_on: +- regex: readbitmap_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=readbitmap diff --git a/prepare/r-reader/PKGBUILD b/prepare/r-reader/PKGBUILD new file mode 100644 index 0000000000..1022a753fd --- /dev/null +++ b/prepare/r-reader/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=reader +_pkgver=1.0.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Suite of Functions to Flexibly Read Data from Files' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ncmisc +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reader/lilac.py b/prepare/r-reader/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reader/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reader/lilac.yaml b/prepare/r-reader/lilac.yaml new file mode 100644 index 0000000000..2d761817cf --- /dev/null +++ b/prepare/r-reader/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ncmisc +update_on: +- regex: reader_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=reader diff --git a/prepare/r-readqpcr/PKGBUILD b/prepare/r-readqpcr/PKGBUILD new file mode 100644 index 0000000000..e63dc3a28b --- /dev/null +++ b/prepare/r-readqpcr/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ReadqPCR +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Read qPCR data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase +) +optdepends=( + r-qpcr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-readqpcr/lilac.py b/prepare/r-readqpcr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-readqpcr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-readqpcr/lilac.yaml b/prepare/r-readqpcr/lilac.yaml new file mode 100644 index 0000000000..ea1c27e641 --- /dev/null +++ b/prepare/r-readqpcr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: ReadqPCR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ReadqPCR diff --git a/prepare/r-readr/PKGBUILD b/prepare/r-readr/PKGBUILD new file mode 100644 index 0000000000..aeb9059551 --- /dev/null +++ b/prepare/r-readr/PKGBUILD @@ -0,0 +1,53 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=readr +_pkgver=2.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Read Rectangular Text Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-cli + r-clipr + r-cpp11 + r-crayon + r-hms + r-lifecycle + r-r6 + r-rlang + r-tibble + r-tzdb + r-vroom +) +optdepends=( + r-covr + r-curl + r-datasets + r-knitr + r-rmarkdown + r-spelling + r-stringi + r-testthat + r-tzdb + r-waldo + r-withr + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-readr/lilac.py b/prepare/r-readr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-readr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-readr/lilac.yaml b/prepare/r-readr/lilac.yaml new file mode 100644 index 0000000000..213f5e70f9 --- /dev/null +++ b/prepare/r-readr/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cli +- r-clipr +- r-cpp11 +- r-crayon +- r-hms +- r-lifecycle +- r-r6 +- r-rlang +- r-tibble +- r-tzdb +- r-vroom +update_on: +- regex: readr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=readr diff --git a/prepare/r-readstata13/PKGBUILD b/prepare/r-readstata13/PKGBUILD new file mode 100644 index 0000000000..d4aceb20ba --- /dev/null +++ b/prepare/r-readstata13/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=readstata13 +_pkgver=0.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Import 'Stata' Data Files" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-readstata13/lilac.py b/prepare/r-readstata13/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-readstata13/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-readstata13/lilac.yaml b/prepare/r-readstata13/lilac.yaml new file mode 100644 index 0000000000..098ddc02ea --- /dev/null +++ b/prepare/r-readstata13/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: readstata13_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=readstata13 diff --git a/prepare/r-readxl/PKGBUILD b/prepare/r-readxl/PKGBUILD new file mode 100644 index 0000000000..7572c2368d --- /dev/null +++ b/prepare/r-readxl/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=readxl +_pkgver=1.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Read Excel Files' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-cellranger + r-progress + r-rcpp + r-tibble +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-rprojroot + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-readxl/lilac.py b/prepare/r-readxl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-readxl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-readxl/lilac.yaml b/prepare/r-readxl/lilac.yaml new file mode 100644 index 0000000000..c3297307ea --- /dev/null +++ b/prepare/r-readxl/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cellranger +- r-progress +- r-rcpp +- r-tibble +update_on: +- regex: readxl_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=readxl diff --git a/prepare/r-rebet/PKGBUILD b/prepare/r-rebet/PKGBUILD new file mode 100644 index 0000000000..133a274b26 --- /dev/null +++ b/prepare/r-rebet/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=REBET +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The subREgion-based BurdEn Test (REBET)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-asset +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rebet/lilac.py b/prepare/r-rebet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rebet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rebet/lilac.yaml b/prepare/r-rebet/lilac.yaml new file mode 100644 index 0000000000..4b7ef9be17 --- /dev/null +++ b/prepare/r-rebet/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-asset +update_on: +- regex: REBET_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/REBET diff --git a/prepare/r-rebook/PKGBUILD b/prepare/r-rebook/PKGBUILD new file mode 100644 index 0000000000..91324ddb49 --- /dev/null +++ b/prepare/r-rebook/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rebook +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Re-using Content in Bioconductor Books' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocstyle + r-codedepends + r-dir.expiry + r-filelock + r-knitr + r-rmarkdown +) +optdepends=( + r-biocmanager + r-biocparallel + r-bookdown + r-igraph + r-osca.intro + r-osca.workflows + r-rappdirs + r-rcurl + r-testthat + r-xml + r-yaml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rebook/lilac.py b/prepare/r-rebook/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rebook/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rebook/lilac.yaml b/prepare/r-rebook/lilac.yaml new file mode 100644 index 0000000000..bb1246368f --- /dev/null +++ b/prepare/r-rebook/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocstyle +- r-codedepends +- r-dir.expiry +- r-filelock +- r-knitr +- r-rmarkdown +update_on: +- regex: rebook_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rebook diff --git a/prepare/r-rebus.base/PKGBUILD b/prepare/r-rebus.base/PKGBUILD new file mode 100644 index 0000000000..0a0eac902d --- /dev/null +++ b/prepare/r-rebus.base/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rebus.base +_pkgver=0.0-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Core Functionality for the 'rebus' Package" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Unlimited') +depends=( + r +) +optdepends=( + r-stringi + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rebus.base/lilac.py b/prepare/r-rebus.base/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rebus.base/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rebus.base/lilac.yaml b/prepare/r-rebus.base/lilac.yaml new file mode 100644 index 0000000000..67d73a7452 --- /dev/null +++ b/prepare/r-rebus.base/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: rebus.base_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rebus.base diff --git a/prepare/r-rebus.datetimes/PKGBUILD b/prepare/r-rebus.datetimes/PKGBUILD new file mode 100644 index 0000000000..542a706bbd --- /dev/null +++ b/prepare/r-rebus.datetimes/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rebus.datetimes +_pkgver=0.0-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Date and Time Extensions for the 'rebus' Package" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Unlimited') +depends=( + r + r-rebus.base +) +optdepends=( + r-stats + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rebus.datetimes/lilac.py b/prepare/r-rebus.datetimes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rebus.datetimes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rebus.datetimes/lilac.yaml b/prepare/r-rebus.datetimes/lilac.yaml new file mode 100644 index 0000000000..f612f3ea66 --- /dev/null +++ b/prepare/r-rebus.datetimes/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rebus.base +update_on: +- regex: rebus.datetimes_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rebus.datetimes diff --git a/prepare/r-rebus.numbers/PKGBUILD b/prepare/r-rebus.numbers/PKGBUILD new file mode 100644 index 0000000000..089f216cc9 --- /dev/null +++ b/prepare/r-rebus.numbers/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rebus.numbers +_pkgver=0.0-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Numeric Extensions for the 'rebus' Package" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Unlimited') +depends=( + r + r-rebus.base +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rebus.numbers/lilac.py b/prepare/r-rebus.numbers/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rebus.numbers/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rebus.numbers/lilac.yaml b/prepare/r-rebus.numbers/lilac.yaml new file mode 100644 index 0000000000..7c4fb18830 --- /dev/null +++ b/prepare/r-rebus.numbers/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rebus.base +update_on: +- regex: rebus.numbers_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rebus.numbers diff --git a/prepare/r-rebus.unicode/PKGBUILD b/prepare/r-rebus.unicode/PKGBUILD new file mode 100644 index 0000000000..0300260baa --- /dev/null +++ b/prepare/r-rebus.unicode/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rebus.unicode +_pkgver=0.0-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Unicode Extensions for the 'rebus' Package" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Unlimited') +depends=( + r + r-rebus.base +) +optdepends=( + r-stringi +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rebus.unicode/lilac.py b/prepare/r-rebus.unicode/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rebus.unicode/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rebus.unicode/lilac.yaml b/prepare/r-rebus.unicode/lilac.yaml new file mode 100644 index 0000000000..1af2ffa940 --- /dev/null +++ b/prepare/r-rebus.unicode/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rebus.base +update_on: +- regex: rebus.unicode_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rebus.unicode diff --git a/prepare/r-rebus/PKGBUILD b/prepare/r-rebus/PKGBUILD new file mode 100644 index 0000000000..168e67c028 --- /dev/null +++ b/prepare/r-rebus/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rebus +_pkgver=0.1-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Build Regular Expressions in a Human Readable Way' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Unlimited') +depends=( + r + r-rebus.base + r-rebus.datetimes + r-rebus.numbers + r-rebus.unicode +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rebus/lilac.py b/prepare/r-rebus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rebus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rebus/lilac.yaml b/prepare/r-rebus/lilac.yaml new file mode 100644 index 0000000000..832aba1049 --- /dev/null +++ b/prepare/r-rebus/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rebus.base +- r-rebus.datetimes +- r-rebus.numbers +- r-rebus.unicode +update_on: +- regex: rebus_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rebus diff --git a/prepare/r-receptloss/PKGBUILD b/prepare/r-receptloss/PKGBUILD new file mode 100644 index 0000000000..862d7532ff --- /dev/null +++ b/prepare/r-receptloss/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=receptLoss +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-ggplot2 + r-magrittr + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-here + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-receptloss/lilac.py b/prepare/r-receptloss/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-receptloss/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-receptloss/lilac.yaml b/prepare/r-receptloss/lilac.yaml new file mode 100644 index 0000000000..dbc4105368 --- /dev/null +++ b/prepare/r-receptloss/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-magrittr +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: receptLoss_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/receptLoss diff --git a/prepare/r-recipes/PKGBUILD b/prepare/r-recipes/PKGBUILD new file mode 100644 index 0000000000..3ddd0186ff --- /dev/null +++ b/prepare/r-recipes/PKGBUILD @@ -0,0 +1,65 @@ +# Maintainer: Guoyi Zhang + +_pkgname=recipes +_pkgver=0.1.17 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Preprocessing and Feature Engineering Steps for Modeling' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-ellipsis + r-generics + r-glue + r-gower + r-ipred + r-lifecycle + r-lubridate + r-magrittr + r-purrr + r-rlang + r-tibble + r-tidyr + r-tidyselect + r-timedate + r-vctrs + r-withr +) +optdepends=( + r-covr + r-ddalpha + r-dimred + r-fastica + r-ggplot2 + r-igraph + r-kernlab + r-knitr + r-modeldata + r-parsnip + r-rann + r-rcpproll + r-rmarkdown + r-rpart + r-rsample + r-rspectra + r-testthat + r-workflows + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-recipes/lilac.py b/prepare/r-recipes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-recipes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-recipes/lilac.yaml b/prepare/r-recipes/lilac.yaml new file mode 100644 index 0000000000..9b57c1c114 --- /dev/null +++ b/prepare/r-recipes/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ellipsis +- r-generics +- r-glue +- r-gower +- r-ipred +- r-lifecycle +- r-lubridate +- r-magrittr +- r-purrr +- r-rlang +- r-tibble +- r-tidyr +- r-tidyselect +- r-timedate +- r-vctrs +- r-withr +update_on: +- regex: recipes_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=recipes diff --git a/prepare/r-reconsi/PKGBUILD b/prepare/r-reconsi/PKGBUILD new file mode 100644 index 0000000000..8573e1a0a4 --- /dev/null +++ b/prepare/r-reconsi/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=reconsi +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Resampling Collapsed Null Distributions for Simultaneous Inference' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-matrixstats + r-phyloseq + r-reshape2 +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reconsi/lilac.py b/prepare/r-reconsi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reconsi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reconsi/lilac.yaml b/prepare/r-reconsi/lilac.yaml new file mode 100644 index 0000000000..f2437affe1 --- /dev/null +++ b/prepare/r-reconsi/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-matrixstats +- r-phyloseq +- r-reshape2 +update_on: +- regex: reconsi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/reconsi diff --git a/prepare/r-recordlinkage/PKGBUILD b/prepare/r-recordlinkage/PKGBUILD new file mode 100644 index 0000000000..e226a1f6a6 --- /dev/null +++ b/prepare/r-recordlinkage/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RecordLinkage +_pkgver=0.4-12.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Record Linkage Functions for Linking and Deduplicating Data Sets' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ada + r-data.table + r-dbi + r-e1071 + r-evd + r-ff + r-ipred + r-rsqlite + r-xtable +) +optdepends=( + r-knitr + r-runit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-recordlinkage/lilac.py b/prepare/r-recordlinkage/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-recordlinkage/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-recordlinkage/lilac.yaml b/prepare/r-recordlinkage/lilac.yaml new file mode 100644 index 0000000000..75688d9ed7 --- /dev/null +++ b/prepare/r-recordlinkage/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ada +- r-data.table +- r-dbi +- r-e1071 +- r-evd +- r-ff +- r-ipred +- r-rsqlite +- r-xtable +update_on: +- regex: RecordLinkage_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RecordLinkage diff --git a/prepare/r-recount/PKGBUILD b/prepare/r-recount/PKGBUILD new file mode 100644 index 0000000000..c93484f4c8 --- /dev/null +++ b/prepare/r-recount/PKGBUILD @@ -0,0 +1,59 @@ +# Maintainer: Guoyi Zhang + +_pkgname=recount +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Explore and download data from the recount project' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-derfinder + r-downloader + r-genomeinfodb + r-genomicranges + r-geoquery + r-iranges + r-rcurl + r-rentrez + r-rtracklayer + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-annotationdbi + r-biocmanager + r-biocstyle + r-covr + r-deseq2 + r-dt + r-edger + r-ensdb.hsapiens.v79 + r-genomicfeatures + r-ggplot2 + r-knitr + r-org.hs.eg.db + r-pheatmap + r-rcolorbrewer + r-refmanager + r-regionreport + r-rmarkdown + r-sessioninfo + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-recount/lilac.py b/prepare/r-recount/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-recount/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-recount/lilac.yaml b/prepare/r-recount/lilac.yaml new file mode 100644 index 0000000000..805527ca50 --- /dev/null +++ b/prepare/r-recount/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-derfinder +- r-downloader +- r-genomeinfodb +- r-genomicranges +- r-geoquery +- r-iranges +- r-rcurl +- r-rentrez +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: recount_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/recount diff --git a/prepare/r-recount3/PKGBUILD b/prepare/r-recount3/PKGBUILD new file mode 100644 index 0000000000..3301483267 --- /dev/null +++ b/prepare/r-recount3/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=recount3 +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Explore and download data from the recount3 project' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocfilecache + r-data.table + r-genomicranges + r-r.utils + r-rcurl + r-rtracklayer + r-s4vectors + r-sessioninfo + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-covr + r-interactivedisplaybase + r-knitcitations + r-knitr + r-pryr + r-recount + r-refmanager + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-recount3/lilac.py b/prepare/r-recount3/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-recount3/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-recount3/lilac.yaml b/prepare/r-recount3/lilac.yaml new file mode 100644 index 0000000000..bf78cca2cc --- /dev/null +++ b/prepare/r-recount3/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-data.table +- r-genomicranges +- r-r.utils +- r-rcurl +- r-rtracklayer +- r-s4vectors +- r-sessioninfo +- r-summarizedexperiment +update_on: +- regex: recount3_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/recount3 diff --git a/prepare/r-recountmethylation/PKGBUILD b/prepare/r-recountmethylation/PKGBUILD new file mode 100644 index 0000000000..8a0d15c6ca --- /dev/null +++ b/prepare/r-recountmethylation/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=recountmethylation +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Access and analyze DNA methylation database compilations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocfilecache + r-hdf5array + r-minfi + r-r.utils + r-rcurl + r-rhdf5 + r-s4vectors +) +optdepends=( + r-annotationhub + r-biocstyle + r-experimenthub + r-genomicranges + r-ggplot2 + r-gridextra + r-knitr + r-limma + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-recountmethylation/lilac.py b/prepare/r-recountmethylation/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-recountmethylation/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-recountmethylation/lilac.yaml b/prepare/r-recountmethylation/lilac.yaml new file mode 100644 index 0000000000..8c8b632e23 --- /dev/null +++ b/prepare/r-recountmethylation/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-hdf5array +- r-minfi +- r-r.utils +- r-rcurl +- r-rhdf5 +- r-s4vectors +update_on: +- regex: recountmethylation_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/recountmethylation diff --git a/prepare/r-recoup/PKGBUILD b/prepare/r-recoup/PKGBUILD new file mode 100644 index 0000000000..efd12d990b --- /dev/null +++ b/prepare/r-recoup/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=recoup +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package for the creation of complex genomic profile plots' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biomart + r-biostrings + r-circlize + r-complexheatmap + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-httr + r-iranges + r-rsamtools + r-rsqlite + r-rtracklayer + r-s4vectors + r-stringr +) +optdepends=( + r-biocmanager + r-biocstyle + r-bsgenome + r-grid + r-knitr + r-rmarkdown + r-rmysql + r-runit + r-zoo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-recoup/lilac.py b/prepare/r-recoup/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-recoup/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-recoup/lilac.yaml b/prepare/r-recoup/lilac.yaml new file mode 100644 index 0000000000..7302e2e16b --- /dev/null +++ b/prepare/r-recoup/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biomart +- r-biostrings +- r-circlize +- r-complexheatmap +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-httr +- r-iranges +- r-rsamtools +- r-rsqlite +- r-rtracklayer +- r-s4vectors +- r-stringr +update_on: +- regex: recoup_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/recoup diff --git a/prepare/r-reder/PKGBUILD b/prepare/r-reder/PKGBUILD new file mode 100644 index 0000000000..fe548d9241 --- /dev/null +++ b/prepare/r-reder/PKGBUILD @@ -0,0 +1,34 @@ +# system requirements: Java Runtime Environment (>= 8) +# Maintainer: Guoyi Zhang + +_pkgname=RedeR +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive visualization and manipulation of nested networks' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-igraph +) +optdepends=( + r-biocstyle + r-knitr + r-pvclust + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reder/lilac.py b/prepare/r-reder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reder/lilac.yaml b/prepare/r-reder/lilac.yaml new file mode 100644 index 0000000000..93b3073789 --- /dev/null +++ b/prepare/r-reder/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +update_on: +- regex: RedeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RedeR diff --git a/prepare/r-redseq/PKGBUILD b/prepare/r-redseq/PKGBUILD new file mode 100644 index 0000000000..fed9fa6ec1 --- /dev/null +++ b/prepare/r-redseq/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=REDseq +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of high-throughput sequencing data processed by restriction enzyme digestion' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocgenerics + r-biostrings + r-bsgenome + r-bsgenome.celegans.ucsc.ce2 + r-chippeakanno + r-iranges + r-multtest +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-redseq/lilac.py b/prepare/r-redseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-redseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-redseq/lilac.yaml b/prepare/r-redseq/lilac.yaml new file mode 100644 index 0000000000..b92cc1e2cc --- /dev/null +++ b/prepare/r-redseq/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-bsgenome.celegans.ucsc.ce2 +- r-chippeakanno +- r-iranges +- r-multtest +update_on: +- regex: REDseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/REDseq diff --git a/prepare/r-reffreeewas/PKGBUILD b/prepare/r-reffreeewas/PKGBUILD new file mode 100644 index 0000000000..ee0ba6a46f --- /dev/null +++ b/prepare/r-reffreeewas/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RefFreeEWAS +_pkgver=2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc=' EWAS using Reference-Free DNA Methylation Mixture Deconvolution' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-quadprog +) +source=("https://github.com/cran/RefFreeEWAS/archive/refs/tags/${pkgver}.tar.gz") +sha256sums=('7d24a61eb1c80e14b42eb21c3a7482149489673e257917b5f4a7e9638ee83039') + +build() { + R CMD INSTALL ${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reffreeewas/lilac.py b/prepare/r-reffreeewas/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reffreeewas/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reffreeewas/lilac.yaml b/prepare/r-reffreeewas/lilac.yaml new file mode 100644 index 0000000000..d0c24a26ba --- /dev/null +++ b/prepare/r-reffreeewas/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-quadprog +update_on: +- regex: github + github: cran/RefFreeEWAS + use_max_tag: true diff --git a/prepare/r-refmanager/PKGBUILD b/prepare/r-refmanager/PKGBUILD new file mode 100644 index 0000000000..4ffdf0e35b --- /dev/null +++ b/prepare/r-refmanager/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RefManageR +_pkgver=1.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-httr + r-jsonlite + r-lubridate + r-plyr + r-stringr + r-xml2 +) +optdepends=( + r-bibtex + r-knitr + r-markdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-refmanager/lilac.yaml b/prepare/r-refmanager/lilac.yaml new file mode 100644 index 0000000000..8947a1278b --- /dev/null +++ b/prepare/r-refmanager/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-httr +- r-jsonlite +- r-lubridate +- r-plyr +- r-stringr +- r-xml2 +update_on: +- regex: RefManageR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RefManageR diff --git a/prepare/r-refplus/PKGBUILD b/prepare/r-refplus/PKGBUILD new file mode 100644 index 0000000000..44fd8da4fd --- /dev/null +++ b/prepare/r-refplus/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RefPlus +_pkgver=1.64.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-affyplm + r-biobase + r-preprocesscore +) +optdepends=( + r-affydata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-refplus/lilac.py b/prepare/r-refplus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-refplus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-refplus/lilac.yaml b/prepare/r-refplus/lilac.yaml new file mode 100644 index 0000000000..0c4847edd6 --- /dev/null +++ b/prepare/r-refplus/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-affyplm +- r-biobase +- r-preprocesscore +update_on: +- regex: RefPlus_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RefPlus diff --git a/prepare/r-regenrich/PKGBUILD b/prepare/r-regenrich/PKGBUILD new file mode 100644 index 0000000000..ee2b9d44eb --- /dev/null +++ b/prepare/r-regenrich/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RegEnrich +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene regulator enrichment analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-biocset + r-deseq2 + r-dose + r-dplyr + r-fgsea + r-ggplot2 + r-limma + r-magrittr + r-randomforest + r-reshape2 + r-s4vectors + r-summarizedexperiment + r-tibble + r-wgcna +) +optdepends=( + r-biocmanager + r-geoquery + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-regenrich/lilac.py b/prepare/r-regenrich/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-regenrich/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-regenrich/lilac.yaml b/prepare/r-regenrich/lilac.yaml new file mode 100644 index 0000000000..09f7ab885b --- /dev/null +++ b/prepare/r-regenrich/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-biocset +- r-deseq2 +- r-dose +- r-dplyr +- r-fgsea +- r-ggplot2 +- r-limma +- r-magrittr +- r-randomforest +- r-reshape2 +- r-s4vectors +- r-summarizedexperiment +- r-tibble +- r-wgcna +update_on: +- regex: RegEnrich_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RegEnrich diff --git a/prepare/r-regioner/PKGBUILD b/prepare/r-regioner/PKGBUILD new file mode 100644 index 0000000000..38a4b7f2be --- /dev/null +++ b/prepare/r-regioner/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=regioneR +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Association analysis of genomic regions based on permutation tests' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-iranges + r-memoise + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19.masked + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-regioner/lilac.py b/prepare/r-regioner/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-regioner/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-regioner/lilac.yaml b/prepare/r-regioner/lilac.yaml new file mode 100644 index 0000000000..11475cc9f5 --- /dev/null +++ b/prepare/r-regioner/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-memoise +- r-rtracklayer +- r-s4vectors +update_on: +- regex: regioneR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/regioneR diff --git a/prepare/r-regionreport/PKGBUILD b/prepare/r-regionreport/PKGBUILD new file mode 100644 index 0000000000..96fe7df3e1 --- /dev/null +++ b/prepare/r-regionreport/PKGBUILD @@ -0,0 +1,58 @@ +# Maintainer: Guoyi Zhang + +_pkgname=regionReport +_pkgver=1.28.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocstyle + r-deformats + r-derfinder + r-deseq2 + r-genomeinfodb + r-genomicranges + r-knitr + r-knitrbootstrap + r-refmanager + r-rmarkdown + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocmanager + r-biovizbase + r-bumphunter + r-derfinderplot + r-dt + r-edger + r-ggbio + r-ggplot2 + r-grid + r-gridextra + r-iranges + r-mgcv + r-pasilla + r-pheatmap + r-rcolorbrewer + r-sessioninfo + r-txdb.hsapiens.ucsc.hg19.knowngene + r-whisker +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-regionreport/lilac.py b/prepare/r-regionreport/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-regionreport/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-regionreport/lilac.yaml b/prepare/r-regionreport/lilac.yaml new file mode 100644 index 0000000000..2c10554ccf --- /dev/null +++ b/prepare/r-regionreport/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocstyle +- r-deformats +- r-derfinder +- r-deseq2 +- r-genomeinfodb +- r-genomicranges +- r-knitr +- r-knitrbootstrap +- r-refmanager +- r-rmarkdown +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: regionReport_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/regionReport diff --git a/prepare/r-registry/PKGBUILD b/prepare/r-registry/PKGBUILD new file mode 100644 index 0000000000..83f2216964 --- /dev/null +++ b/prepare/r-registry/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=registry +_pkgver=0.5-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Infrastructure for R Package Registries' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-registry/lilac.py b/prepare/r-registry/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-registry/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-registry/lilac.yaml b/prepare/r-registry/lilac.yaml new file mode 100644 index 0000000000..2f274f6041 --- /dev/null +++ b/prepare/r-registry/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: registry_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=registry diff --git a/prepare/r-regsplice/PKGBUILD b/prepare/r-regsplice/PKGBUILD new file mode 100644 index 0000000000..870bbec7ff --- /dev/null +++ b/prepare/r-regsplice/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=regsplice +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='L1-regularization based methods for detection of differential splicing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-edger + r-glmnet + r-limma + r-pbapply + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-regsplice/lilac.py b/prepare/r-regsplice/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-regsplice/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-regsplice/lilac.yaml b/prepare/r-regsplice/lilac.yaml new file mode 100644 index 0000000000..831a50d6b5 --- /dev/null +++ b/prepare/r-regsplice/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-edger +- r-glmnet +- r-limma +- r-pbapply +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: regsplice_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/regsplice diff --git a/prepare/r-regutools/PKGBUILD b/prepare/r-regutools/PKGBUILD new file mode 100644 index 0000000000..c79e98aeb7 --- /dev/null +++ b/prepare/r-regutools/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=regutools +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='regutools: an R package for data extraction from RegulonDB' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-annotationhub + r-biocfilecache + r-biostrings + r-dbi + r-genomicranges + r-gviz + r-iranges + r-rcy3 + r-rsqlite + r-s4vectors +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-refmanager + r-rmarkdown + r-sessioninfo + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-regutools/lilac.py b/prepare/r-regutools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-regutools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-regutools/lilac.yaml b/prepare/r-regutools/lilac.yaml new file mode 100644 index 0000000000..60a1836800 --- /dev/null +++ b/prepare/r-regutools/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-biocfilecache +- r-biostrings +- r-dbi +- r-genomicranges +- r-gviz +- r-iranges +- r-rcy3 +- r-rsqlite +- r-s4vectors +update_on: +- regex: regutools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/regutools diff --git a/prepare/r-relations/PKGBUILD b/prepare/r-relations/PKGBUILD new file mode 100644 index 0000000000..a89185f476 --- /dev/null +++ b/prepare/r-relations/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=relations +_pkgver=0.6-10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data Structures and Algorithms for Relations' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-sets + r-slam +) +optdepends=( + r-clue + r-lpsolve + r-methods + r-rcplex + r-rglpk + r-rgraphviz + r-rsymphony + r-seriation +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-relations/lilac.py b/prepare/r-relations/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-relations/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-relations/lilac.yaml b/prepare/r-relations/lilac.yaml new file mode 100644 index 0000000000..c36a11284e --- /dev/null +++ b/prepare/r-relations/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-sets +- r-slam +update_on: +- regex: relations_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=relations diff --git a/prepare/r-reldist/PKGBUILD b/prepare/r-reldist/PKGBUILD new file mode 100644 index 0000000000..c447939925 --- /dev/null +++ b/prepare/r-reldist/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=reldist +_pkgver=1.7-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Relative Distribution Methods' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-densestbayes + r-hmisc +) +optdepends=( + r-locfit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reldist/lilac.py b/prepare/r-reldist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reldist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reldist/lilac.yaml b/prepare/r-reldist/lilac.yaml new file mode 100644 index 0000000000..208a0fb540 --- /dev/null +++ b/prepare/r-reldist/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-densestbayes +- r-hmisc +update_on: +- regex: reldist_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=reldist diff --git a/prepare/r-relimp/PKGBUILD b/prepare/r-relimp/PKGBUILD new file mode 100644 index 0000000000..5ae6c464e5 --- /dev/null +++ b/prepare/r-relimp/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=relimp +_pkgver=1.0-5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Relative Contribution of Effects in a Regression Model' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-mass + r-nnet + r-rcmdr + r-tcltk +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-relimp/lilac.py b/prepare/r-relimp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-relimp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-relimp/lilac.yaml b/prepare/r-relimp/lilac.yaml new file mode 100644 index 0000000000..74a51d701e --- /dev/null +++ b/prepare/r-relimp/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: relimp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=relimp diff --git a/prepare/r-rematch/PKGBUILD b/prepare/r-rematch/PKGBUILD new file mode 100644 index 0000000000..85f395042e --- /dev/null +++ b/prepare/r-rematch/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rematch +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Match Regular Expressions with a Nicer 'API'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rematch/lilac.py b/prepare/r-rematch/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rematch/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rematch/lilac.yaml b/prepare/r-rematch/lilac.yaml new file mode 100644 index 0000000000..26e32ed315 --- /dev/null +++ b/prepare/r-rematch/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: rematch_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rematch diff --git a/prepare/r-rematch2/PKGBUILD b/prepare/r-rematch2/PKGBUILD new file mode 100644 index 0000000000..7b2f7d412d --- /dev/null +++ b/prepare/r-rematch2/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rematch2 +_pkgver=2.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tidy Output from Regular Expression Matching' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-tibble +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rematch2/lilac.py b/prepare/r-rematch2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rematch2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rematch2/lilac.yaml b/prepare/r-rematch2/lilac.yaml new file mode 100644 index 0000000000..de929a6212 --- /dev/null +++ b/prepare/r-rematch2/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-tibble +update_on: +- regex: rematch2_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rematch2 diff --git a/prepare/r-remotes/PKGBUILD b/prepare/r-remotes/PKGBUILD new file mode 100644 index 0000000000..d41514aff1 --- /dev/null +++ b/prepare/r-remotes/PKGBUILD @@ -0,0 +1,45 @@ +# system requirements: Subversion for install_svn, git for install_git +# Maintainer: Guoyi Zhang + +_pkgname=remotes +_pkgver=2.4.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="R Package Installation from Remote Repositories, Including 'GitHub'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-brew + r-callr + r-codetools + r-covr + r-curl + r-git2r + r-knitr + r-mockery + r-pingr + r-pkgbuild + r-rmarkdown + r-rprojroot + r-testthat + r-webfakes + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-remotes/lilac.py b/prepare/r-remotes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-remotes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-remotes/lilac.yaml b/prepare/r-remotes/lilac.yaml new file mode 100644 index 0000000000..3d43d3794f --- /dev/null +++ b/prepare/r-remotes/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: remotes_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=remotes diff --git a/prepare/r-remp/PKGBUILD b/prepare/r-remp/PKGBUILD new file mode 100644 index 0000000000..fe061bbe14 --- /dev/null +++ b/prepare/r-remp/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=REMP +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Repetitive Element Methylation Prediction' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationhub + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-caret + r-doparallel + r-foreach + r-genomeinfodb + r-genomicranges + r-impute + r-iranges + r-iterators + r-kernlab + r-minfi + r-org.hs.eg.db + r-ranger + r-readr + r-rtracklayer + r-s4vectors + r-settings + r-summarizedexperiment +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.hsapiens.ucsc.hg38 + r-illuminahumanmethylation450kanno.ilmn12.hg19 + r-illuminahumanmethylationepicanno.ilm10b2.hg19 + r-knitr + r-minfidataepic + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-remp/lilac.py b/prepare/r-remp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-remp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-remp/lilac.yaml b/prepare/r-remp/lilac.yaml new file mode 100644 index 0000000000..8a306cf5e4 --- /dev/null +++ b/prepare/r-remp/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-caret +- r-doparallel +- r-foreach +- r-genomeinfodb +- r-genomicranges +- r-impute +- r-iranges +- r-iterators +- r-kernlab +- r-minfi +- r-org.hs.eg.db +- r-ranger +- r-readr +- r-rtracklayer +- r-s4vectors +- r-settings +- r-summarizedexperiment +update_on: +- regex: REMP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/REMP diff --git a/prepare/r-rentrez/PKGBUILD b/prepare/r-rentrez/PKGBUILD new file mode 100644 index 0000000000..2d74993e8d --- /dev/null +++ b/prepare/r-rentrez/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rentrez +_pkgver=1.2.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'Entrez' in R" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-httr + r-jsonlite + r-xml +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rentrez/lilac.py b/prepare/r-rentrez/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rentrez/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rentrez/lilac.yaml b/prepare/r-rentrez/lilac.yaml new file mode 100644 index 0000000000..4926ac09e4 --- /dev/null +++ b/prepare/r-rentrez/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-httr +- r-jsonlite +- r-xml +update_on: +- regex: rentrez_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rentrez diff --git a/prepare/r-renv/PKGBUILD b/prepare/r-renv/PKGBUILD new file mode 100644 index 0000000000..5744b8adee --- /dev/null +++ b/prepare/r-renv/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=renv +_pkgver=0.15.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Project Environments' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-biocmanager + r-cli + r-covr + r-devtools + r-knitr + r-miniui + r-packrat + r-pak + r-r6 + r-remotes + r-reticulate + r-rmarkdown + r-rstudioapi + r-shiny + r-testthat + r-uuid + r-yaml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-renv/lilac.py b/prepare/r-renv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-renv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-renv/lilac.yaml b/prepare/r-renv/lilac.yaml new file mode 100644 index 0000000000..0b9a5e2d97 --- /dev/null +++ b/prepare/r-renv/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: renv_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=renv diff --git a/prepare/r-reordercluster/PKGBUILD b/prepare/r-reordercluster/PKGBUILD new file mode 100644 index 0000000000..d711b5adc9 --- /dev/null +++ b/prepare/r-reordercluster/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ReorderCluster +_pkgver=1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Reordering the dendrogram according to the class labels' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-gplots + r-rcpp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reordercluster/lilac.py b/prepare/r-reordercluster/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reordercluster/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reordercluster/lilac.yaml b/prepare/r-reordercluster/lilac.yaml new file mode 100644 index 0000000000..0b0948d894 --- /dev/null +++ b/prepare/r-reordercluster/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gplots +- r-rcpp +update_on: +- regex: ReorderCluster_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ReorderCluster diff --git a/prepare/r-repitools/PKGBUILD b/prepare/r-repitools/PKGBUILD new file mode 100644 index 0000000000..33d6c410f5 --- /dev/null +++ b/prepare/r-repitools/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Repitools +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Epigenomic tools' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biocgenerics + r-biostrings + r-bsgenome + r-dnacopy + r-edger + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-gplots + r-gsmoothr + r-iranges + r-ringo + r-rsamtools + r-rsolnp + r-rtracklayer + r-s4vectors +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg18 + r-shortread +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-repitools/lilac.py b/prepare/r-repitools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-repitools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-repitools/lilac.yaml b/prepare/r-repitools/lilac.yaml new file mode 100644 index 0000000000..7aff21bc0b --- /dev/null +++ b/prepare/r-repitools/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-dnacopy +- r-edger +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-gplots +- r-gsmoothr +- r-iranges +- r-ringo +- r-rsamtools +- r-rsolnp +- r-rtracklayer +- r-s4vectors +update_on: +- regex: Repitools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Repitools diff --git a/prepare/r-repmis/PKGBUILD b/prepare/r-repmis/PKGBUILD new file mode 100644 index 0000000000..436ca3bc7e --- /dev/null +++ b/prepare/r-repmis/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=repmis +_pkgver=0.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Miscellaneous Tools for Reproducible Research' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-digest + r-httr + r-plyr + r-r.cache +) +optdepends=( + r-xlsx +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-repmis/lilac.py b/prepare/r-repmis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-repmis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-repmis/lilac.yaml b/prepare/r-repmis/lilac.yaml new file mode 100644 index 0000000000..1edc91096e --- /dev/null +++ b/prepare/r-repmis/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-digest +- r-httr +- r-plyr +- r-r.cache +update_on: +- regex: repmis_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=repmis diff --git a/prepare/r-repo/PKGBUILD b/prepare/r-repo/PKGBUILD new file mode 100644 index 0000000000..2992efd8a5 --- /dev/null +++ b/prepare/r-repo/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=repo +_pkgver=2.1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Data-Centered Data Flow Manager' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-digest +) +optdepends=( + r-igraph + r-knitr + r-shiny + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-repo/lilac.py b/prepare/r-repo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-repo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-repo/lilac.yaml b/prepare/r-repo/lilac.yaml new file mode 100644 index 0000000000..077c9a9712 --- /dev/null +++ b/prepare/r-repo/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +update_on: +- regex: repo_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=repo diff --git a/prepare/r-reportingtools/PKGBUILD b/prepare/r-reportingtools/PKGBUILD new file mode 100644 index 0000000000..67cee52363 --- /dev/null +++ b/prepare/r-reportingtools/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ReportingTools +_pkgver=2.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for making reports in various formats' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-category + r-deseq2 + r-edger + r-ggbio + r-ggplot2 + r-gostats + r-gseabase + r-hwriter + r-iranges + r-knitr + r-limma + r-pfam.db + r-r.utils + r-xml +) +optdepends=( + r-all + r-hgu95av2.db + r-markdown + r-org.mm.eg.db + r-org.sc.sgd.db + r-pasilla + r-rmarkdown + r-runit + r-shiny +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reportingtools/lilac.py b/prepare/r-reportingtools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reportingtools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reportingtools/lilac.yaml b/prepare/r-reportingtools/lilac.yaml new file mode 100644 index 0000000000..1113d7f98e --- /dev/null +++ b/prepare/r-reportingtools/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-category +- r-deseq2 +- r-edger +- r-ggbio +- r-ggplot2 +- r-gostats +- r-gseabase +- r-hwriter +- r-iranges +- r-knitr +- r-limma +- r-pfam.db +- r-r.utils +- r-xml +update_on: +- regex: ReportingTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ReportingTools diff --git a/prepare/r-reportr/PKGBUILD b/prepare/r-reportr/PKGBUILD new file mode 100644 index 0000000000..f246a385a4 --- /dev/null +++ b/prepare/r-reportr/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=reportr +_pkgver=1.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A General Message and Error Reporting System' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ore +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reportr/lilac.py b/prepare/r-reportr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reportr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reportr/lilac.yaml b/prepare/r-reportr/lilac.yaml new file mode 100644 index 0000000000..a3d1ff8c93 --- /dev/null +++ b/prepare/r-reportr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ore +update_on: +- regex: reportr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=reportr diff --git a/prepare/r-reportroc/PKGBUILD b/prepare/r-reportroc/PKGBUILD new file mode 100644 index 0000000000..25635da733 --- /dev/null +++ b/prepare/r-reportroc/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=reportROC +_pkgver=3.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Easy Way to Report ROC Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-proc +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reportroc/lilac.py b/prepare/r-reportroc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reportroc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reportroc/lilac.yaml b/prepare/r-reportroc/lilac.yaml new file mode 100644 index 0000000000..ada4343d9a --- /dev/null +++ b/prepare/r-reportroc/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-proc +update_on: +- regex: reportROC_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=reportROC diff --git a/prepare/r-repr/PKGBUILD b/prepare/r-repr/PKGBUILD new file mode 100644 index 0000000000..9083fe2868 --- /dev/null +++ b/prepare/r-repr/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=repr +_pkgver=1.1.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Serializable Representations' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-base64enc + r-htmltools + r-jsonlite + r-pillar +) +optdepends=( + r-cairo + r-data.table + r-geojsonio + r-highr + r-htmlwidgets + r-leaflet + r-methods + r-plotly + r-stringr + r-testthat + r-tibble + r-vegalite +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-repr/lilac.py b/prepare/r-repr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-repr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-repr/lilac.yaml b/prepare/r-repr/lilac.yaml new file mode 100644 index 0000000000..baeb4bf031 --- /dev/null +++ b/prepare/r-repr/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-htmltools +- r-jsonlite +- r-pillar +update_on: +- regex: repr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=repr diff --git a/prepare/r-reprex/PKGBUILD b/prepare/r-reprex/PKGBUILD new file mode 100644 index 0000000000..1015e35470 --- /dev/null +++ b/prepare/r-reprex/PKGBUILD @@ -0,0 +1,50 @@ +# system requirements: pandoc (>= 2.0) - http://pandoc.org +# Maintainer: Guoyi Zhang + +_pkgname=reprex +_pkgver=2.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Prepare Reproducible Example Code via the Clipboard' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-callr + r-cli + r-clipr + r-fs + r-glue + r-knitr + r-rlang + r-rmarkdown + r-rstudioapi + r-withr +) +optdepends=( + r-covr + r-fortunes + r-miniui + r-mockr + r-rprojroot + r-sessioninfo + r-shiny + r-spelling + r-styler + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reprex/lilac.py b/prepare/r-reprex/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reprex/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reprex/lilac.yaml b/prepare/r-reprex/lilac.yaml new file mode 100644 index 0000000000..cf142b19cb --- /dev/null +++ b/prepare/r-reprex/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-callr +- r-cli +- r-clipr +- r-fs +- r-glue +- r-knitr +- r-rlang +- r-rmarkdown +- r-rstudioapi +- r-withr +update_on: +- regex: reprex_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=reprex diff --git a/prepare/r-repviz/PKGBUILD b/prepare/r-repviz/PKGBUILD new file mode 100644 index 0000000000..addeb3d2ad --- /dev/null +++ b/prepare/r-repviz/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RepViz +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Replicate oriented Visualization of a genomic region' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-genomicranges + r-iranges + r-rsamtools + r-s4vectors +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-repviz/lilac.py b/prepare/r-repviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-repviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-repviz/lilac.yaml b/prepare/r-repviz/lilac.yaml new file mode 100644 index 0000000000..2546e6b597 --- /dev/null +++ b/prepare/r-repviz/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-genomicranges +- r-iranges +- r-rsamtools +- r-s4vectors +update_on: +- regex: RepViz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RepViz diff --git a/prepare/r-reqon/PKGBUILD b/prepare/r-reqon/PKGBUILD new file mode 100644 index 0000000000..4b4d0a8a67 --- /dev/null +++ b/prepare/r-reqon/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: Java version >= 1.6 +# Maintainer: Guoyi Zhang + +_pkgname=ReQON +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Recalibrating Quality Of Nucleotides' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rjava + r-rsamtools + r-seqbias +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reqon/lilac.py b/prepare/r-reqon/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reqon/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reqon/lilac.yaml b/prepare/r-reqon/lilac.yaml new file mode 100644 index 0000000000..956dddeaea --- /dev/null +++ b/prepare/r-reqon/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rjava +- r-rsamtools +- r-seqbias +update_on: +- regex: ReQON_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ReQON diff --git a/prepare/r-reshape/PKGBUILD b/prepare/r-reshape/PKGBUILD new file mode 100644 index 0000000000..bec55f47c3 --- /dev/null +++ b/prepare/r-reshape/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=reshape +_pkgver=0.8.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Flexibly Reshape Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-plyr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reshape/lilac.py b/prepare/r-reshape/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reshape/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reshape/lilac.yaml b/prepare/r-reshape/lilac.yaml new file mode 100644 index 0000000000..cc19fc0504 --- /dev/null +++ b/prepare/r-reshape/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-plyr +update_on: +- regex: reshape_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=reshape diff --git a/prepare/r-reshape2/PKGBUILD b/prepare/r-reshape2/PKGBUILD new file mode 100644 index 0000000000..cdbc4eb8e9 --- /dev/null +++ b/prepare/r-reshape2/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=reshape2 +_pkgver=1.4.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Flexibly Reshape Data: A Reboot of the Reshape Package' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-plyr + r-rcpp + r-stringr +) +optdepends=( + r-covr + r-lattice + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reshape2/lilac.py b/prepare/r-reshape2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reshape2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reshape2/lilac.yaml b/prepare/r-reshape2/lilac.yaml new file mode 100644 index 0000000000..3ab9bdbf94 --- /dev/null +++ b/prepare/r-reshape2/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-plyr +- r-rcpp +- r-stringr +update_on: +- regex: reshape2_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=reshape2 diff --git a/prepare/r-residualmatrix/PKGBUILD b/prepare/r-residualmatrix/PKGBUILD new file mode 100644 index 0000000000..26ffb1eef8 --- /dev/null +++ b/prepare/r-residualmatrix/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ResidualMatrix +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Creating a DelayedMatrix of Regression Residuals' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-delayedarray + r-s4vectors +) +optdepends=( + r-biocsingular + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-residualmatrix/lilac.py b/prepare/r-residualmatrix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-residualmatrix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-residualmatrix/lilac.yaml b/prepare/r-residualmatrix/lilac.yaml new file mode 100644 index 0000000000..286a71a9aa --- /dev/null +++ b/prepare/r-residualmatrix/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-delayedarray +- r-s4vectors +update_on: +- regex: ResidualMatrix_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ResidualMatrix diff --git a/prepare/r-restfulse/PKGBUILD b/prepare/r-restfulse/PKGBUILD new file mode 100644 index 0000000000..eb6073dd80 --- /dev/null +++ b/prepare/r-restfulse/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=restfulSE +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-annotationhub + r-bigrquery + r-biobase + r-dbi + r-delayedarray + r-dplyr + r-experimenthub + r-go.db + r-magrittr + r-reshape2 + r-rhdf5client + r-rlang + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-org.hs.eg.db + r-org.mm.eg.db + r-restfulsedata + r-rmarkdown + r-rtsne + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-restfulse/lilac.py b/prepare/r-restfulse/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-restfulse/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-restfulse/lilac.yaml b/prepare/r-restfulse/lilac.yaml new file mode 100644 index 0000000000..6b09419c46 --- /dev/null +++ b/prepare/r-restfulse/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-bigrquery +- r-biobase +- r-dbi +- r-delayedarray +- r-dplyr +- r-experimenthub +- r-go.db +- r-magrittr +- r-reshape2 +- r-rhdf5client +- r-rlang +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: restfulSE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/restfulSE diff --git a/prepare/r-reticulate/PKGBUILD b/prepare/r-reticulate/PKGBUILD new file mode 100644 index 0000000000..5619ca277c --- /dev/null +++ b/prepare/r-reticulate/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: Python (>= 2.7.0) +# Maintainer: Guoyi Zhang + +_pkgname=reticulate +_pkgver=1.22 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Interface to 'Python'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-here + r-jsonlite + r-png + r-rappdirs + r-rcpp + r-withr +) +optdepends=( + r-callr + r-knitr + r-rlang + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-reticulate/lilac.py b/prepare/r-reticulate/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-reticulate/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-reticulate/lilac.yaml b/prepare/r-reticulate/lilac.yaml new file mode 100644 index 0000000000..73119b0b53 --- /dev/null +++ b/prepare/r-reticulate/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-here +- r-jsonlite +- r-png +- r-rappdirs +- r-rcpp +- r-withr +update_on: +- regex: reticulate_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=reticulate diff --git a/prepare/r-rex/PKGBUILD b/prepare/r-rex/PKGBUILD new file mode 100644 index 0000000000..527e40afa8 --- /dev/null +++ b/prepare/r-rex/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rex +_pkgver=1.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Friendly Regular Expressions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-lazyeval +) +optdepends=( + r-covr + r-dplyr + r-ggplot2 + r-hmisc + r-knitr + r-magrittr + r-rmarkdown + r-roxygen2 + r-rvest + r-stringr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rex/lilac.py b/prepare/r-rex/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rex/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rex/lilac.yaml b/prepare/r-rex/lilac.yaml new file mode 100644 index 0000000000..83ed349fcc --- /dev/null +++ b/prepare/r-rex/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lazyeval +update_on: +- regex: rex_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rex diff --git a/prepare/r-rexposome/PKGBUILD b/prepare/r-rexposome/PKGBUILD new file mode 100644 index 0000000000..e9eb099b94 --- /dev/null +++ b/prepare/r-rexposome/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rexposome +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Exposome exploration and outcome data analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-circlize + r-corrplot + r-factominer + r-ggplot2 + r-ggrepel + r-glmnet + r-gplots + r-gridextra + r-gtools + r-hmisc + r-imputelcmd + r-lme4 + r-lsr + r-mice + r-pryr + r-reshape2 + r-s4vectors + r-scales + r-scatterplot3d + r-stringr +) +optdepends=( + r-biocstyle + r-flexmix + r-knitr + r-mclust + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rexposome/lilac.py b/prepare/r-rexposome/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rexposome/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rexposome/lilac.yaml b/prepare/r-rexposome/lilac.yaml new file mode 100644 index 0000000000..1a5b879430 --- /dev/null +++ b/prepare/r-rexposome/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-circlize +- r-corrplot +- r-factominer +- r-ggplot2 +- r-ggrepel +- r-glmnet +- r-gplots +- r-gridextra +- r-gtools +- r-hmisc +- r-imputelcmd +- r-lme4 +- r-lsr +- r-mice +- r-pryr +- r-reshape2 +- r-s4vectors +- r-scales +- r-scatterplot3d +- r-stringr +update_on: +- regex: rexposome_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rexposome diff --git a/prepare/r-rfarm/PKGBUILD b/prepare/r-rfarm/PKGBUILD new file mode 100644 index 0000000000..f2bf2b7f4c --- /dev/null +++ b/prepare/r-rfarm/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rfaRm +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R interface to the Rfam database' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-data.table + r-httr + r-iranges + r-magick + r-rsvg + r-rvest + r-s4vectors + r-stringi + r-xml2 +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-r4rna + r-rmarkdown + r-treeio +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rfarm/lilac.py b/prepare/r-rfarm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rfarm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rfarm/lilac.yaml b/prepare/r-rfarm/lilac.yaml new file mode 100644 index 0000000000..d7fd8b8038 --- /dev/null +++ b/prepare/r-rfarm/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-data.table +- r-httr +- r-iranges +- r-magick +- r-rsvg +- r-rvest +- r-s4vectors +- r-stringi +- r-xml2 +update_on: +- regex: rfaRm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rfaRm diff --git a/prepare/r-rfast/PKGBUILD b/prepare/r-rfast/PKGBUILD new file mode 100644 index 0000000000..03ff938908 --- /dev/null +++ b/prepare/r-rfast/PKGBUILD @@ -0,0 +1,30 @@ +# system requirements: C++17 +# Maintainer: Guoyi Zhang + +_pkgname=Rfast +_pkgver=2.0.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Collection of Efficient and Extremely Fast R Functions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcpparmadillo + r-rcppziggurat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rfast/lilac.py b/prepare/r-rfast/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rfast/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rfast/lilac.yaml b/prepare/r-rfast/lilac.yaml new file mode 100644 index 0000000000..c84265343a --- /dev/null +++ b/prepare/r-rfast/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcpparmadillo +- r-rcppziggurat +update_on: +- regex: Rfast_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rfast diff --git a/prepare/r-rfastp/PKGBUILD b/prepare/r-rfastp/PKGBUILD new file mode 100644 index 0000000000..8cdaf2a378 --- /dev/null +++ b/prepare/r-rfastp/PKGBUILD @@ -0,0 +1,39 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=Rfastp +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing).' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-rcpp + r-reshape2 + r-rhtslib + r-rjson + r-zlibbioc +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rfastp/lilac.py b/prepare/r-rfastp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rfastp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rfastp/lilac.yaml b/prepare/r-rfastp/lilac.yaml new file mode 100644 index 0000000000..3c13fca8a0 --- /dev/null +++ b/prepare/r-rfastp/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-rcpp +- r-reshape2 +- r-rhtslib +- r-rjson +- r-zlibbioc +update_on: +- regex: Rfastp_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rfastp diff --git a/prepare/r-rfoc/PKGBUILD b/prepare/r-rfoc/PKGBUILD new file mode 100644 index 0000000000..11999dc95e --- /dev/null +++ b/prepare/r-rfoc/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RFOC +_pkgver=3.4-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Graphics for Spherical Distributions and Earthquake Focal Mechanisms' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-geomap + r-rpmg + r-rseis + r-splancs +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rfoc/lilac.py b/prepare/r-rfoc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rfoc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rfoc/lilac.yaml b/prepare/r-rfoc/lilac.yaml new file mode 100644 index 0000000000..fc0c6843f5 --- /dev/null +++ b/prepare/r-rfoc/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-geomap +- r-rpmg +- r-rseis +- r-splancs +update_on: +- regex: RFOC_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RFOC diff --git a/prepare/r-rfpred/PKGBUILD b/prepare/r-rfpred/PKGBUILD new file mode 100644 index 0000000000..6e936ab54c --- /dev/null +++ b/prepare/r-rfpred/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rfPred +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assign rfPred functional prediction scores to a missense variants list' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-genomicranges + r-iranges + r-rsamtools +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rfpred/lilac.py b/prepare/r-rfpred/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rfpred/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rfpred/lilac.yaml b/prepare/r-rfpred/lilac.yaml new file mode 100644 index 0000000000..47eb6214fa --- /dev/null +++ b/prepare/r-rfpred/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-genomicranges +- r-iranges +- r-rsamtools +update_on: +- regex: rfPred_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rfPred diff --git a/prepare/r-rgadem/PKGBUILD b/prepare/r-rgadem/PKGBUILD new file mode 100644 index 0000000000..311e1696ca --- /dev/null +++ b/prepare/r-rgadem/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rGADEM +_pkgver=2.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='de novo motif discovery' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-bsgenome + r-genomicranges + r-iranges + r-seqlogo +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg19 + r-rtracklayer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rgadem/lilac.py b/prepare/r-rgadem/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rgadem/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rgadem/lilac.yaml b/prepare/r-rgadem/lilac.yaml new file mode 100644 index 0000000000..e6ba441382 --- /dev/null +++ b/prepare/r-rgadem/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome +- r-genomicranges +- r-iranges +- r-seqlogo +update_on: +- regex: rGADEM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rGADEM diff --git a/prepare/r-rgalaxy/PKGBUILD b/prepare/r-rgalaxy/PKGBUILD new file mode 100644 index 0000000000..faf945d908 --- /dev/null +++ b/prepare/r-rgalaxy/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RGalaxy +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Make an R function available in the Galaxy web platform' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-optparse + r-roxygen2 + r-xml +) +optdepends=( + r-annotationdbi + r-formatr + r-hgu95av2.db + r-knitr + r-markdown + r-rsclient + r-rserve + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rgalaxy/lilac.py b/prepare/r-rgalaxy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rgalaxy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rgalaxy/lilac.yaml b/prepare/r-rgalaxy/lilac.yaml new file mode 100644 index 0000000000..557f487c2a --- /dev/null +++ b/prepare/r-rgalaxy/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-optparse +- r-roxygen2 +- r-xml +update_on: +- regex: RGalaxy_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RGalaxy diff --git a/prepare/r-rgenometracks/PKGBUILD b/prepare/r-rgenometracks/PKGBUILD new file mode 100644 index 0000000000..e62cd20b8b --- /dev/null +++ b/prepare/r-rgenometracks/PKGBUILD @@ -0,0 +1,35 @@ +# system requirements: pyGenomeTracks (prefered to useinstall_pyGenomeTracks()) +# Maintainer: Guoyi Zhang + +_pkgname=rGenomeTracks +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integerated visualization of epigenomic data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-imager + r-reticulate + r-rgenometracksdata +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rgenometracks/lilac.py b/prepare/r-rgenometracks/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rgenometracks/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rgenometracks/lilac.yaml b/prepare/r-rgenometracks/lilac.yaml new file mode 100644 index 0000000000..6d774aaed0 --- /dev/null +++ b/prepare/r-rgenometracks/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-imager +- r-reticulate +- r-rgenometracksdata +update_on: +- regex: rGenomeTracks_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rGenomeTracks diff --git a/prepare/r-rgenometracksdata/PKGBUILD b/prepare/r-rgenometracksdata/PKGBUILD new file mode 100644 index 0000000000..747410970d --- /dev/null +++ b/prepare/r-rgenometracksdata/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rGenomeTracksData +_pkgver=0.99.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Demonstration Data from rGenomeTracks Package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationhub +) +optdepends=( + r-biocmanager + r-devtools + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rgenometracksdata/lilac.py b/prepare/r-rgenometracksdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rgenometracksdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rgenometracksdata/lilac.yaml b/prepare/r-rgenometracksdata/lilac.yaml new file mode 100644 index 0000000000..8581339abd --- /dev/null +++ b/prepare/r-rgenometracksdata/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +update_on: +- regex: rGenomeTracksData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rGenomeTracksData diff --git a/prepare/r-rgeos/PKGBUILD b/prepare/r-rgeos/PKGBUILD new file mode 100644 index 0000000000..a7d209d69d --- /dev/null +++ b/prepare/r-rgeos/PKGBUILD @@ -0,0 +1,35 @@ +# system requirements: GEOS (>= 3.2.0); for building from source: GEOSfrom https://libgeos.org; GEOS OSX frameworks built by WilliamKyngesburye at http://www.kyngchaos.com/ may be used for sourceinstalls on OSX. +# Maintainer: Guoyi Zhang + +_pkgname=rgeos +_pkgver=0.5-9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Interface to Geometry Engine - Open Source ('GEOS')" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-sp +) +optdepends=( + r-maps + r-maptools + r-rgdal + r-testthat + r-xml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rgeos/lilac.py b/prepare/r-rgeos/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rgeos/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rgeos/lilac.yaml b/prepare/r-rgeos/lilac.yaml new file mode 100644 index 0000000000..dce11504be --- /dev/null +++ b/prepare/r-rgeos/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-sp +update_on: +- regex: rgeos_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rgeos diff --git a/prepare/r-rgin/PKGBUILD b/prepare/r-rgin/PKGBUILD new file mode 100644 index 0000000000..3d1028a1ac --- /dev/null +++ b/prepare/r-rgin/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rgin +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='gin in R' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-rcppeigen +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rgin/lilac.py b/prepare/r-rgin/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rgin/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rgin/lilac.yaml b/prepare/r-rgin/lilac.yaml new file mode 100644 index 0000000000..a0ba372d28 --- /dev/null +++ b/prepare/r-rgin/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcppeigen +update_on: +- regex: Rgin_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rgin diff --git a/prepare/r-rgl/PKGBUILD b/prepare/r-rgl/PKGBUILD new file mode 100644 index 0000000000..854c8ac3f5 --- /dev/null +++ b/prepare/r-rgl/PKGBUILD @@ -0,0 +1,59 @@ +# system requirements: OpenGL, GLU Library, XQuartz (on OSX), zlib(optional), libpng (>=1.2.9, optional), FreeType (optional),pandoc (>=1.14, needed for vignettes; if not present, markdownpackage will be used) +# Maintainer: Guoyi Zhang + +_pkgname=rgl +_pkgver=0.108.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='3D Visualization Using OpenGL' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-htmltools + r-htmlwidgets + r-jsonlite + r-knitr + r-magrittr + r-r6 +) +optdepends=( + r-akima + r-alphashape3d + r-crosstalk + r-deldir + r-downlit + r-extrafont + r-interp + r-js + r-lattice + r-magick + r-manipulatewidget + r-markdown + r-mass + r-misc3d + r-orientlib + r-pkgdown + r-plotrix + r-rmarkdown + r-shiny + r-tcltk + r-testthat + r-tripack + r-waldo + r-webshot2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rgl/lilac.py b/prepare/r-rgl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rgl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rgl/lilac.yaml b/prepare/r-rgl/lilac.yaml new file mode 100644 index 0000000000..c4baa08295 --- /dev/null +++ b/prepare/r-rgl/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-htmlwidgets +- r-jsonlite +- r-knitr +- r-magrittr +- r-r6 +update_on: +- regex: rgl_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rgl diff --git a/prepare/r-rgmql/PKGBUILD b/prepare/r-rgmql/PKGBUILD new file mode 100644 index 0000000000..5328a2f99f --- /dev/null +++ b/prepare/r-rgmql/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RGMQL +_pkgver=1.14.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GenoMetric Query Language for R/Bioconductor' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-data.table + r-dplyr + r-genomicranges + r-glue + r-httr + r-plyr + r-rgmqllib + r-rjava + r-rtracklayer + r-s4vectors + r-xml2 +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rgmql/lilac.py b/prepare/r-rgmql/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rgmql/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rgmql/lilac.yaml b/prepare/r-rgmql/lilac.yaml new file mode 100644 index 0000000000..dc3f026c22 --- /dev/null +++ b/prepare/r-rgmql/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-data.table +- r-dplyr +- r-genomicranges +- r-glue +- r-httr +- r-plyr +- r-rgmqllib +- r-rjava +- r-rtracklayer +- r-s4vectors +- r-xml2 +update_on: +- regex: RGMQL_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RGMQL diff --git a/prepare/r-rgmqllib/PKGBUILD b/prepare/r-rgmqllib/PKGBUILD new file mode 100644 index 0000000000..224584be58 --- /dev/null +++ b/prepare/r-rgmqllib/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RGMQLlib +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RGMQLlib, java libraries to run GMQL scala API' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rgmqllib/lilac.py b/prepare/r-rgmqllib/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rgmqllib/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rgmqllib/lilac.yaml b/prepare/r-rgmqllib/lilac.yaml new file mode 100644 index 0000000000..04768e7acd --- /dev/null +++ b/prepare/r-rgmqllib/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RGMQLlib_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RGMQLlib diff --git a/prepare/r-rgraph2js/PKGBUILD b/prepare/r-rgraph2js/PKGBUILD new file mode 100644 index 0000000000..2134e04cb5 --- /dev/null +++ b/prepare/r-rgraph2js/PKGBUILD @@ -0,0 +1,38 @@ +# system requirements: jQuery, jQueryUI, qTip2, D3js and Raphael arerequired Javascript libraries made available via the onlineCDNJS service (http://cdnjs.cloudflare.com). +# Maintainer: Guoyi Zhang + +_pkgname=RGraph2js +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Convert a Graph into a D3js Script' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-digest + r-graph + r-rjson + r-whisker +) +optdepends=( + r-biocgenerics + r-biocstyle + r-runit + r-sna + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rgraph2js/lilac.py b/prepare/r-rgraph2js/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rgraph2js/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rgraph2js/lilac.yaml b/prepare/r-rgraph2js/lilac.yaml new file mode 100644 index 0000000000..dbc813412e --- /dev/null +++ b/prepare/r-rgraph2js/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-graph +- r-rjson +- r-whisker +update_on: +- regex: RGraph2js_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RGraph2js diff --git a/prepare/r-rgraphviz/PKGBUILD b/prepare/r-rgraphviz/PKGBUILD new file mode 100644 index 0000000000..d04fe8cc57 --- /dev/null +++ b/prepare/r-rgraphviz/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: optionally Graphviz (>= 2.16) +# Maintainer: Guoyi Zhang + +_pkgname=Rgraphviz +_pkgver=2.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Provides plotting capabilities for R graph objects' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('EPL') +depends=( + r + r-graph +) +optdepends=( + r-biocgenerics + r-runit + r-xml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rgraphviz/lilac.py b/prepare/r-rgraphviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rgraphviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rgraphviz/lilac.yaml b/prepare/r-rgraphviz/lilac.yaml new file mode 100644 index 0000000000..7a0bafbad0 --- /dev/null +++ b/prepare/r-rgraphviz/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +update_on: +- regex: Rgraphviz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rgraphviz diff --git a/prepare/r-rgreat/PKGBUILD b/prepare/r-rgreat/PKGBUILD new file mode 100644 index 0000000000..bdb42409fa --- /dev/null +++ b/prepare/r-rgreat/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rGREAT +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Client for GREAT Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-genomicranges + r-getoptlong + r-iranges + r-rcurl + r-rjson +) +optdepends=( + r-circlize + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rgreat/lilac.py b/prepare/r-rgreat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rgreat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rgreat/lilac.yaml b/prepare/r-rgreat/lilac.yaml new file mode 100644 index 0000000000..d4256ef8a1 --- /dev/null +++ b/prepare/r-rgreat/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-getoptlong +- r-iranges +- r-rcurl +- r-rjson +update_on: +- regex: rGREAT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rGREAT diff --git a/prepare/r-rgsea/PKGBUILD b/prepare/r-rgsea/PKGBUILD new file mode 100644 index 0000000000..a881483d51 --- /dev/null +++ b/prepare/r-rgsea/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RGSEA +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Random Gene Set Enrichment Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics +) +optdepends=( + r-biocstyle + r-geoquery + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rgsea/lilac.py b/prepare/r-rgsea/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rgsea/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rgsea/lilac.yaml b/prepare/r-rgsea/lilac.yaml new file mode 100644 index 0000000000..1e12dcba4d --- /dev/null +++ b/prepare/r-rgsea/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +update_on: +- regex: RGSEA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RGSEA diff --git a/prepare/r-rgsepd/PKGBUILD b/prepare/r-rgsepd/PKGBUILD new file mode 100644 index 0000000000..7018613514 --- /dev/null +++ b/prepare/r-rgsepd/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rgsepd +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Set Enrichment / Projection Displays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biomart + r-deseq2 + r-go.db + r-goseq + r-gplots + r-hash + r-org.hs.eg.db + r-summarizedexperiment +) +optdepends=( + r-biocgenerics + r-boot + r-knitr + r-tools + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rgsepd/lilac.py b/prepare/r-rgsepd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rgsepd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rgsepd/lilac.yaml b/prepare/r-rgsepd/lilac.yaml new file mode 100644 index 0000000000..486d997dce --- /dev/null +++ b/prepare/r-rgsepd/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biomart +- r-deseq2 +- r-go.db +- r-goseq +- r-gplots +- r-hash +- r-org.hs.eg.db +- r-summarizedexperiment +update_on: +- regex: rgsepd_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rgsepd diff --git a/prepare/r-rhandsontable/PKGBUILD b/prepare/r-rhandsontable/PKGBUILD new file mode 100644 index 0000000000..2ab8d17d27 --- /dev/null +++ b/prepare/r-rhandsontable/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rhandsontable +_pkgver=0.3.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Interface to the 'Handsontable.js' Library" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmlwidgets + r-jsonlite + r-magrittr +) +optdepends=( + r-htmltools + r-knitr + r-miniui + r-rmarkdown + r-rstudioapi + r-shiny +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rhandsontable/lilac.py b/prepare/r-rhandsontable/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rhandsontable/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rhandsontable/lilac.yaml b/prepare/r-rhandsontable/lilac.yaml new file mode 100644 index 0000000000..ba5c81302c --- /dev/null +++ b/prepare/r-rhandsontable/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmlwidgets +- r-jsonlite +- r-magrittr +update_on: +- regex: rhandsontable_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rhandsontable diff --git a/prepare/r-rhdf5/PKGBUILD b/prepare/r-rhdf5/PKGBUILD new file mode 100644 index 0000000000..4ae0da52cd --- /dev/null +++ b/prepare/r-rhdf5/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=rhdf5 +_pkgver=2.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Interface to HDF5' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-rhdf5filters + r-rhdf5lib +) +optdepends=( + r-biocstyle + r-bit64 + r-dplyr + r-ggplot2 + r-knitr + r-microbenchmark + r-mockery + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rhdf5/lilac.py b/prepare/r-rhdf5/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rhdf5/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rhdf5/lilac.yaml b/prepare/r-rhdf5/lilac.yaml new file mode 100644 index 0000000000..945a31657d --- /dev/null +++ b/prepare/r-rhdf5/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rhdf5filters +- r-rhdf5lib +update_on: +- regex: rhdf5_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rhdf5 diff --git a/prepare/r-rhdf5client/PKGBUILD b/prepare/r-rhdf5client/PKGBUILD new file mode 100644 index 0000000000..0cd4f6b6dd --- /dev/null +++ b/prepare/r-rhdf5client/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rhdf5client +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Access HDF5 content from h5serv' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-delayedarray +) +optdepends=( + r-knitr + r-testthat + r-biocstyle + r-dt + r-markdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rhdf5client/lilac.py b/prepare/r-rhdf5client/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rhdf5client/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rhdf5client/lilac.yaml b/prepare/r-rhdf5client/lilac.yaml new file mode 100644 index 0000000000..5d501da289 --- /dev/null +++ b/prepare/r-rhdf5client/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-delayedarray +update_on: +- regex: rhdf5client_(\d.+\d+.\d+).tar.gz + source: regex + url: https://bioconductor.org/packages/rhdf5client diff --git a/prepare/r-rhdf5filters/PKGBUILD b/prepare/r-rhdf5filters/PKGBUILD new file mode 100644 index 0000000000..e1afe56517 --- /dev/null +++ b/prepare/r-rhdf5filters/PKGBUILD @@ -0,0 +1,36 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=rhdf5filters +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='HDF5 Compression Filters' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-rhdf5lib +) +optdepends=( + r-biocstyle + r-knitr + r-rhdf5 + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rhdf5filters/lilac.py b/prepare/r-rhdf5filters/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rhdf5filters/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rhdf5filters/lilac.yaml b/prepare/r-rhdf5filters/lilac.yaml new file mode 100644 index 0000000000..3cc10b9001 --- /dev/null +++ b/prepare/r-rhdf5filters/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rhdf5lib +update_on: +- regex: rhdf5filters_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rhdf5filters diff --git a/prepare/r-rhdf5lib/PKGBUILD b/prepare/r-rhdf5lib/PKGBUILD new file mode 100644 index 0000000000..973efe468e --- /dev/null +++ b/prepare/r-rhdf5lib/PKGBUILD @@ -0,0 +1,34 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=Rhdf5lib +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='hdf5 library as an R package' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-biocstyle + r-knitr + r-mockery + r-rmarkdown + r-tinytest +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rhdf5lib/lilac.py b/prepare/r-rhdf5lib/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rhdf5lib/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rhdf5lib/lilac.yaml b/prepare/r-rhdf5lib/lilac.yaml new file mode 100644 index 0000000000..14e9adac8d --- /dev/null +++ b/prepare/r-rhdf5lib/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Rhdf5lib_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rhdf5lib diff --git a/prepare/r-rhisat2/PKGBUILD b/prepare/r-rhisat2/PKGBUILD new file mode 100644 index 0000000000..b6846db937 --- /dev/null +++ b/prepare/r-rhisat2/PKGBUILD @@ -0,0 +1,36 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=Rhisat2 +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Wrapper for HISAT2 Aligner' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicfeatures + r-genomicranges + r-sgseq +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rhisat2/lilac.py b/prepare/r-rhisat2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rhisat2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rhisat2/lilac.yaml b/prepare/r-rhisat2/lilac.yaml new file mode 100644 index 0000000000..3780011232 --- /dev/null +++ b/prepare/r-rhisat2/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicfeatures +- r-genomicranges +- r-sgseq +update_on: +- regex: Rhisat2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rhisat2 diff --git a/prepare/r-rhpcblasctl/PKGBUILD b/prepare/r-rhpcblasctl/PKGBUILD new file mode 100644 index 0000000000..a99e17c994 --- /dev/null +++ b/prepare/r-rhpcblasctl/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RhpcBLASctl +_pkgver=0.21-247.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Control the Number of Threads on 'BLAS'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('AGPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rhpcblasctl/lilac.py b/prepare/r-rhpcblasctl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rhpcblasctl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rhpcblasctl/lilac.yaml b/prepare/r-rhpcblasctl/lilac.yaml new file mode 100644 index 0000000000..3c5fbd33c4 --- /dev/null +++ b/prepare/r-rhpcblasctl/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RhpcBLASctl_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RhpcBLASctl diff --git a/prepare/r-rhtslib/PKGBUILD b/prepare/r-rhtslib/PKGBUILD new file mode 100644 index 0000000000..56fe79075e --- /dev/null +++ b/prepare/r-rhtslib/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: libbz2 & liblzma & libcurl (with header files), GNUmake +# Maintainer: Guoyi Zhang + +_pkgname=Rhtslib +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='HTSlib high-throughput sequencing library as an R package' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-zlibbioc +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rhtslib/lilac.py b/prepare/r-rhtslib/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rhtslib/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rhtslib/lilac.yaml b/prepare/r-rhtslib/lilac.yaml new file mode 100644 index 0000000000..166dcd879e --- /dev/null +++ b/prepare/r-rhtslib/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-zlibbioc +update_on: +- regex: Rhtslib_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rhtslib diff --git a/prepare/r-ribocrypt/PKGBUILD b/prepare/r-ribocrypt/PKGBUILD new file mode 100644 index 0000000000..33ad7b0baa --- /dev/null +++ b/prepare/r-ribocrypt/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RiboCrypt +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive visualization in genomics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-data.table + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-orfik + r-plotly + r-rlang +) +optdepends=( + r-biocstyle + r-bsgenome + r-bsgenome.hsapiens.ucsc.hg19 + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ribocrypt/lilac.py b/prepare/r-ribocrypt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ribocrypt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ribocrypt/lilac.yaml b/prepare/r-ribocrypt/lilac.yaml new file mode 100644 index 0000000000..e0efbbbb96 --- /dev/null +++ b/prepare/r-ribocrypt/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-data.table +- r-dplyr +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-orfik +- r-plotly +- r-rlang +update_on: +- regex: RiboCrypt_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RiboCrypt diff --git a/prepare/r-ribodipa/PKGBUILD b/prepare/r-ribodipa/PKGBUILD new file mode 100644 index 0000000000..15e7c36625 --- /dev/null +++ b/prepare/r-ribodipa/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RiboDiPA +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential pattern analysis for Ribo-seq data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biocfilecache + r-data.table + r-deseq2 + r-doparallel + r-elitism + r-foreach + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-matrixstats + r-qvalue + r-rcpp + r-reldist + r-rsamtools + r-s4vectors +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ribodipa/lilac.py b/prepare/r-ribodipa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ribodipa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ribodipa/lilac.yaml b/prepare/r-ribodipa/lilac.yaml new file mode 100644 index 0000000000..245c1d2c01 --- /dev/null +++ b/prepare/r-ribodipa/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-data.table +- r-deseq2 +- r-doparallel +- r-elitism +- r-foreach +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-matrixstats +- r-qvalue +- r-rcpp +- r-reldist +- r-rsamtools +- r-s4vectors +update_on: +- regex: RiboDiPA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RiboDiPA diff --git a/prepare/r-riboprofiling/PKGBUILD b/prepare/r-riboprofiling/PKGBUILD new file mode 100644 index 0000000000..c911767ebd --- /dev/null +++ b/prepare/r-riboprofiling/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RiboProfiling +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-data.table + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggbio + r-ggplot2 + r-iranges + r-plyr + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors + r-sqldf +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-knitr + r-summarizedexperiment + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-riboprofiling/lilac.py b/prepare/r-riboprofiling/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-riboprofiling/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-riboprofiling/lilac.yaml b/prepare/r-riboprofiling/lilac.yaml new file mode 100644 index 0000000000..d621439660 --- /dev/null +++ b/prepare/r-riboprofiling/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-data.table +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggbio +- r-ggplot2 +- r-iranges +- r-plyr +- r-reshape2 +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-sqldf +update_on: +- regex: RiboProfiling_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RiboProfiling diff --git a/prepare/r-ribor/PKGBUILD b/prepare/r-ribor/PKGBUILD new file mode 100644 index 0000000000..1281e827eb --- /dev/null +++ b/prepare/r-ribor/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ribor +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R Interface for Ribo Files' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-ggplot2 + r-hash + r-rhdf5 + r-rlang + r-s4vectors + r-tidyr + r-yaml +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ribor/lilac.py b/prepare/r-ribor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ribor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ribor/lilac.yaml b/prepare/r-ribor/lilac.yaml new file mode 100644 index 0000000000..8e6a523cc2 --- /dev/null +++ b/prepare/r-ribor/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-hash +- r-rhdf5 +- r-rlang +- r-s4vectors +- r-tidyr +- r-yaml +update_on: +- regex: ribor_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ribor diff --git a/prepare/r-riboseqr/PKGBUILD b/prepare/r-riboseqr/PKGBUILD new file mode 100644 index 0000000000..648a2c6a5c --- /dev/null +++ b/prepare/r-riboseqr/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=riboSeqR +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of sequencing data from ribosome profiling experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-bayseq + r-genomeinfodb + r-genomicranges + r-iranges + r-rsamtools + r-seqlogo +) +optdepends=( + r-biocgenerics + r-biocstyle + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-riboseqr/lilac.py b/prepare/r-riboseqr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-riboseqr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-riboseqr/lilac.yaml b/prepare/r-riboseqr/lilac.yaml new file mode 100644 index 0000000000..12f925e86a --- /dev/null +++ b/prepare/r-riboseqr/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-bayseq +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rsamtools +- r-seqlogo +update_on: +- regex: riboSeqR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/riboSeqR diff --git a/prepare/r-ribosomeprofilingqc/PKGBUILD b/prepare/r-ribosomeprofilingqc/PKGBUILD new file mode 100644 index 0000000000..3cb4c4af9d --- /dev/null +++ b/prepare/r-ribosomeprofilingqc/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ribosomeProfilingQC +_pkgver=1.6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Ribosome Profiling Quality Control' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocgenerics + r-biostrings + r-bsgenome + r-edaseq + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggfittext + r-ggplot2 + r-ggrepel + r-iranges + r-motifstack + r-rsamtools + r-rsubread + r-rtracklayer + r-ruvseq + r-s4vectors + r-scales + r-xvector +) +optdepends=( + r-biocstyle + r-bsgenome.drerio.ucsc.danrer10 + r-edger + r-knitr + r-limma + r-rmarkdown + r-runit + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ribosomeprofilingqc/lilac.py b/prepare/r-ribosomeprofilingqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ribosomeprofilingqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ribosomeprofilingqc/lilac.yaml b/prepare/r-ribosomeprofilingqc/lilac.yaml new file mode 100644 index 0000000000..96529f9dcc --- /dev/null +++ b/prepare/r-ribosomeprofilingqc/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-edaseq +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggfittext +- r-ggplot2 +- r-ggrepel +- r-iranges +- r-motifstack +- r-rsamtools +- r-rsubread +- r-rtracklayer +- r-ruvseq +- r-s4vectors +- r-scales +- r-xvector +update_on: +- regex: ribosomeProfilingQC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ribosomeProfilingQC diff --git a/prepare/r-rimmport/PKGBUILD b/prepare/r-rimmport/PKGBUILD new file mode 100644 index 0000000000..8376a1f743 --- /dev/null +++ b/prepare/r-rimmport/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RImmPort +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RImmPort: Enabling Ready-for-analysis Immunology Research Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-dbi + r-dplyr + r-plyr + r-reshape2 + r-rsqlite + r-sqldf +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rimmport/lilac.py b/prepare/r-rimmport/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rimmport/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rimmport/lilac.yaml b/prepare/r-rimmport/lilac.yaml new file mode 100644 index 0000000000..4ee9c84228 --- /dev/null +++ b/prepare/r-rimmport/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-dbi +- r-dplyr +- r-plyr +- r-reshape2 +- r-rsqlite +- r-sqldf +update_on: +- regex: RImmPort_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RImmPort diff --git a/prepare/r-ringo/PKGBUILD b/prepare/r-ringo/PKGBUILD new file mode 100644 index 0000000000..2c49a8ca38 --- /dev/null +++ b/prepare/r-ringo/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Ringo +_pkgver=1.58.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Investigation of ChIP-chip Oligoarrays' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-genefilter + r-limma + r-rcolorbrewer + r-vsn +) +optdepends=( + r-mclust + r-rtracklayer + r-topgo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ringo/lilac.py b/prepare/r-ringo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ringo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ringo/lilac.yaml b/prepare/r-ringo/lilac.yaml new file mode 100644 index 0000000000..d99b343172 --- /dev/null +++ b/prepare/r-ringo/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-genefilter +- r-limma +- r-rcolorbrewer +- r-vsn +update_on: +- regex: Ringo_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Ringo diff --git a/prepare/r-rintrojs/PKGBUILD b/prepare/r-rintrojs/PKGBUILD new file mode 100644 index 0000000000..12cac2ac8b --- /dev/null +++ b/prepare/r-rintrojs/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rintrojs +_pkgver=0.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Wrapper for the 'Intro.js' Library" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('AGPL') +depends=( + r + r-jsonlite + r-shiny +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rintrojs/lilac.py b/prepare/r-rintrojs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rintrojs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rintrojs/lilac.yaml b/prepare/r-rintrojs/lilac.yaml new file mode 100644 index 0000000000..06be076333 --- /dev/null +++ b/prepare/r-rintrojs/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-jsonlite +- r-shiny +update_on: +- regex: rintrojs_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rintrojs diff --git a/prepare/r-rio/PKGBUILD b/prepare/r-rio/PKGBUILD new file mode 100644 index 0000000000..f77afcfb80 --- /dev/null +++ b/prepare/r-rio/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rio +_pkgver=0.5.29 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Swiss-Army Knife for Data I/O' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-curl + r-data.table + r-haven + r-openxlsx + r-readxl + r-tibble +) +optdepends=( + r-arrow + r-bit64 + r-clipr + r-datasets + r-feather + r-fst + r-hexview + r-jsonlite + r-knitr + r-magrittr + r-pzfx + r-readods + r-readr + r-rmarkdown + r-rmatio + r-testthat + r-xml2 + r-yaml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rio/lilac.py b/prepare/r-rio/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rio/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rio/lilac.yaml b/prepare/r-rio/lilac.yaml new file mode 100644 index 0000000000..38c0eff58f --- /dev/null +++ b/prepare/r-rio/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-data.table +- r-haven +- r-openxlsx +- r-readxl +- r-tibble +update_on: +- regex: rio_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rio diff --git a/prepare/r-ripat/PKGBUILD b/prepare/r-ripat/PKGBUILD new file mode 100644 index 0000000000..1d525bdceb --- /dev/null +++ b/prepare/r-ripat/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RIPAT +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Retroviral Integration Pattern Analysis Tool (RIPAT)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biomart + r-genomicranges + r-ggplot2 + r-iranges + r-karyoploter + r-openxlsx + r-plyr + r-regioner + r-rtracklayer + r-stringr +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ripat/lilac.py b/prepare/r-ripat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ripat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ripat/lilac.yaml b/prepare/r-ripat/lilac.yaml new file mode 100644 index 0000000000..59570e7c1e --- /dev/null +++ b/prepare/r-ripat/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-karyoploter +- r-openxlsx +- r-plyr +- r-regioner +- r-rtracklayer +- r-stringr +update_on: +- regex: RIPAT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RIPAT diff --git a/prepare/r-risa/PKGBUILD b/prepare/r-risa/PKGBUILD new file mode 100644 index 0000000000..011267c21d --- /dev/null +++ b/prepare/r-risa/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Risa +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Converting experimental metadata from ISA-tab into Bioconductor data structures' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-affy + r-biobase + r-biocviews + r-rcpp + r-xcms +) +optdepends=( + r-faahko +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-risa/lilac.py b/prepare/r-risa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-risa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-risa/lilac.yaml b/prepare/r-risa/lilac.yaml new file mode 100644 index 0000000000..139bf243d6 --- /dev/null +++ b/prepare/r-risa/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +- r-biocviews +- r-rcpp +- r-xcms +update_on: +- regex: Risa_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Risa diff --git a/prepare/r-rismed/PKGBUILD b/prepare/r-rismed/PKGBUILD new file mode 100644 index 0000000000..91b89a18d8 --- /dev/null +++ b/prepare/r-rismed/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RISmed +_pkgver=2.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Download Content from NCBI Databases' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-httr + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rismed/lilac.py b/prepare/r-rismed/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rismed/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rismed/lilac.yaml b/prepare/r-rismed/lilac.yaml new file mode 100644 index 0000000000..b6479aa941 --- /dev/null +++ b/prepare/r-rismed/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-httr +- r-xml2 +update_on: +- regex: RISmed_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RISmed diff --git a/prepare/r-ritan/PKGBUILD b/prepare/r-ritan/PKGBUILD new file mode 100644 index 0000000000..8d176b3c21 --- /dev/null +++ b/prepare/r-ritan/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RITAN +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Rapid Integration of Term Annotation and Network resources' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-bgeedb + r-dynamictreecut + r-ggplot2 + r-gplots + r-gridextra + r-gsubfn + r-hash + r-igraph + r-knitr + r-linkcomm + r-mcl + r-plotrix + r-png + r-rcolorbrewer + r-reshape2 + r-ritandata + r-sqldf + r-stringdb +) +optdepends=( + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ritan/lilac.py b/prepare/r-ritan/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ritan/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ritan/lilac.yaml b/prepare/r-ritan/lilac.yaml new file mode 100644 index 0000000000..516e7ec273 --- /dev/null +++ b/prepare/r-ritan/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bgeedb +- r-dynamictreecut +- r-ggplot2 +- r-gplots +- r-gridextra +- r-gsubfn +- r-hash +- r-igraph +- r-knitr +- r-linkcomm +- r-mcl +- r-plotrix +- r-png +- r-rcolorbrewer +- r-reshape2 +- r-ritandata +- r-sqldf +- r-stringdb +update_on: +- regex: RITAN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RITAN diff --git a/prepare/r-ritandata/PKGBUILD b/prepare/r-ritandata/PKGBUILD new file mode 100644 index 0000000000..b51ca347ca --- /dev/null +++ b/prepare/r-ritandata/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RITANdata +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='This package contains the annotation and network data sets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ritandata/lilac.py b/prepare/r-ritandata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ritandata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ritandata/lilac.yaml b/prepare/r-ritandata/lilac.yaml new file mode 100644 index 0000000000..562ea024e7 --- /dev/null +++ b/prepare/r-ritandata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RITANdata_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RITANdata diff --git a/prepare/r-river/PKGBUILD b/prepare/r-river/PKGBUILD new file mode 100644 index 0000000000..27a6e2920d --- /dev/null +++ b/prepare/r-river/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RIVER +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R package for RIVER (RNA-Informed Variant Effect on Regulation)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-ggplot2 + r-glmnet + r-proc +) +optdepends=( + r-biocstyle + r-devtools + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-river/lilac.py b/prepare/r-river/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-river/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-river/lilac.yaml b/prepare/r-river/lilac.yaml new file mode 100644 index 0000000000..ad9847c75f --- /dev/null +++ b/prepare/r-river/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-ggplot2 +- r-glmnet +- r-proc +update_on: +- regex: RIVER_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RIVER diff --git a/prepare/r-rjags/PKGBUILD b/prepare/r-rjags/PKGBUILD new file mode 100644 index 0000000000..dd28b9ce84 --- /dev/null +++ b/prepare/r-rjags/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: JAGS 4.x.y +# Maintainer: Guoyi Zhang + +_pkgname=rjags +_pkgver=4-12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian Graphical Models using MCMC' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-coda +) +optdepends=( + r-tcltk +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rjags/lilac.py b/prepare/r-rjags/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rjags/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rjags/lilac.yaml b/prepare/r-rjags/lilac.yaml new file mode 100644 index 0000000000..763d89fd02 --- /dev/null +++ b/prepare/r-rjags/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-coda +update_on: +- regex: rjags_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rjags diff --git a/prepare/r-rjava/PKGBUILD b/prepare/r-rjava/PKGBUILD new file mode 100644 index 0000000000..503c99f0a7 --- /dev/null +++ b/prepare/r-rjava/PKGBUILD @@ -0,0 +1,27 @@ +# system requirements: Java JDK 1.2 or higher (for JRI/REngine JDK 1.4 orhigher), GNU make +# Maintainer: Guoyi Zhang + +_pkgname=rJava +_pkgver=1.0-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Low-Level R to Java Interface' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rjava/lilac.py b/prepare/r-rjava/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rjava/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rjava/lilac.yaml b/prepare/r-rjava/lilac.yaml new file mode 100644 index 0000000000..26ffe16007 --- /dev/null +++ b/prepare/r-rjava/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: rJava_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rJava diff --git a/prepare/r-rjmcmcnucleosomes/PKGBUILD b/prepare/r-rjmcmcnucleosomes/PKGBUILD new file mode 100644 index 0000000000..f8a3f0d563 --- /dev/null +++ b/prepare/r-rjmcmcnucleosomes/PKGBUILD @@ -0,0 +1,42 @@ +# system requirements: Rcpp +# Maintainer: Guoyi Zhang + +_pkgname=RJMCMCNucleosomes +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biocparallel + r-consensusseeker + r-genomeinfodb + r-genomicranges + r-iranges + r-rcpp + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-nucleosim + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rjmcmcnucleosomes/lilac.py b/prepare/r-rjmcmcnucleosomes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rjmcmcnucleosomes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rjmcmcnucleosomes/lilac.yaml b/prepare/r-rjmcmcnucleosomes/lilac.yaml new file mode 100644 index 0000000000..1b9cfbf459 --- /dev/null +++ b/prepare/r-rjmcmcnucleosomes/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-consensusseeker +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rcpp +- r-s4vectors +update_on: +- regex: RJMCMCNucleosomes_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RJMCMCNucleosomes diff --git a/prepare/r-rjsonio/PKGBUILD b/prepare/r-rjsonio/PKGBUILD new file mode 100644 index 0000000000..aaa73a9820 --- /dev/null +++ b/prepare/r-rjsonio/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RJSONIO +_pkgver=1.3-1.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Serialize R Objects to JSON, JavaScript Object Notation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rjsonio/lilac.py b/prepare/r-rjsonio/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rjsonio/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rjsonio/lilac.yaml b/prepare/r-rjsonio/lilac.yaml new file mode 100644 index 0000000000..fea88c2356 --- /dev/null +++ b/prepare/r-rjsonio/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RJSONIO_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RJSONIO diff --git a/prepare/r-rlab/PKGBUILD b/prepare/r-rlab/PKGBUILD new file mode 100644 index 0000000000..3e3c82e8de --- /dev/null +++ b/prepare/r-rlab/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rlab +_pkgver=2.15.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions and Datasets Required for ST370 class' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rlab/lilac.py b/prepare/r-rlab/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rlab/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rlab/lilac.yaml b/prepare/r-rlab/lilac.yaml new file mode 100644 index 0000000000..a7dbf411b0 --- /dev/null +++ b/prepare/r-rlab/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Rlab_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rlab diff --git a/prepare/r-rlabkey/PKGBUILD b/prepare/r-rlabkey/PKGBUILD new file mode 100644 index 0000000000..9fc1182bd9 --- /dev/null +++ b/prepare/r-rlabkey/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rlabkey +_pkgver=2.8.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Data Exchange Between R and 'LabKey' Server" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-httr + r-jsonlite + r-rcpp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rlabkey/lilac.py b/prepare/r-rlabkey/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rlabkey/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rlabkey/lilac.yaml b/prepare/r-rlabkey/lilac.yaml new file mode 100644 index 0000000000..601af9ce9d --- /dev/null +++ b/prepare/r-rlabkey/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-httr +- r-jsonlite +- r-rcpp +update_on: +- regex: Rlabkey_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rlabkey diff --git a/prepare/r-rlassocox/PKGBUILD b/prepare/r-rlassocox/PKGBUILD new file mode 100644 index 0000000000..7ec95b271e --- /dev/null +++ b/prepare/r-rlassocox/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RLassoCox +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A reweighted Lasso-Cox by integrating gene interaction information' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-glmnet + r-igraph +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rlassocox/lilac.py b/prepare/r-rlassocox/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rlassocox/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rlassocox/lilac.yaml b/prepare/r-rlassocox/lilac.yaml new file mode 100644 index 0000000000..96418a2f9e --- /dev/null +++ b/prepare/r-rlassocox/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-glmnet +- r-igraph +update_on: +- regex: RLassoCox_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RLassoCox diff --git a/prepare/r-rlhub/PKGBUILD b/prepare/r-rlhub/PKGBUILD new file mode 100644 index 0000000000..c79ed85630 --- /dev/null +++ b/prepare/r-rlhub/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RLHub +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An ExperimentHub package for accessing processed RLSuite data sets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationhub + r-experimenthub +) +optdepends=( + r-biocstyle + r-dt + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rlhub/lilac.py b/prepare/r-rlhub/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rlhub/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rlhub/lilac.yaml b/prepare/r-rlhub/lilac.yaml new file mode 100644 index 0000000000..ae8ea9d344 --- /dev/null +++ b/prepare/r-rlhub/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-experimenthub +update_on: +- regex: RLHub_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RLHub diff --git a/prepare/r-rlist/PKGBUILD b/prepare/r-rlist/PKGBUILD new file mode 100644 index 0000000000..1f3f2ed9c9 --- /dev/null +++ b/prepare/r-rlist/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rlist +_pkgver=0.4.6.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Toolbox for Non-Tabular Data Manipulation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-data.table + r-jsonlite + r-xml + r-yaml +) +optdepends=( + r-stringdist + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rlist/lilac.py b/prepare/r-rlist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rlist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rlist/lilac.yaml b/prepare/r-rlist/lilac.yaml new file mode 100644 index 0000000000..eb5da47407 --- /dev/null +++ b/prepare/r-rlist/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-jsonlite +- r-xml +- r-yaml +update_on: +- regex: rlist_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rlist diff --git a/prepare/r-rlmm/PKGBUILD b/prepare/r-rlmm/PKGBUILD new file mode 100644 index 0000000000..f7bd3aa8fc --- /dev/null +++ b/prepare/r-rlmm/PKGBUILD @@ -0,0 +1,27 @@ +# system requirements: Internal files Xba.CQV, Xba.regions (or otherregions file) +# Maintainer: Guoyi Zhang + +_pkgname=RLMM +_pkgver=1.56.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Genotype Calling Algorithm for Affymetrix SNP Arrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rlmm/lilac.py b/prepare/r-rlmm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rlmm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rlmm/lilac.yaml b/prepare/r-rlmm/lilac.yaml new file mode 100644 index 0000000000..84b30218d9 --- /dev/null +++ b/prepare/r-rlmm/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RLMM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RLMM diff --git a/prepare/r-rlseq/PKGBUILD b/prepare/r-rlseq/PKGBUILD new file mode 100644 index 0000000000..527335acff --- /dev/null +++ b/prepare/r-rlseq/PKGBUILD @@ -0,0 +1,73 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RLSeq +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RLSeq: An analysis package for R-loop mapping data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationhub + r-aws.s3 + r-callr + r-caretensemble + r-circlize + r-complexheatmap + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggplotify + r-ggprism + r-pheatmap + r-rcolorbrewer + r-regioner + r-rlhub + r-rtracklayer + r-valr + r-venndiagram +) +optdepends=( + r-annotationdbi + r-biocstyle + r-covr + r-dt + r-futile.logger + r-httr + r-jsonlite + r-kableextra + r-kernlab + r-knitr + r-lintr + r-magick + r-mass + r-org.hs.eg.db + r-r.utils + r-randomforest + r-rcmdcheck + r-readr + r-rmarkdown + r-rpart + r-testthat + r-tibble + r-tidyr + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rlseq/lilac.py b/prepare/r-rlseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rlseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rlseq/lilac.yaml b/prepare/r-rlseq/lilac.yaml new file mode 100644 index 0000000000..824d4a6224 --- /dev/null +++ b/prepare/r-rlseq/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-aws.s3 +- r-callr +- r-caretensemble +- r-circlize +- r-complexheatmap +- r-dplyr +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-ggplotify +- r-ggprism +- r-pheatmap +- r-rcolorbrewer +- r-regioner +- r-rlhub +- r-rtracklayer +- r-valr +- r-venndiagram +update_on: +- regex: RLSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RLSeq diff --git a/prepare/r-rmagic/PKGBUILD b/prepare/r-rmagic/PKGBUILD new file mode 100644 index 0000000000..960aebda4c --- /dev/null +++ b/prepare/r-rmagic/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rmagic +_pkgver=2.0.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MAGIC - Markov Affinity-Based Graph Imputation of Cells' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-reticulate +) +optdepends=( + r-phater + r-readr + r-seurat + r-viridis +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmagic/lilac.py b/prepare/r-rmagic/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmagic/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmagic/lilac.yaml b/prepare/r-rmagic/lilac.yaml new file mode 100644 index 0000000000..682608f43e --- /dev/null +++ b/prepare/r-rmagic/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-reticulate +update_on: +- regex: Rmagic_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rmagic diff --git a/prepare/r-rmagpie/PKGBUILD b/prepare/r-rmagpie/PKGBUILD new file mode 100644 index 0000000000..5691622475 --- /dev/null +++ b/prepare/r-rmagpie/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rmagpie +_pkgver=1.50.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='MicroArray Gene-expression-based Program In Error rate estimation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-e1071 + r-kernlab + r-pamr +) +optdepends=( + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmagpie/lilac.py b/prepare/r-rmagpie/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmagpie/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmagpie/lilac.yaml b/prepare/r-rmagpie/lilac.yaml new file mode 100644 index 0000000000..35584e0e42 --- /dev/null +++ b/prepare/r-rmagpie/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-e1071 +- r-kernlab +- r-pamr +update_on: +- regex: Rmagpie_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rmagpie diff --git a/prepare/r-rmallow/PKGBUILD b/prepare/r-rmallow/PKGBUILD new file mode 100644 index 0000000000..c4c9d49dfd --- /dev/null +++ b/prepare/r-rmallow/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RMallow +_pkgver=1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Fit Multi-Modal Mallows' Models to Ranking Data" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-combinat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmallow/lilac.py b/prepare/r-rmallow/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmallow/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmallow/lilac.yaml b/prepare/r-rmallow/lilac.yaml new file mode 100644 index 0000000000..93421cb160 --- /dev/null +++ b/prepare/r-rmallow/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-combinat +update_on: +- regex: RMallow_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RMallow diff --git a/prepare/r-rmarkdown/PKGBUILD b/prepare/r-rmarkdown/PKGBUILD new file mode 100644 index 0000000000..e59ada3bb7 --- /dev/null +++ b/prepare/r-rmarkdown/PKGBUILD @@ -0,0 +1,50 @@ +# system requirements: pandoc (>= 1.14) - http://pandoc.org +# Maintainer: Guoyi Zhang + +_pkgname=rmarkdown +_pkgver=2.11 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Dynamic Documents for R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-evaluate + r-htmltools + r-jquerylib + r-jsonlite + r-knitr + r-stringr + r-tinytex + r-xfun + r-yaml +) +optdepends=( + r-bslib + r-digest + r-dygraphs + r-fs + r-rsconnect + r-sass + r-shiny + r-testthat + r-tibble + r-tufte + r-vctrs + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmarkdown/lilac.py b/prepare/r-rmarkdown/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmarkdown/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmarkdown/lilac.yaml b/prepare/r-rmarkdown/lilac.yaml new file mode 100644 index 0000000000..3239918040 --- /dev/null +++ b/prepare/r-rmarkdown/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-evaluate +- r-htmltools +- r-jquerylib +- r-jsonlite +- r-knitr +- r-stringr +- r-tinytex +- r-xfun +- r-yaml +update_on: +- regex: rmarkdown_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rmarkdown diff --git a/prepare/r-rmassbank/PKGBUILD b/prepare/r-rmassbank/PKGBUILD new file mode 100644 index 0000000000..09a3d985ff --- /dev/null +++ b/prepare/r-rmassbank/PKGBUILD @@ -0,0 +1,51 @@ +# system requirements: OpenBabel +# Maintainer: Guoyi Zhang + +_pkgname=RMassBank +_pkgver=3.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Workflow to process tandem MS files and build MassBank records' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-assertthat + r-biobase + r-digest + r-envipat + r-httr + r-logger + r-msnbase + r-mzr + r-rcdk + r-rcpp + r-rcurl + r-rjson + r-s4vectors + r-xml + r-yaml +) +optdepends=( + r-biocstyle + r-camera + r-gplots + r-knitr + r-rmassbankdata + r-runit + r-xcms +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmassbank/lilac.py b/prepare/r-rmassbank/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmassbank/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmassbank/lilac.yaml b/prepare/r-rmassbank/lilac.yaml new file mode 100644 index 0000000000..0821b9db79 --- /dev/null +++ b/prepare/r-rmassbank/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biobase +- r-digest +- r-envipat +- r-httr +- r-logger +- r-msnbase +- r-mzr +- r-rcdk +- r-rcpp +- r-rcurl +- r-rjson +- r-s4vectors +- r-xml +- r-yaml +update_on: +- regex: RMassBank_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RMassBank diff --git a/prepare/r-rmdformats/PKGBUILD b/prepare/r-rmdformats/PKGBUILD new file mode 100644 index 0000000000..9469669332 --- /dev/null +++ b/prepare/r-rmdformats/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rmdformats +_pkgver=1.0.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="HTML Output Formats and Templates for 'rmarkdown' Documents" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bookdown + r-htmltools + r-knitr + r-rmarkdown +) +optdepends=( + r-dt + r-ggplot2 + r-palmerpenguins + r-questionr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmdformats/lilac.py b/prepare/r-rmdformats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmdformats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmdformats/lilac.yaml b/prepare/r-rmdformats/lilac.yaml new file mode 100644 index 0000000000..e5a8d3747a --- /dev/null +++ b/prepare/r-rmdformats/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bookdown +- r-htmltools +- r-knitr +- r-rmarkdown +update_on: +- regex: rmdformats_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rmdformats diff --git a/prepare/r-rmelting/PKGBUILD b/prepare/r-rmelting/PKGBUILD new file mode 100644 index 0000000000..1ad1d464af --- /dev/null +++ b/prepare/r-rmelting/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: Java +# Maintainer: Guoyi Zhang + +_pkgname=rmelting +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Interface to MELTING 5' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rdpack + r-rjava +) +optdepends=( + r-knitr + r-pander + r-readxl + r-reshape2 + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmelting/lilac.py b/prepare/r-rmelting/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmelting/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmelting/lilac.yaml b/prepare/r-rmelting/lilac.yaml new file mode 100644 index 0000000000..8bfb155fe2 --- /dev/null +++ b/prepare/r-rmelting/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rdpack +- r-rjava +update_on: +- regex: rmelting_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rmelting diff --git a/prepare/r-rmeta/PKGBUILD b/prepare/r-rmeta/PKGBUILD new file mode 100644 index 0000000000..88d3564c62 --- /dev/null +++ b/prepare/r-rmeta/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rmeta +_pkgver=3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Meta-Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmeta/lilac.py b/prepare/r-rmeta/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmeta/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmeta/lilac.yaml b/prepare/r-rmeta/lilac.yaml new file mode 100644 index 0000000000..812b9b3e54 --- /dev/null +++ b/prepare/r-rmeta/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: rmeta_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rmeta diff --git a/prepare/r-rmio/PKGBUILD b/prepare/r-rmio/PKGBUILD new file mode 100644 index 0000000000..07fe3c15ce --- /dev/null +++ b/prepare/r-rmio/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rmio +_pkgver=0.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Provides 'mio' C++11 Header Files" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmio/lilac.py b/prepare/r-rmio/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmio/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmio/lilac.yaml b/prepare/r-rmio/lilac.yaml new file mode 100644 index 0000000000..5dc0fd5979 --- /dev/null +++ b/prepare/r-rmio/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: rmio_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rmio diff --git a/prepare/r-rmir.hs.mirna/PKGBUILD b/prepare/r-rmir.hs.mirna/PKGBUILD new file mode 100644 index 0000000000..5f3cbeb6b5 --- /dev/null +++ b/prepare/r-rmir.hs.mirna/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RmiR.Hs.miRNA +_pkgver=1.0.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Various databases of microRNA Targets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi +) +optdepends=( + r-hgug4112a.db + r-methods +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmir.hs.mirna/lilac.py b/prepare/r-rmir.hs.mirna/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmir.hs.mirna/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmir.hs.mirna/lilac.yaml b/prepare/r-rmir.hs.mirna/lilac.yaml new file mode 100644 index 0000000000..c8aafff8b3 --- /dev/null +++ b/prepare/r-rmir.hs.mirna/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +update_on: +- regex: RmiR.Hs.miRNA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RmiR.Hs.miRNA diff --git a/prepare/r-rmir/PKGBUILD b/prepare/r-rmir/PKGBUILD new file mode 100644 index 0000000000..ccff61f41b --- /dev/null +++ b/prepare/r-rmir/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RmiR +_pkgver=1.49.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Package to work with miRNAs and miRNA targets with R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-dbi + r-rmir.hs.mirna + r-rsvgtipsdevice +) +optdepends=( + r-hgug4112a.db + r-org.hs.eg.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmir/lilac.py b/prepare/r-rmir/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmir/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmir/lilac.yaml b/prepare/r-rmir/lilac.yaml new file mode 100644 index 0000000000..d2d0c60a5f --- /dev/null +++ b/prepare/r-rmir/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dbi +- r-rmir.hs.mirna +- r-rsvgtipsdevice +update_on: +- regex: RmiR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RmiR diff --git a/prepare/r-rmisc/PKGBUILD b/prepare/r-rmisc/PKGBUILD new file mode 100644 index 0000000000..64776d4189 --- /dev/null +++ b/prepare/r-rmisc/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rmisc +_pkgver=1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Rmisc: Ryan Miscellaneous' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-plyr +) +optdepends=( + r-hmisc + r-latticeextra + r-stats4 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmisc/lilac.py b/prepare/r-rmisc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmisc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmisc/lilac.yaml b/prepare/r-rmisc/lilac.yaml new file mode 100644 index 0000000000..6a1e494142 --- /dev/null +++ b/prepare/r-rmisc/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-plyr +update_on: +- regex: Rmisc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rmisc diff --git a/prepare/r-rmixmod/PKGBUILD b/prepare/r-rmixmod/PKGBUILD new file mode 100644 index 0000000000..8c184f4f80 --- /dev/null +++ b/prepare/r-rmixmod/PKGBUILD @@ -0,0 +1,29 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=Rmixmod +_pkgver=2.1.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Classification with Mixture Modelling' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcppeigen +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmixmod/lilac.py b/prepare/r-rmixmod/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmixmod/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmixmod/lilac.yaml b/prepare/r-rmixmod/lilac.yaml new file mode 100644 index 0000000000..e38ace2e6a --- /dev/null +++ b/prepare/r-rmixmod/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcppeigen +update_on: +- regex: Rmixmod_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rmixmod diff --git a/prepare/r-rmmquant/PKGBUILD b/prepare/r-rmmquant/PKGBUILD new file mode 100644 index 0000000000..7e466744e1 --- /dev/null +++ b/prepare/r-rmmquant/PKGBUILD @@ -0,0 +1,42 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=Rmmquant +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RNA-Seq multi-mapping Reads Quantification Tool' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocstyle + r-deseq2 + r-devtools + r-genomicranges + r-org.mm.eg.db + r-rcpp + r-s4vectors + r-summarizedexperiment + r-tbx20bamsubset + r-txdb.mmusculus.ucsc.mm9.knowngene +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmmquant/lilac.py b/prepare/r-rmmquant/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmmquant/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmmquant/lilac.yaml b/prepare/r-rmmquant/lilac.yaml new file mode 100644 index 0000000000..0153c81f1f --- /dev/null +++ b/prepare/r-rmmquant/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocstyle +- r-deseq2 +- r-devtools +- r-genomicranges +- r-org.mm.eg.db +- r-rcpp +- r-s4vectors +- r-summarizedexperiment +- r-tbx20bamsubset +- r-txdb.mmusculus.ucsc.mm9.knowngene +update_on: +- regex: Rmmquant_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rmmquant diff --git a/prepare/r-rmpfr/PKGBUILD b/prepare/r-rmpfr/PKGBUILD new file mode 100644 index 0000000000..56e32411e3 --- /dev/null +++ b/prepare/r-rmpfr/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: gmp (>= 4.2.3), mpfr (>= 3.0.0), pdfcrop (part ofTexLive) is required to rebuild the vignettes. +# Maintainer: Guoyi Zhang + +_pkgname=Rmpfr +_pkgver=0.8-7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R MPFR - Multiple Precision Floating-Point Reliable' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-gmp +) +optdepends=( + r-bessel + r-dfoptim + r-mass + r-matrix + r-polynom + r-pracma + r-sfsmisc +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmpfr/lilac.py b/prepare/r-rmpfr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmpfr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmpfr/lilac.yaml b/prepare/r-rmpfr/lilac.yaml new file mode 100644 index 0000000000..68a347ebcd --- /dev/null +++ b/prepare/r-rmpfr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gmp +update_on: +- regex: Rmpfr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rmpfr diff --git a/prepare/r-rmpi/PKGBUILD b/prepare/r-rmpi/PKGBUILD new file mode 100644 index 0000000000..2c1253827c --- /dev/null +++ b/prepare/r-rmpi/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rmpi +_pkgver=0.6-9.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interface (Wrapper) to MPI (Message-Passing Interface)' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmpi/lilac.py b/prepare/r-rmpi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmpi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmpi/lilac.yaml b/prepare/r-rmpi/lilac.yaml new file mode 100644 index 0000000000..df81e63579 --- /dev/null +++ b/prepare/r-rmpi/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Rmpi_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rmpi diff --git a/prepare/r-rms/PKGBUILD b/prepare/r-rms/PKGBUILD new file mode 100644 index 0000000000..07c2e39879 --- /dev/null +++ b/prepare/r-rms/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rms +_pkgver=6.2-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Regression Modeling Strategies' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-digest + r-ggplot2 + r-hmisc + r-htmltable + r-htmltools + r-multcomp + r-polspline + r-quantreg + r-sparsem +) +optdepends=( + r-boot + r-knitr + r-mice + r-plotly + r-rmsb + r-tcltk +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rms/lilac.py b/prepare/r-rms/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rms/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rms/lilac.yaml b/prepare/r-rms/lilac.yaml new file mode 100644 index 0000000000..48e89f713c --- /dev/null +++ b/prepare/r-rms/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-ggplot2 +- r-hmisc +- r-htmltable +- r-htmltools +- r-multcomp +- r-polspline +- r-quantreg +- r-sparsem +update_on: +- regex: rms_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rms diff --git a/prepare/r-rmsnumpress/PKGBUILD b/prepare/r-rmsnumpress/PKGBUILD new file mode 100644 index 0000000000..0802b3ee76 --- /dev/null +++ b/prepare/r-rmsnumpress/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RMSNumpress +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'Rcpp' Bindings to Native C++ Implementation of MS Numpress" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-rcpp +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmsnumpress/lilac.py b/prepare/r-rmsnumpress/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmsnumpress/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmsnumpress/lilac.yaml b/prepare/r-rmsnumpress/lilac.yaml new file mode 100644 index 0000000000..bd72f927cd --- /dev/null +++ b/prepare/r-rmsnumpress/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: RMSNumpress_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RMSNumpress diff --git a/prepare/r-rmspc/PKGBUILD b/prepare/r-rmspc/PKGBUILD new file mode 100644 index 0000000000..69f9f171f4 --- /dev/null +++ b/prepare/r-rmspc/PKGBUILD @@ -0,0 +1,38 @@ +# system requirements: .NET 5.0 +# Maintainer: Guoyi Zhang + +_pkgname=rmspc +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multiple Sample Peak Calling' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocmanager + r-genomicranges + r-processx + r-rtracklayer + r-stringr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmspc/lilac.py b/prepare/r-rmspc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmspc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmspc/lilac.yaml b/prepare/r-rmspc/lilac.yaml new file mode 100644 index 0000000000..1740ec66aa --- /dev/null +++ b/prepare/r-rmspc/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocmanager +- r-genomicranges +- r-processx +- r-rtracklayer +- r-stringr +update_on: +- regex: rmspc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rmspc diff --git a/prepare/r-rmtstat/PKGBUILD b/prepare/r-rmtstat/PKGBUILD new file mode 100644 index 0000000000..7e19434cfe --- /dev/null +++ b/prepare/r-rmtstat/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RMTstat +_pkgver=0.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Distributions, Statistics and Tests derived from Random Matrix Theory' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmtstat/lilac.py b/prepare/r-rmtstat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmtstat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmtstat/lilac.yaml b/prepare/r-rmtstat/lilac.yaml new file mode 100644 index 0000000000..c2f7f1047b --- /dev/null +++ b/prepare/r-rmtstat/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RMTstat_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RMTstat diff --git a/prepare/r-rmutil/PKGBUILD b/prepare/r-rmutil/PKGBUILD new file mode 100644 index 0000000000..fb956f7657 --- /dev/null +++ b/prepare/r-rmutil/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rmutil +_pkgver=1.1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities for Nonlinear Regression and Repeated Measurements Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmutil/lilac.py b/prepare/r-rmutil/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmutil/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmutil/lilac.yaml b/prepare/r-rmutil/lilac.yaml new file mode 100644 index 0000000000..82839d27b0 --- /dev/null +++ b/prepare/r-rmutil/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: rmutil_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rmutil diff --git a/prepare/r-rmysql/PKGBUILD b/prepare/r-rmysql/PKGBUILD new file mode 100644 index 0000000000..259e4badbe --- /dev/null +++ b/prepare/r-rmysql/PKGBUILD @@ -0,0 +1,32 @@ +# system requirements: libmariadb-client-dev | libmariadb-client-lgpl-dev| libmysqlclient-dev (deb), mariadb-devel (rpm), mariadb |mysql-connector-c (brew), mysql56_dev (csw) +# Maintainer: Guoyi Zhang + +_pkgname=RMySQL +_pkgver=0.10.23 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Database Interface and 'MySQL' Driver for R" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dbi +) +optdepends=( + r-curl + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rmysql/lilac.py b/prepare/r-rmysql/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rmysql/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rmysql/lilac.yaml b/prepare/r-rmysql/lilac.yaml new file mode 100644 index 0000000000..d77dcb15cb --- /dev/null +++ b/prepare/r-rmysql/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dbi +update_on: +- regex: RMySQL_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RMySQL diff --git a/prepare/r-rnaagecalc/PKGBUILD b/prepare/r-rnaagecalc/PKGBUILD new file mode 100644 index 0000000000..e1ab21fdb9 --- /dev/null +++ b/prepare/r-rnaagecalc/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RNAAgeCalc +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A multi-tissue transcriptional age calculator' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-ggplot2 + r-impute + r-org.hs.eg.db + r-recount + r-summarizedexperiment +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnaagecalc/lilac.py b/prepare/r-rnaagecalc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnaagecalc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnaagecalc/lilac.yaml b/prepare/r-rnaagecalc/lilac.yaml new file mode 100644 index 0000000000..404ccb567c --- /dev/null +++ b/prepare/r-rnaagecalc/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-ggplot2 +- r-impute +- r-org.hs.eg.db +- r-recount +- r-summarizedexperiment +update_on: +- regex: RNAAgeCalc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RNAAgeCalc diff --git a/prepare/r-rnadecay/PKGBUILD b/prepare/r-rnadecay/PKGBUILD new file mode 100644 index 0000000000..315e92c134 --- /dev/null +++ b/prepare/r-rnadecay/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RNAdecay +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Maximum Likelihood Decay Modeling of RNA Degradation Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-gplots + r-nloptr + r-scales + r-tmb +) +optdepends=( + r-knitr + r-parallel + r-reshape2 + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnadecay/lilac.py b/prepare/r-rnadecay/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnadecay/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnadecay/lilac.yaml b/prepare/r-rnadecay/lilac.yaml new file mode 100644 index 0000000000..6cd9a9db4b --- /dev/null +++ b/prepare/r-rnadecay/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gplots +- r-nloptr +- r-scales +- r-tmb +update_on: +- regex: RNAdecay_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RNAdecay diff --git a/prepare/r-rnaeditr/PKGBUILD b/prepare/r-rnaeditr/PKGBUILD new file mode 100644 index 0000000000..2989d3ff57 --- /dev/null +++ b/prepare/r-rnaeditr/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rnaEditr +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical analysis of RNA editing sites and hyper-editing regions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-bumphunter + r-corrplot + r-genomeinfodb + r-genomicranges + r-iranges + r-logistf + r-plyr + r-s4vectors +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnaeditr/lilac.py b/prepare/r-rnaeditr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnaeditr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnaeditr/lilac.yaml b/prepare/r-rnaeditr/lilac.yaml new file mode 100644 index 0000000000..bddd2f0430 --- /dev/null +++ b/prepare/r-rnaeditr/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-bumphunter +- r-corrplot +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-logistf +- r-plyr +- r-s4vectors +update_on: +- regex: rnaEditr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rnaEditr diff --git a/prepare/r-rnainteract/PKGBUILD b/prepare/r-rnainteract/PKGBUILD new file mode 100644 index 0000000000..5b5cde7fb7 --- /dev/null +++ b/prepare/r-rnainteract/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RNAinteract +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimate Pairwise Interactions from multidimensional features' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-abind + r-biobase + r-cellhts2 + r-geneplotter + r-gplots + r-hwriter + r-ics + r-icsnp + r-latticeextra + r-limma + r-locfit + r-rcolorbrewer + r-splots +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnainteract/lilac.py b/prepare/r-rnainteract/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnainteract/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnainteract/lilac.yaml b/prepare/r-rnainteract/lilac.yaml new file mode 100644 index 0000000000..d87301ff1b --- /dev/null +++ b/prepare/r-rnainteract/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-biobase +- r-cellhts2 +- r-geneplotter +- r-gplots +- r-hwriter +- r-ics +- r-icsnp +- r-latticeextra +- r-limma +- r-locfit +- r-rcolorbrewer +- r-splots +update_on: +- regex: RNAinteract_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RNAinteract diff --git a/prepare/r-rnamodr.alkanilineseq/PKGBUILD b/prepare/r-rnamodr.alkanilineseq/PKGBUILD new file mode 100644 index 0000000000..740514f62d --- /dev/null +++ b/prepare/r-rnamodr.alkanilineseq/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RNAmodR.AlkAnilineSeq +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detection of m7G, m3C and D modification by AlkAnilineSeq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-genomicranges + r-gviz + r-iranges + r-rnamodr + r-s4vectors +) +optdepends=( + r-biocstyle + r-biostrings + r-knitr + r-rmarkdown + r-rnamodr.data + r-rtracklayer + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnamodr.alkanilineseq/lilac.py b/prepare/r-rnamodr.alkanilineseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnamodr.alkanilineseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnamodr.alkanilineseq/lilac.yaml b/prepare/r-rnamodr.alkanilineseq/lilac.yaml new file mode 100644 index 0000000000..8c03848989 --- /dev/null +++ b/prepare/r-rnamodr.alkanilineseq/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomicranges +- r-gviz +- r-iranges +- r-rnamodr +- r-s4vectors +update_on: +- regex: RNAmodR.AlkAnilineSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RNAmodR.AlkAnilineSeq diff --git a/prepare/r-rnamodr.ml/PKGBUILD b/prepare/r-rnamodr.ml/PKGBUILD new file mode 100644 index 0000000000..dab13f236f --- /dev/null +++ b/prepare/r-rnamodr.ml/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RNAmodR.ML +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detecting patterns of post-transcriptional modifications using machine learning' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-genomicranges + r-iranges + r-ranger + r-rnamodr + r-s4vectors +) +optdepends=( + r-biocstyle + r-genomicfeatures + r-keras + r-knitr + r-rmarkdown + r-rnamodr.alkanilineseq + r-rnamodr.data + r-rsamtools + r-rtracklayer + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnamodr.ml/lilac.py b/prepare/r-rnamodr.ml/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnamodr.ml/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnamodr.ml/lilac.yaml b/prepare/r-rnamodr.ml/lilac.yaml new file mode 100644 index 0000000000..eb9f90b8b9 --- /dev/null +++ b/prepare/r-rnamodr.ml/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomicranges +- r-iranges +- r-ranger +- r-rnamodr +- r-s4vectors +update_on: +- regex: RNAmodR.ML_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RNAmodR.ML diff --git a/prepare/r-rnamodr.ribomethseq/PKGBUILD b/prepare/r-rnamodr.ribomethseq/PKGBUILD new file mode 100644 index 0000000000..644ba024a4 --- /dev/null +++ b/prepare/r-rnamodr.ribomethseq/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RNAmodR.RiboMethSeq +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Detection of 2'-O methylations by RiboMethSeq" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-genomicranges + r-gviz + r-iranges + r-rnamodr + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-rnamodr.data + r-rtracklayer + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnamodr.ribomethseq/lilac.py b/prepare/r-rnamodr.ribomethseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnamodr.ribomethseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnamodr.ribomethseq/lilac.yaml b/prepare/r-rnamodr.ribomethseq/lilac.yaml new file mode 100644 index 0000000000..fd0a0a95d6 --- /dev/null +++ b/prepare/r-rnamodr.ribomethseq/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomicranges +- r-gviz +- r-iranges +- r-rnamodr +- r-s4vectors +update_on: +- regex: RNAmodR.RiboMethSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RNAmodR.RiboMethSeq diff --git a/prepare/r-rnamodr/PKGBUILD b/prepare/r-rnamodr/PKGBUILD new file mode 100644 index 0000000000..4a9a0d967f --- /dev/null +++ b/prepare/r-rnamodr/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RNAmodR +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detection of post-transcriptional modifications in high throughput sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-colorramps + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-gviz + r-iranges + r-matrixstats + r-modstrings + r-rcolorbrewer + r-reshape2 + r-rocr + r-rsamtools + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-rnamodr.data + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnamodr/lilac.py b/prepare/r-rnamodr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnamodr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnamodr/lilac.yaml b/prepare/r-rnamodr/lilac.yaml new file mode 100644 index 0000000000..f4772d0c33 --- /dev/null +++ b/prepare/r-rnamodr/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-colorramps +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-gviz +- r-iranges +- r-matrixstats +- r-modstrings +- r-rcolorbrewer +- r-reshape2 +- r-rocr +- r-rsamtools +- r-rtracklayer +- r-s4vectors +update_on: +- regex: RNAmodR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RNAmodR diff --git a/prepare/r-rnasense/PKGBUILD b/prepare/r-rnasense/PKGBUILD new file mode 100644 index 0000000000..03a7849e25 --- /dev/null +++ b/prepare/r-rnasense/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RNAsense +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Time-Resolved RNA-Seq Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-nbpseq + r-qvalue + r-summarizedexperiment +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnasense/lilac.py b/prepare/r-rnasense/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnasense/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnasense/lilac.yaml b/prepare/r-rnasense/lilac.yaml new file mode 100644 index 0000000000..dd8e40890b --- /dev/null +++ b/prepare/r-rnasense/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-nbpseq +- r-qvalue +- r-summarizedexperiment +update_on: +- regex: RNAsense_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RNAsense diff --git a/prepare/r-rnaseqcomp/PKGBUILD b/prepare/r-rnaseqcomp/PKGBUILD new file mode 100644 index 0000000000..8ddbefaee6 --- /dev/null +++ b/prepare/r-rnaseqcomp/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rnaseqcomp +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Benchmarks for RNA-seq Quantification Pipelines' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rcolorbrewer +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnaseqcomp/lilac.py b/prepare/r-rnaseqcomp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnaseqcomp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnaseqcomp/lilac.yaml b/prepare/r-rnaseqcomp/lilac.yaml new file mode 100644 index 0000000000..39103eb505 --- /dev/null +++ b/prepare/r-rnaseqcomp/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcolorbrewer +update_on: +- regex: rnaseqcomp_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rnaseqcomp diff --git a/prepare/r-rnaseqpower/PKGBUILD b/prepare/r-rnaseqpower/PKGBUILD new file mode 100644 index 0000000000..a8915afa1e --- /dev/null +++ b/prepare/r-rnaseqpower/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RNASeqPower +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sample size for RNAseq studies' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +makedepends=( + git + tar +) +optdepends=( + r-dgeobj.utils +) +source=("git+https://git.bioconductor.org/packages/${_pkgname}.git") +sha256sums=('SKIP') + +build() { + tar -zcvf ${_pkgname}.tar.gz ${_pkgname} + R CMD INSTALL ${_pkgname}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnaseqpower/lilac.py b/prepare/r-rnaseqpower/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnaseqpower/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnaseqpower/lilac.yaml b/prepare/r-rnaseqpower/lilac.yaml new file mode 100644 index 0000000000..9391ba86ad --- /dev/null +++ b/prepare/r-rnaseqpower/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Version(\d+.\d+.\d+) + source: regex + url: https://bioconductor.org/packages/RNASeqPower diff --git a/prepare/r-rnaseqr/PKGBUILD b/prepare/r-rnaseqr/PKGBUILD new file mode 100644 index 0000000000..80ba3e16c1 --- /dev/null +++ b/prepare/r-rnaseqr/PKGBUILD @@ -0,0 +1,57 @@ +# system requirements: RNASeqR only support Linux and macOS. Window is notsupported. Python2 is highly recommended. If your machine isPython3, make sure '2to3' command is available. +# Maintainer: Guoyi Zhang + +_pkgname=RNASeqR +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RNASeqR: an R package for automated two-group RNA-Seq analysis workflow' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ballgown + r-biostrings + r-clusterprofiler + r-corrplot + r-deseq2 + r-dose + r-edger + r-factoextra + r-factominer + r-ggplot2 + r-gridextra + r-org.hs.eg.db + r-org.sc.sgd.db + r-pathview + r-performanceanalytics + r-pheatmap + r-rafalib + r-reshape2 + r-reticulate + r-rsamtools + r-stringr + r-systempiper + r-systempiperdata +) +optdepends=( + r-grid + r-knitr + r-png + r-rmarkdown + r-rnaseqrdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnaseqr/lilac.py b/prepare/r-rnaseqr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnaseqr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnaseqr/lilac.yaml b/prepare/r-rnaseqr/lilac.yaml new file mode 100644 index 0000000000..8dc55fe166 --- /dev/null +++ b/prepare/r-rnaseqr/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ballgown +- r-biostrings +- r-clusterprofiler +- r-corrplot +- r-deseq2 +- r-dose +- r-edger +- r-factoextra +- r-factominer +- r-ggplot2 +- r-gridextra +- r-org.hs.eg.db +- r-org.sc.sgd.db +- r-pathview +- r-performanceanalytics +- r-pheatmap +- r-rafalib +- r-reshape2 +- r-reticulate +- r-rsamtools +- r-stringr +- r-systempiper +- r-systempiperdata +update_on: +- regex: RNASeqR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RNASeqR diff --git a/prepare/r-rnaseqsamplesize/PKGBUILD b/prepare/r-rnaseqsamplesize/PKGBUILD new file mode 100644 index 0000000000..bde17cf435 --- /dev/null +++ b/prepare/r-rnaseqsamplesize/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RnaSeqSampleSize +_pkgver=2.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RnaSeqSampleSize' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-edger + r-heatmap3 + r-keggrest + r-matlab + r-rcpp + r-rnaseqsamplesizedata +) +optdepends=( + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnaseqsamplesize/lilac.py b/prepare/r-rnaseqsamplesize/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnaseqsamplesize/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnaseqsamplesize/lilac.yaml b/prepare/r-rnaseqsamplesize/lilac.yaml new file mode 100644 index 0000000000..0f8f014e85 --- /dev/null +++ b/prepare/r-rnaseqsamplesize/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-edger +- r-heatmap3 +- r-keggrest +- r-matlab +- r-rcpp +- r-rnaseqsamplesizedata +update_on: +- regex: RnaSeqSampleSize_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RnaSeqSampleSize diff --git a/prepare/r-rnaseqsamplesizedata/PKGBUILD b/prepare/r-rnaseqsamplesizedata/PKGBUILD new file mode 100644 index 0000000000..cd04a169fa --- /dev/null +++ b/prepare/r-rnaseqsamplesizedata/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RnaSeqSampleSizeData +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RnaSeqSampleSizeData' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-edger +) +optdepends=( + r-biocstyle + r-knitr +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnaseqsamplesizedata/lilac.py b/prepare/r-rnaseqsamplesizedata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnaseqsamplesizedata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnaseqsamplesizedata/lilac.yaml b/prepare/r-rnaseqsamplesizedata/lilac.yaml new file mode 100644 index 0000000000..ec75ede491 --- /dev/null +++ b/prepare/r-rnaseqsamplesizedata/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-edger +update_on: +- regex: RnaSeqSampleSizeData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RnaSeqSampleSizeData diff --git a/prepare/r-rnbeads.hg19/PKGBUILD b/prepare/r-rnbeads.hg19/PKGBUILD new file mode 100644 index 0000000000..20891a5cc2 --- /dev/null +++ b/prepare/r-rnbeads.hg19/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RnBeads.hg19 +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RnBeads.hg19' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicranges +) +optdepends=( + r-rnbeads +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnbeads.hg19/lilac.py b/prepare/r-rnbeads.hg19/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnbeads.hg19/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnbeads.hg19/lilac.yaml b/prepare/r-rnbeads.hg19/lilac.yaml new file mode 100644 index 0000000000..50e652bb51 --- /dev/null +++ b/prepare/r-rnbeads.hg19/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +update_on: +- regex: RnBeads.hg19_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RnBeads.hg19 diff --git a/prepare/r-rnbeads/PKGBUILD b/prepare/r-rnbeads/PKGBUILD new file mode 100644 index 0000000000..cdecd37c3e --- /dev/null +++ b/prepare/r-rnbeads/PKGBUILD @@ -0,0 +1,85 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RnBeads +_pkgver=2.12.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RnBeads' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-ff + r-fields + r-genomicranges + r-ggplot2 + r-gplots + r-gridextra + r-illuminaio + r-iranges + r-limma + r-matrixstats + r-methylumi + r-plyr + r-s4vectors +) +optdepends=( + r-annotate + r-argparse + r-biomart + r-category + r-doparallel + r-foreach + r-ggbio + r-glad + r-glmnet + r-gostats + r-gviz + r-hexbin + r-illuminahumanmethylation450kanno.ilmn12.hg19 + r-illuminahumanmethylation450kmanifest + r-impute + r-isva + r-mclust + r-methylseekr + r-mgcv + r-minfi + r-missmethyl + r-nlme + r-org.hs.eg.db + r-org.mm.eg.db + r-org.rn.eg.db + r-plotrix + r-quadprog + r-qvalue + r-qvalue + r-reffreeewas + r-rnbeads.hg19 + r-rnbeads.mm9 + r-rpmm + r-rtracklayer + r-runit + r-scales + r-sesame + r-shiny + r-shinyjs + r-sva + r-watermelon + r-wordcloud + r-xml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnbeads/lilac.py b/prepare/r-rnbeads/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnbeads/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnbeads/lilac.yaml b/prepare/r-rnbeads/lilac.yaml new file mode 100644 index 0000000000..7231cd132a --- /dev/null +++ b/prepare/r-rnbeads/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-ff +- r-fields +- r-genomicranges +- r-ggplot2 +- r-gplots +- r-gridextra +- r-illuminaio +- r-iranges +- r-limma +- r-matrixstats +- r-methylumi +- r-plyr +- r-s4vectors +update_on: +- regex: RnBeads_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RnBeads diff --git a/prepare/r-rncl/PKGBUILD b/prepare/r-rncl/PKGBUILD new file mode 100644 index 0000000000..8cd93d0f28 --- /dev/null +++ b/prepare/r-rncl/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rncl +_pkgver=0.8.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Interface to the Nexus Class Library' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-progress + r-rcpp +) +optdepends=( + r-ape + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rncl/lilac.py b/prepare/r-rncl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rncl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rncl/lilac.yaml b/prepare/r-rncl/lilac.yaml new file mode 100644 index 0000000000..8c11b79cd5 --- /dev/null +++ b/prepare/r-rncl/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-progress +- r-rcpp +update_on: +- regex: rncl_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rncl diff --git a/prepare/r-rnexml/PKGBUILD b/prepare/r-rnexml/PKGBUILD new file mode 100644 index 0000000000..6debd064d5 --- /dev/null +++ b/prepare/r-rnexml/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RNeXML +_pkgver=2.4.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Semantically Rich I/O for the 'NeXML' Format" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-ape + r-dplyr + r-httr + r-lazyeval + r-plyr + r-reshape2 + r-stringi + r-stringr + r-tidyr + r-uuid + r-xml + r-xml2 +) +optdepends=( + r-covr + r-geiger + r-knitcitations + r-knitr + r-phytools + r-rdflib + r-rfigshare + r-rlang + r-rmarkdown + r-spelling + r-taxadb + r-testthat + r-xslt +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnexml/lilac.py b/prepare/r-rnexml/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnexml/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnexml/lilac.yaml b/prepare/r-rnexml/lilac.yaml new file mode 100644 index 0000000000..fdc0176588 --- /dev/null +++ b/prepare/r-rnexml/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-dplyr +- r-httr +- r-lazyeval +- r-plyr +- r-reshape2 +- r-stringi +- r-stringr +- r-tidyr +- r-uuid +- r-xml +- r-xml2 +update_on: +- regex: RNeXML_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RNeXML diff --git a/prepare/r-rngtools/PKGBUILD b/prepare/r-rngtools/PKGBUILD new file mode 100644 index 0000000000..29003f402c --- /dev/null +++ b/prepare/r-rngtools/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rngtools +_pkgver=1.5.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utility Functions for Working with Random Number Generators' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-digest +) +optdepends=( + r-covr + r-runit + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rngtools/lilac.py b/prepare/r-rngtools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rngtools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rngtools/lilac.yaml b/prepare/r-rngtools/lilac.yaml new file mode 100644 index 0000000000..7cc285c79b --- /dev/null +++ b/prepare/r-rngtools/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +update_on: +- regex: rngtools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rngtools diff --git a/prepare/r-rnifti/PKGBUILD b/prepare/r-rnifti/PKGBUILD new file mode 100644 index 0000000000..6746f01eb6 --- /dev/null +++ b/prepare/r-rnifti/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RNifti +_pkgver=1.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast R and C++ Access to NIfTI Images' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-covr + r-oro.nifti + r-reportr + r-shades + r-testthat + r-tractor.base +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnifti/lilac.py b/prepare/r-rnifti/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnifti/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnifti/lilac.yaml b/prepare/r-rnifti/lilac.yaml new file mode 100644 index 0000000000..a3118165f8 --- /dev/null +++ b/prepare/r-rnifti/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: RNifti_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RNifti diff --git a/prepare/r-rnits/PKGBUILD b/prepare/r-rnits/PKGBUILD new file mode 100644 index 0000000000..831d60a062 --- /dev/null +++ b/prepare/r-rnits/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rnits +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Normalization and Inference of Time Series data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-biobase + r-ggplot2 + r-impute + r-limma + r-qvalue + r-reshape2 +) +optdepends=( + r-biocstyle + r-geoquery + r-knitr + r-stringr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnits/lilac.py b/prepare/r-rnits/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnits/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnits/lilac.yaml b/prepare/r-rnits/lilac.yaml new file mode 100644 index 0000000000..0f924e88d8 --- /dev/null +++ b/prepare/r-rnits/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +- r-ggplot2 +- r-impute +- r-limma +- r-qvalue +- r-reshape2 +update_on: +- regex: Rnits_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rnits diff --git a/prepare/r-rnomni/PKGBUILD b/prepare/r-rnomni/PKGBUILD new file mode 100644 index 0000000000..8b2381da56 --- /dev/null +++ b/prepare/r-rnomni/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RNOmni +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Rank Normal Transformation Omnibus Test' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-plyr + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-r.rsp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rnomni/lilac.py b/prepare/r-rnomni/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rnomni/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rnomni/lilac.yaml b/prepare/r-rnomni/lilac.yaml new file mode 100644 index 0000000000..1d7a78f316 --- /dev/null +++ b/prepare/r-rnomni/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-plyr +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: RNOmni_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RNOmni diff --git a/prepare/r-roar/PKGBUILD b/prepare/r-roar/PKGBUILD new file mode 100644 index 0000000000..542c44904b --- /dev/null +++ b/prepare/r-roar/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=roar +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identify differential APA usage from RNA-seq alignments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-rtracklayer + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-rnaseqdata.hnrnpc.bam.chr14 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-roar/lilac.py b/prepare/r-roar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-roar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-roar/lilac.yaml b/prepare/r-roar/lilac.yaml new file mode 100644 index 0000000000..59d439029e --- /dev/null +++ b/prepare/r-roar/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: roar_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/roar diff --git a/prepare/r-robust/PKGBUILD b/prepare/r-robust/PKGBUILD new file mode 100644 index 0000000000..2ce10c4501 --- /dev/null +++ b/prepare/r-robust/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=robust +_pkgver=0.6-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Port of the S+ "Robust Library"' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-fit.models + r-robustbase + r-rrcov +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-robust/lilac.py b/prepare/r-robust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-robust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-robust/lilac.yaml b/prepare/r-robust/lilac.yaml new file mode 100644 index 0000000000..ad43280a7a --- /dev/null +++ b/prepare/r-robust/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fit.models +- r-robustbase +- r-rrcov +update_on: +- regex: robust_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=robust diff --git a/prepare/r-robustbase/PKGBUILD b/prepare/r-robustbase/PKGBUILD new file mode 100644 index 0000000000..3f75135b4c --- /dev/null +++ b/prepare/r-robustbase/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=robustbase +_pkgver=0.93-9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Basic Robust Statistics' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-deoptimr +) +optdepends=( + r-boot + r-catdata + r-cluster + r-doparallel + r-fit.models + r-foreach + r-ggally + r-ggplot2 + r-grid + r-hmisc + r-lattice + r-mass + r-matrix + r-matrixstats + r-mpv + r-quantreg + r-rcolorbrewer + r-reshape2 + r-robust + r-robustx + r-rrcov + r-sfsmisc + r-skewt + r-xtable +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-robustbase/lilac.py b/prepare/r-robustbase/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-robustbase/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-robustbase/lilac.yaml b/prepare/r-robustbase/lilac.yaml new file mode 100644 index 0000000000..c895830cfc --- /dev/null +++ b/prepare/r-robustbase/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-deoptimr +update_on: +- regex: robustbase_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=robustbase diff --git a/prepare/r-robustrankaggreg/PKGBUILD b/prepare/r-robustrankaggreg/PKGBUILD new file mode 100644 index 0000000000..465b3154b2 --- /dev/null +++ b/prepare/r-robustrankaggreg/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RobustRankAggreg +_pkgver=1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methods for robust rank aggregation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-robustrankaggreg/lilac.py b/prepare/r-robustrankaggreg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-robustrankaggreg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-robustrankaggreg/lilac.yaml b/prepare/r-robustrankaggreg/lilac.yaml new file mode 100644 index 0000000000..b64333f5ff --- /dev/null +++ b/prepare/r-robustrankaggreg/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RobustRankAggreg_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RobustRankAggreg diff --git a/prepare/r-roc/PKGBUILD b/prepare/r-roc/PKGBUILD new file mode 100644 index 0000000000..cb3077e5ca --- /dev/null +++ b/prepare/r-roc/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ROC +_pkgver=1.70.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='utilities for ROC, with microarray focus' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-knitr +) +optdepends=( + r-biobase + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-roc/lilac.py b/prepare/r-roc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-roc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-roc/lilac.yaml b/prepare/r-roc/lilac.yaml new file mode 100644 index 0000000000..0e104ced66 --- /dev/null +++ b/prepare/r-roc/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-knitr +update_on: +- regex: ROC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ROC diff --git a/prepare/r-rocit/PKGBUILD b/prepare/r-rocit/PKGBUILD new file mode 100644 index 0000000000..39033c8ca1 --- /dev/null +++ b/prepare/r-rocit/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ROCit +_pkgver=2.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Performance Assessment of Binary Classifier with Visualization' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rocit/lilac.py b/prepare/r-rocit/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rocit/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rocit/lilac.yaml b/prepare/r-rocit/lilac.yaml new file mode 100644 index 0000000000..2e2d95d0cd --- /dev/null +++ b/prepare/r-rocit/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ROCit_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ROCit diff --git a/prepare/r-rocpai/PKGBUILD b/prepare/r-rocpai/PKGBUILD new file mode 100644 index 0000000000..1a85530727 --- /dev/null +++ b/prepare/r-rocpai/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ROCpAI +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-fission + r-knitr + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rocpai/lilac.py b/prepare/r-rocpai/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rocpai/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rocpai/lilac.yaml b/prepare/r-rocpai/lilac.yaml new file mode 100644 index 0000000000..e8159bbf23 --- /dev/null +++ b/prepare/r-rocpai/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fission +- r-knitr +- r-summarizedexperiment +update_on: +- regex: ROCpAI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ROCpAI diff --git a/prepare/r-rocr/PKGBUILD b/prepare/r-rocr/PKGBUILD new file mode 100644 index 0000000000..84e87c1444 --- /dev/null +++ b/prepare/r-rocr/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ROCR +_pkgver=1.0-11 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualizing the Performance of Scoring Classifiers' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-gplots +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rocr/lilac.py b/prepare/r-rocr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rocr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rocr/lilac.yaml b/prepare/r-rocr/lilac.yaml new file mode 100644 index 0000000000..6499e5db59 --- /dev/null +++ b/prepare/r-rocr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gplots +update_on: +- regex: ROCR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ROCR diff --git a/prepare/r-roi.plugin.lpsolve/PKGBUILD b/prepare/r-roi.plugin.lpsolve/PKGBUILD new file mode 100644 index 0000000000..cbc6416ac6 --- /dev/null +++ b/prepare/r-roi.plugin.lpsolve/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ROI.plugin.lpsolve +_pkgver=1.0-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'lp_solve' Plugin for the 'R' Optimization Infrastructure" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-lpsolveapi + r-roi +) +optdepends=( + r-slam +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-roi.plugin.lpsolve/lilac.py b/prepare/r-roi.plugin.lpsolve/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-roi.plugin.lpsolve/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-roi.plugin.lpsolve/lilac.yaml b/prepare/r-roi.plugin.lpsolve/lilac.yaml new file mode 100644 index 0000000000..3b62e79e7c --- /dev/null +++ b/prepare/r-roi.plugin.lpsolve/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-lpsolveapi +- r-roi +update_on: +- regex: ROI.plugin.lpsolve_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ROI.plugin.lpsolve diff --git a/prepare/r-roi/PKGBUILD b/prepare/r-roi/PKGBUILD new file mode 100644 index 0000000000..045c959323 --- /dev/null +++ b/prepare/r-roi/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ROI +_pkgver=1.0-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Optimization Infrastructure' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-registry + r-slam +) +optdepends=( + r-numderiv +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-roi/lilac.py b/prepare/r-roi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-roi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-roi/lilac.yaml b/prepare/r-roi/lilac.yaml new file mode 100644 index 0000000000..83971c0116 --- /dev/null +++ b/prepare/r-roi/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-registry +- r-slam +update_on: +- regex: ROI_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ROI diff --git a/prepare/r-rols/PKGBUILD b/prepare/r-rols/PKGBUILD new file mode 100644 index 0000000000..0e90760111 --- /dev/null +++ b/prepare/r-rols/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rols +_pkgver=2.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R interface to the Ontology Lookup Service' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-httr + r-jsonlite + r-progress +) +optdepends=( + r-biocstyle + r-dt + r-go.db + r-knitr + r-lubridate + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rols/lilac.py b/prepare/r-rols/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rols/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rols/lilac.yaml b/prepare/r-rols/lilac.yaml new file mode 100644 index 0000000000..6d59ee54cb --- /dev/null +++ b/prepare/r-rols/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-httr +- r-jsonlite +- r-progress +update_on: +- regex: rols_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rols diff --git a/prepare/r-rontotools/PKGBUILD b/prepare/r-rontotools/PKGBUILD new file mode 100644 index 0000000000..858c8a294c --- /dev/null +++ b/prepare/r-rontotools/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ROntoTools +_pkgver=2.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Onto-Tools suite' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CCPL:by-nc-sa') +depends=( + r + r-graph + r-kegggraph + r-keggrest + r-rgraphviz +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rontotools/lilac.py b/prepare/r-rontotools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rontotools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rontotools/lilac.yaml b/prepare/r-rontotools/lilac.yaml new file mode 100644 index 0000000000..4db0d85c62 --- /dev/null +++ b/prepare/r-rontotools/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +- r-kegggraph +- r-keggrest +- r-rgraphviz +update_on: +- regex: ROntoTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ROntoTools diff --git a/prepare/r-rook/PKGBUILD b/prepare/r-rook/PKGBUILD new file mode 100644 index 0000000000..3c90ae5846 --- /dev/null +++ b/prepare/r-rook/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rook +_pkgver=1.1-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Rook - a web server interface for R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-brew +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rook/lilac.py b/prepare/r-rook/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rook/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rook/lilac.yaml b/prepare/r-rook/lilac.yaml new file mode 100644 index 0000000000..38e901ec42 --- /dev/null +++ b/prepare/r-rook/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-brew +update_on: +- regex: Rook_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rook diff --git a/prepare/r-rootsolve/PKGBUILD b/prepare/r-rootsolve/PKGBUILD new file mode 100644 index 0000000000..33f09ed437 --- /dev/null +++ b/prepare/r-rootsolve/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rootSolve +_pkgver=1.8.2.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rootsolve/lilac.py b/prepare/r-rootsolve/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rootsolve/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rootsolve/lilac.yaml b/prepare/r-rootsolve/lilac.yaml new file mode 100644 index 0000000000..ce07cbee73 --- /dev/null +++ b/prepare/r-rootsolve/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: rootSolve_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rootSolve diff --git a/prepare/r-ropls/PKGBUILD b/prepare/r-ropls/PKGBUILD new file mode 100644 index 0000000000..f17dc69ea9 --- /dev/null +++ b/prepare/r-ropls/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ropls +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CeCILL') +depends=( + r + r-biobase + r-multidataset +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-multtest + r-omicade4 + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ropls/lilac.py b/prepare/r-ropls/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ropls/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ropls/lilac.yaml b/prepare/r-ropls/lilac.yaml new file mode 100644 index 0000000000..54065a5504 --- /dev/null +++ b/prepare/r-ropls/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-multidataset +update_on: +- regex: ropls_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ropls diff --git a/prepare/r-roptim/PKGBUILD b/prepare/r-roptim/PKGBUILD new file mode 100644 index 0000000000..88e2e112a7 --- /dev/null +++ b/prepare/r-roptim/PKGBUILD @@ -0,0 +1,32 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=roptim +_pkgver=0.1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='General Purpose Optimization in R using C++' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-r.rsp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-roptim/lilac.py b/prepare/r-roptim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-roptim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-roptim/lilac.yaml b/prepare/r-roptim/lilac.yaml new file mode 100644 index 0000000000..10318acf49 --- /dev/null +++ b/prepare/r-roptim/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: roptim_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=roptim diff --git a/prepare/r-roseq/PKGBUILD b/prepare/r-roseq/PKGBUILD new file mode 100644 index 0000000000..183deb8d3f --- /dev/null +++ b/prepare/r-roseq/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ROSeq +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-Seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-edger + r-limma + r-pbmcapply +) +optdepends=( + r-biocgenerics + r-knitr + r-rmarkdown + r-runit + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-roseq/lilac.py b/prepare/r-roseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-roseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-roseq/lilac.yaml b/prepare/r-roseq/lilac.yaml new file mode 100644 index 0000000000..eac79b95e8 --- /dev/null +++ b/prepare/r-roseq/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-edger +- r-limma +- r-pbmcapply +update_on: +- regex: ROSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ROSeq diff --git a/prepare/r-rots/PKGBUILD b/prepare/r-rots/PKGBUILD new file mode 100644 index 0000000000..de867268da --- /dev/null +++ b/prepare/r-rots/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ROTS +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Reproducibility-Optimized Test Statistic' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-rcpp +) +optdepends=( + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rots/lilac.py b/prepare/r-rots/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rots/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rots/lilac.yaml b/prepare/r-rots/lilac.yaml new file mode 100644 index 0000000000..7e57d99f26 --- /dev/null +++ b/prepare/r-rots/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-rcpp +update_on: +- regex: ROTS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ROTS diff --git a/prepare/r-roxygen2/PKGBUILD b/prepare/r-roxygen2/PKGBUILD new file mode 100644 index 0000000000..5f2e1e1722 --- /dev/null +++ b/prepare/r-roxygen2/PKGBUILD @@ -0,0 +1,49 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=roxygen2 +_pkgver=7.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='In-Line Documentation for R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-brew + r-commonmark + r-cpp11 + r-desc + r-digest + r-knitr + r-pkgload + r-purrr + r-r6 + r-rlang + r-stringi + r-stringr + r-xml2 +) +optdepends=( + r-covr + r-devtools + r-r.methodss3 + r-r.oo + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-roxygen2/lilac.py b/prepare/r-roxygen2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-roxygen2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-roxygen2/lilac.yaml b/prepare/r-roxygen2/lilac.yaml new file mode 100644 index 0000000000..42017bfbc4 --- /dev/null +++ b/prepare/r-roxygen2/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-brew +- r-commonmark +- r-cpp11 +- r-desc +- r-digest +- r-knitr +- r-pkgload +- r-purrr +- r-r6 +- r-rlang +- r-stringi +- r-stringr +- r-xml2 +update_on: +- regex: roxygen2_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=roxygen2 diff --git a/prepare/r-rpa/PKGBUILD b/prepare/r-rpa/PKGBUILD new file mode 100644 index 0000000000..918e64b8d3 --- /dev/null +++ b/prepare/r-rpa/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RPA +_pkgver=1.50.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RPA: Robust Probabilistic Averaging for probe-level analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-affy + r-biocgenerics + r-biocstyle + r-phyloseq + r-rmarkdown +) +optdepends=( + r-affydata + r-knitr + r-parallel +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rpa/lilac.py b/prepare/r-rpa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rpa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rpa/lilac.yaml b/prepare/r-rpa/lilac.yaml new file mode 100644 index 0000000000..9f72ccfae3 --- /dev/null +++ b/prepare/r-rpa/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biocgenerics +- r-biocstyle +- r-phyloseq +- r-rmarkdown +update_on: +- regex: RPA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RPA diff --git a/prepare/r-rpart.plot/PKGBUILD b/prepare/r-rpart.plot/PKGBUILD new file mode 100644 index 0000000000..d35b04b611 --- /dev/null +++ b/prepare/r-rpart.plot/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rpart.plot +_pkgver=3.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-earth +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rpart.plot/lilac.py b/prepare/r-rpart.plot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rpart.plot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rpart.plot/lilac.yaml b/prepare/r-rpart.plot/lilac.yaml new file mode 100644 index 0000000000..ae9fd70f41 --- /dev/null +++ b/prepare/r-rpart.plot/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: rpart.plot_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rpart.plot diff --git a/prepare/r-rpmg/PKGBUILD b/prepare/r-rpmg/PKGBUILD new file mode 100644 index 0000000000..32411b2efb --- /dev/null +++ b/prepare/r-rpmg/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RPMG +_pkgver=2.2-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Graphical User Interface (GUI) for Interactive R Analysis Sessions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rpmg/lilac.py b/prepare/r-rpmg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rpmg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rpmg/lilac.yaml b/prepare/r-rpmg/lilac.yaml new file mode 100644 index 0000000000..1e7cfaae7d --- /dev/null +++ b/prepare/r-rpmg/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RPMG_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RPMG diff --git a/prepare/r-rpmm/PKGBUILD b/prepare/r-rpmm/PKGBUILD new file mode 100644 index 0000000000..1f4bc23efb --- /dev/null +++ b/prepare/r-rpmm/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RPMM +_pkgver=1.25 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Recursively Partitioned Mixture Model' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rpmm/lilac.py b/prepare/r-rpmm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rpmm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rpmm/lilac.yaml b/prepare/r-rpmm/lilac.yaml new file mode 100644 index 0000000000..54af31f04b --- /dev/null +++ b/prepare/r-rpmm/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RPMM_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RPMM diff --git a/prepare/r-rpostgresql/PKGBUILD b/prepare/r-rpostgresql/PKGBUILD new file mode 100644 index 0000000000..dd2789ffff --- /dev/null +++ b/prepare/r-rpostgresql/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RPostgreSQL +_pkgver=0.7-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="R Interface to the 'PostgreSQL' Database System" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dbi +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rpostgresql/lilac.py b/prepare/r-rpostgresql/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rpostgresql/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rpostgresql/lilac.yaml b/prepare/r-rpostgresql/lilac.yaml new file mode 100644 index 0000000000..b3c84996d7 --- /dev/null +++ b/prepare/r-rpostgresql/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dbi +update_on: +- regex: RPostgreSQL_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RPostgreSQL diff --git a/prepare/r-rpref/PKGBUILD b/prepare/r-rpref/PKGBUILD new file mode 100644 index 0000000000..ae3b7a52ca --- /dev/null +++ b/prepare/r-rpref/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: C++11, GNU make, Windows: cmd.exe and cscript.exe +# Maintainer: Guoyi Zhang + +_pkgname=rPref +_pkgver=1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Database Preferences and Skyline Computation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-igraph + r-lazyeval + r-rcpp + r-rcppparallel +) +optdepends=( + r-ggplot2 + r-graph + r-knitr + r-rgraphviz + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rpref/lilac.py b/prepare/r-rpref/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rpref/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rpref/lilac.yaml b/prepare/r-rpref/lilac.yaml new file mode 100644 index 0000000000..82466a65d1 --- /dev/null +++ b/prepare/r-rpref/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-igraph +- r-lazyeval +- r-rcpp +- r-rcppparallel +update_on: +- regex: rPref_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rPref diff --git a/prepare/r-rprojroot/PKGBUILD b/prepare/r-rprojroot/PKGBUILD new file mode 100644 index 0000000000..a0d9344494 --- /dev/null +++ b/prepare/r-rprojroot/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rprojroot +_pkgver=2.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Finding Files in Project Subdirectories' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-covr + r-knitr + r-lifecycle + r-mockr + r-rmarkdown + r-testthat + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rprojroot/lilac.py b/prepare/r-rprojroot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rprojroot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rprojroot/lilac.yaml b/prepare/r-rprojroot/lilac.yaml new file mode 100644 index 0000000000..cd5b5a725c --- /dev/null +++ b/prepare/r-rprojroot/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: rprojroot_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rprojroot diff --git a/prepare/r-rprotobuflib/PKGBUILD b/prepare/r-rprotobuflib/PKGBUILD new file mode 100644 index 0000000000..d0f08f8541 --- /dev/null +++ b/prepare/r-rprotobuflib/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=RProtoBufLib +_pkgver=2.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='C++ headers and static libraries of Protocol buffers' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rprotobuflib/lilac.py b/prepare/r-rprotobuflib/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rprotobuflib/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rprotobuflib/lilac.yaml b/prepare/r-rprotobuflib/lilac.yaml new file mode 100644 index 0000000000..7e2a023d38 --- /dev/null +++ b/prepare/r-rprotobuflib/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RProtoBufLib_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RProtoBufLib diff --git a/prepare/r-rpsixml/PKGBUILD b/prepare/r-rpsixml/PKGBUILD new file mode 100644 index 0000000000..97365a66f3 --- /dev/null +++ b/prepare/r-rpsixml/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RpsiXML +_pkgver=2.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R interface to PSI-MI 2.5 files' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-annotate + r-annotationdbi + r-biobase + r-graph + r-hypergraph + r-rbgl + r-xml +) +optdepends=( + r-org.dm.eg.db + r-org.hs.eg.db + r-org.mm.eg.db + r-org.rn.eg.db + r-org.sc.sgd.db + r-ppistats + r-rgraphviz + r-scisi + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rpsixml/lilac.py b/prepare/r-rpsixml/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rpsixml/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rpsixml/lilac.yaml b/prepare/r-rpsixml/lilac.yaml new file mode 100644 index 0000000000..bc0dd6136f --- /dev/null +++ b/prepare/r-rpsixml/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-biobase +- r-graph +- r-hypergraph +- r-rbgl +- r-xml +update_on: +- regex: RpsiXML_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RpsiXML diff --git a/prepare/r-rpx/PKGBUILD b/prepare/r-rpx/PKGBUILD new file mode 100644 index 0000000000..b4631ba271 --- /dev/null +++ b/prepare/r-rpx/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rpx +_pkgver=2.1.12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Interface to the ProteomeXchange Repository' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocfilecache + r-curl + r-jsonlite + r-rcurl + r-xml2 +) +optdepends=( + r-biocstyle + r-biostrings + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rpx/lilac.py b/prepare/r-rpx/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rpx/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rpx/lilac.yaml b/prepare/r-rpx/lilac.yaml new file mode 100644 index 0000000000..4dfdd377d3 --- /dev/null +++ b/prepare/r-rpx/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-curl +- r-jsonlite +- r-rcurl +- r-xml2 +update_on: +- regex: rpx_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rpx diff --git a/prepare/r-rqc/PKGBUILD b/prepare/r-rqc/PKGBUILD new file mode 100644 index 0000000000..de66c5521e --- /dev/null +++ b/prepare/r-rqc/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rqc +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quality Control Tool for High-Throughput Sequencing Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-biocstyle + r-biostrings + r-biovizbase + r-genomicalignments + r-genomicfiles + r-ggplot2 + r-iranges + r-knitr + r-markdown + r-plyr + r-rcpp + r-reshape2 + r-rsamtools + r-s4vectors + r-shiny + r-shortread +) +optdepends=( + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rqc/lilac.py b/prepare/r-rqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rqc/lilac.yaml b/prepare/r-rqc/lilac.yaml new file mode 100644 index 0000000000..7b1a4137cf --- /dev/null +++ b/prepare/r-rqc/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biocstyle +- r-biostrings +- r-biovizbase +- r-genomicalignments +- r-genomicfiles +- r-ggplot2 +- r-iranges +- r-knitr +- r-markdown +- r-plyr +- r-rcpp +- r-reshape2 +- r-rsamtools +- r-s4vectors +- r-shiny +- r-shortread +update_on: +- regex: Rqc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rqc diff --git a/prepare/r-rqt/PKGBUILD b/prepare/r-rqt/PKGBUILD new file mode 100644 index 0000000000..bf6d91cc08 --- /dev/null +++ b/prepare/r-rqt/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rqt +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='rqt: utilities for gene-level meta-analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-car + r-compquadform + r-glmnet + r-metap + r-pls + r-ropls + r-runit + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rqt/lilac.py b/prepare/r-rqt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rqt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rqt/lilac.yaml b/prepare/r-rqt/lilac.yaml new file mode 100644 index 0000000000..907a69c8b7 --- /dev/null +++ b/prepare/r-rqt/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-car +- r-compquadform +- r-glmnet +- r-metap +- r-pls +- r-ropls +- r-runit +- r-summarizedexperiment +update_on: +- regex: rqt_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rqt diff --git a/prepare/r-rqubic/PKGBUILD b/prepare/r-rqubic/PKGBUILD new file mode 100644 index 0000000000..be1239244a --- /dev/null +++ b/prepare/r-rqubic/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rqubic +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Qualitative biclustering algorithm for expression data analysis in R' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biclust + r-biobase + r-biocgenerics +) +optdepends=( + r-rcolorbrewer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rqubic/lilac.py b/prepare/r-rqubic/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rqubic/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rqubic/lilac.yaml b/prepare/r-rqubic/lilac.yaml new file mode 100644 index 0000000000..f357e558e9 --- /dev/null +++ b/prepare/r-rqubic/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biclust +- r-biobase +- r-biocgenerics +update_on: +- regex: rqubic_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rqubic diff --git a/prepare/r-rrcov/PKGBUILD b/prepare/r-rrcov/PKGBUILD new file mode 100644 index 0000000000..98cfbb81e5 --- /dev/null +++ b/prepare/r-rrcov/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rrcov +_pkgver=1.6-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Scalable Robust Estimators with High Breakdown Point' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mvtnorm + r-pcapp + r-robustbase +) +optdepends=( + r-grid + r-mass +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rrcov/lilac.py b/prepare/r-rrcov/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rrcov/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rrcov/lilac.yaml b/prepare/r-rrcov/lilac.yaml new file mode 100644 index 0000000000..7d7cbce5dc --- /dev/null +++ b/prepare/r-rrcov/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mvtnorm +- r-pcapp +- r-robustbase +update_on: +- regex: rrcov_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rrcov diff --git a/prepare/r-rrdp/PKGBUILD b/prepare/r-rrdp/PKGBUILD new file mode 100644 index 0000000000..d48768f715 --- /dev/null +++ b/prepare/r-rrdp/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: Java +# Maintainer: Guoyi Zhang + +_pkgname=rRDP +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interface to the RDP Classifier' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings +) +optdepends=( + r-rrdpdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rrdp/lilac.py b/prepare/r-rrdp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rrdp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rrdp/lilac.yaml b/prepare/r-rrdp/lilac.yaml new file mode 100644 index 0000000000..bffea86860 --- /dev/null +++ b/prepare/r-rrdp/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +update_on: +- regex: rRDP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rRDP diff --git a/prepare/r-rrho/PKGBUILD b/prepare/r-rrho/PKGBUILD new file mode 100644 index 0000000000..7aa5d36e6a --- /dev/null +++ b/prepare/r-rrho/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RRHO +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Inference on agreement between ordered lists' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-venndiagram +) +optdepends=( + r-lattice +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rrho/lilac.py b/prepare/r-rrho/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rrho/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rrho/lilac.yaml b/prepare/r-rrho/lilac.yaml new file mode 100644 index 0000000000..23808f28be --- /dev/null +++ b/prepare/r-rrho/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-venndiagram +update_on: +- regex: RRHO_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RRHO diff --git a/prepare/r-rrvgo/PKGBUILD b/prepare/r-rrvgo/PKGBUILD new file mode 100644 index 0000000000..5ab8e57ae2 --- /dev/null +++ b/prepare/r-rrvgo/PKGBUILD @@ -0,0 +1,70 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rrvgo +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Reduce + Visualize GO' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-ggplot2 + r-ggrepel + r-go.db + r-gosemsim + r-pheatmap + r-shiny + r-tm + r-treemap + r-wordcloud +) +optdepends=( + r-biocstyle + r-clusterprofiler + r-dose + r-dt + r-heatmaply + r-knitr + r-magrittr + r-org.ag.eg.db + r-org.at.tair.db + r-org.bt.eg.db + r-org.ce.eg.db + r-org.cf.eg.db + r-org.dm.eg.db + r-org.dr.eg.db + r-org.eck12.eg.db + r-org.ecsakai.eg.db + r-org.gg.eg.db + r-org.hs.eg.db + r-org.mm.eg.db + r-org.mmu.eg.db + r-org.pf.plasmo.db + r-org.pt.eg.db + r-org.rn.eg.db + r-org.sc.sgd.db + r-org.ss.eg.db + r-org.xl.eg.db + r-plotly + r-rmarkdown + r-shinydashboard + r-slam + r-testthat + r-utils +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rrvgo/lilac.py b/prepare/r-rrvgo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rrvgo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rrvgo/lilac.yaml b/prepare/r-rrvgo/lilac.yaml new file mode 100644 index 0000000000..11768cd209 --- /dev/null +++ b/prepare/r-rrvgo/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-ggplot2 +- r-ggrepel +- r-go.db +- r-gosemsim +- r-pheatmap +- r-shiny +- r-tm +- r-treemap +- r-wordcloud +update_on: +- regex: rrvgo_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rrvgo diff --git a/prepare/r-rsample/PKGBUILD b/prepare/r-rsample/PKGBUILD new file mode 100644 index 0000000000..c2d6164775 --- /dev/null +++ b/prepare/r-rsample/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rsample +_pkgver=0.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='General Resampling Infrastructure' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-ellipsis + r-furrr + r-generics + r-lifecycle + r-purrr + r-rlang + r-slider + r-tibble + r-tidyr + r-tidyselect + r-vctrs +) +optdepends=( + r-broom + r-covr + r-ggplot2 + r-knitr + r-modeldata + r-recipes + r-rmarkdown + r-stats + r-testthat + r-utils + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rsample/lilac.py b/prepare/r-rsample/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rsample/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rsample/lilac.yaml b/prepare/r-rsample/lilac.yaml new file mode 100644 index 0000000000..a3c8849335 --- /dev/null +++ b/prepare/r-rsample/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ellipsis +- r-furrr +- r-generics +- r-lifecycle +- r-purrr +- r-rlang +- r-slider +- r-tibble +- r-tidyr +- r-tidyselect +- r-vctrs +update_on: +- regex: rsample_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rsample diff --git a/prepare/r-rsamtools/PKGBUILD b/prepare/r-rsamtools/PKGBUILD new file mode 100644 index 0000000000..7bbb79660a --- /dev/null +++ b/prepare/r-rsamtools/PKGBUILD @@ -0,0 +1,49 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=Rsamtools +_pkgver=2.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-bitops + r-genomeinfodb + r-genomicranges + r-iranges + r-rhtslib + r-s4vectors + r-xvector + r-zlibbioc +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-genomicalignments + r-genomicfeatures + r-rnaseqdata.hnrnpc.bam.chr14 + r-runit + r-shortread + r-txdb.dmelanogaster.ucsc.dm3.ensgene + r-txdb.hsapiens.ucsc.hg18.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rsamtools/lilac.py b/prepare/r-rsamtools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rsamtools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rsamtools/lilac.yaml b/prepare/r-rsamtools/lilac.yaml new file mode 100644 index 0000000000..8cc0b2607f --- /dev/null +++ b/prepare/r-rsamtools/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bitops +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rhtslib +- r-s4vectors +- r-xvector +- r-zlibbioc +update_on: +- regex: Rsamtools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rsamtools diff --git a/prepare/r-rsbml/PKGBUILD b/prepare/r-rsbml/PKGBUILD new file mode 100644 index 0000000000..2810474671 --- /dev/null +++ b/prepare/r-rsbml/PKGBUILD @@ -0,0 +1,29 @@ +# system requirements: libsbml (==5.10.2) +# Maintainer: Guoyi Zhang + +_pkgname=rsbml +_pkgver=2.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R support for SBML, using libsbml' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-graph +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rsbml/lilac.py b/prepare/r-rsbml/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rsbml/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rsbml/lilac.yaml b/prepare/r-rsbml/lilac.yaml new file mode 100644 index 0000000000..537a85dff0 --- /dev/null +++ b/prepare/r-rsbml/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-graph +update_on: +- regex: rsbml_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rsbml diff --git a/prepare/r-rscudo/PKGBUILD b/prepare/r-rscudo/PKGBUILD new file mode 100644 index 0000000000..1832d3aaea --- /dev/null +++ b/prepare/r-rscudo/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rScudo +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Signature-based Clustering for Diagnostic Purposes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-igraph + r-s4vectors + r-stringr + r-summarizedexperiment +) +optdepends=( + r-all + r-biocstyle + r-caret + r-doparallel + r-e1071 + r-knitr + r-parallel + r-rcy3 + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rscudo/lilac.py b/prepare/r-rscudo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rscudo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rscudo/lilac.yaml b/prepare/r-rscudo/lilac.yaml new file mode 100644 index 0000000000..91c9685faf --- /dev/null +++ b/prepare/r-rscudo/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-igraph +- r-s4vectors +- r-stringr +- r-summarizedexperiment +update_on: +- regex: rScudo_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rScudo diff --git a/prepare/r-rseis/PKGBUILD b/prepare/r-rseis/PKGBUILD new file mode 100644 index 0000000000..01019fac34 --- /dev/null +++ b/prepare/r-rseis/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RSEIS +_pkgver=4.0-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Seismic Time Series Analysis Tools' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rpmg + r-rwave +) +optdepends=( + r-stats +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rseis/lilac.py b/prepare/r-rseis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rseis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rseis/lilac.yaml b/prepare/r-rseis/lilac.yaml new file mode 100644 index 0000000000..164ee95676 --- /dev/null +++ b/prepare/r-rseis/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rpmg +- r-rwave +update_on: +- regex: RSEIS_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RSEIS diff --git a/prepare/r-rsemmed/PKGBUILD b/prepare/r-rsemmed/PKGBUILD new file mode 100644 index 0000000000..44a8533e69 --- /dev/null +++ b/prepare/r-rsemmed/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rsemmed +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An interface to the Semantic MEDLINE database' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-dplyr + r-igraph + r-magrittr + r-stringr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rsemmed/lilac.py b/prepare/r-rsemmed/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rsemmed/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rsemmed/lilac.yaml b/prepare/r-rsemmed/lilac.yaml new file mode 100644 index 0000000000..46cb2e8b82 --- /dev/null +++ b/prepare/r-rsemmed/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-igraph +- r-magrittr +- r-stringr +update_on: +- regex: rsemmed_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rsemmed diff --git a/prepare/r-rseqan/PKGBUILD b/prepare/r-rseqan/PKGBUILD new file mode 100644 index 0000000000..33d6e4b701 --- /dev/null +++ b/prepare/r-rseqan/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RSeqAn +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R SeqAn' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-rcpp +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rseqan/lilac.py b/prepare/r-rseqan/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rseqan/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rseqan/lilac.yaml b/prepare/r-rseqan/lilac.yaml new file mode 100644 index 0000000000..33a17d1524 --- /dev/null +++ b/prepare/r-rseqan/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: RSeqAn_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RSeqAn diff --git a/prepare/r-rslurm/PKGBUILD b/prepare/r-rslurm/PKGBUILD new file mode 100644 index 0000000000..fcd8a545ec --- /dev/null +++ b/prepare/r-rslurm/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rslurm +_pkgver=0.6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Submit R Calculations to a 'Slurm' Cluster" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-whisker +) +optdepends=( + r-knitr + r-markdown + r-parallel + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rslurm/lilac.py b/prepare/r-rslurm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rslurm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rslurm/lilac.yaml b/prepare/r-rslurm/lilac.yaml new file mode 100644 index 0000000000..6b3cfb7f84 --- /dev/null +++ b/prepare/r-rslurm/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-whisker +update_on: +- regex: rslurm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rslurm diff --git a/prepare/r-rsm/PKGBUILD b/prepare/r-rsm/PKGBUILD new file mode 100644 index 0000000000..371a629636 --- /dev/null +++ b/prepare/r-rsm/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rsm +_pkgver=2.10.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Response-Surface Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-estimability +) +optdepends=( + r-conf.design + r-doe.base + r-emmeans + r-frf2 + r-vdgraph +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rsm/lilac.py b/prepare/r-rsm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rsm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rsm/lilac.yaml b/prepare/r-rsm/lilac.yaml new file mode 100644 index 0000000000..87387ca73e --- /dev/null +++ b/prepare/r-rsm/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-estimability +update_on: +- regex: rsm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rsm diff --git a/prepare/r-rsnns/PKGBUILD b/prepare/r-rsnns/PKGBUILD new file mode 100644 index 0000000000..833c5e90bb --- /dev/null +++ b/prepare/r-rsnns/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RSNNS +_pkgver=0.4-14 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Neural Networks using the Stuttgart Neural Network Simulator (SNNS)' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-rcpp +) +optdepends=( + r-neuralnettools + r-scatterplot3d +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rsnns/lilac.py b/prepare/r-rsnns/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rsnns/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rsnns/lilac.yaml b/prepare/r-rsnns/lilac.yaml new file mode 100644 index 0000000000..6cb8bbecfb --- /dev/null +++ b/prepare/r-rsnns/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: RSNNS_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RSNNS diff --git a/prepare/r-rsnps/PKGBUILD b/prepare/r-rsnps/PKGBUILD new file mode 100644 index 0000000000..c730143368 --- /dev/null +++ b/prepare/r-rsnps/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rsnps +_pkgver=0.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Get 'SNP' ('Single-Nucleotide' 'Polymorphism') Data on the Web" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-crul + r-data.table + r-httr + r-jsonlite + r-plyr + r-rjsonio + r-stringr +) +optdepends=( + r-knitr + r-markdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rsnps/lilac.py b/prepare/r-rsnps/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rsnps/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rsnps/lilac.yaml b/prepare/r-rsnps/lilac.yaml new file mode 100644 index 0000000000..bd79700f32 --- /dev/null +++ b/prepare/r-rsnps/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-crul +- r-data.table +- r-httr +- r-jsonlite +- r-plyr +- r-rjsonio +- r-stringr +update_on: +- regex: rsnps_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rsnps diff --git a/prepare/r-rsolnp/PKGBUILD b/prepare/r-rsolnp/PKGBUILD new file mode 100644 index 0000000000..223a862aab --- /dev/null +++ b/prepare/r-rsolnp/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rsolnp +_pkgver=1.16 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='General Non-Linear Optimization' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-truncnorm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rsolnp/lilac.py b/prepare/r-rsolnp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rsolnp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rsolnp/lilac.yaml b/prepare/r-rsolnp/lilac.yaml new file mode 100644 index 0000000000..3e0fc32fb1 --- /dev/null +++ b/prepare/r-rsolnp/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-truncnorm +update_on: +- regex: Rsolnp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rsolnp diff --git a/prepare/r-rsparse/PKGBUILD b/prepare/r-rsparse/PKGBUILD new file mode 100644 index 0000000000..2092a8eae3 --- /dev/null +++ b/prepare/r-rsparse/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rsparse +_pkgver=0.5.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Learning on Sparse Matrices' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-float + r-lgr + r-matrixextra + r-rcpp + r-rcpparmadillo + r-rhpcblasctl +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rsparse/lilac.py b/prepare/r-rsparse/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rsparse/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rsparse/lilac.yaml b/prepare/r-rsparse/lilac.yaml new file mode 100644 index 0000000000..8703910eca --- /dev/null +++ b/prepare/r-rsparse/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-float +- r-lgr +- r-matrixextra +- r-rcpp +- r-rcpparmadillo +- r-rhpcblasctl +update_on: +- regex: rsparse_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rsparse diff --git a/prepare/r-rspectra/PKGBUILD b/prepare/r-rspectra/PKGBUILD new file mode 100644 index 0000000000..6de26cc40b --- /dev/null +++ b/prepare/r-rspectra/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RSpectra +_pkgver=0.16-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Solvers for Large-Scale Eigenvalue and SVD Problems' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MPL2') +depends=( + r + r-rcpp + r-rcppeigen +) +optdepends=( + r-knitr + r-prettydoc + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rspectra/lilac.py b/prepare/r-rspectra/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rspectra/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rspectra/lilac.yaml b/prepare/r-rspectra/lilac.yaml new file mode 100644 index 0000000000..1c0baab0ed --- /dev/null +++ b/prepare/r-rspectra/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcppeigen +update_on: +- regex: RSpectra_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RSpectra diff --git a/prepare/r-rsq/PKGBUILD b/prepare/r-rsq/PKGBUILD new file mode 100644 index 0000000000..ddc9e9a216 --- /dev/null +++ b/prepare/r-rsq/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rsq +_pkgver=2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R-Squared and Related Measures' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-deriv + r-lme4 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rsq/lilac.py b/prepare/r-rsq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rsq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rsq/lilac.yaml b/prepare/r-rsq/lilac.yaml new file mode 100644 index 0000000000..150ba9a874 --- /dev/null +++ b/prepare/r-rsq/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-deriv +- r-lme4 +update_on: +- regex: rsq_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rsq diff --git a/prepare/r-rstan/PKGBUILD b/prepare/r-rstan/PKGBUILD new file mode 100644 index 0000000000..b7fbb6748f --- /dev/null +++ b/prepare/r-rstan/PKGBUILD @@ -0,0 +1,52 @@ +# system requirements: GNU make, pandoc +# Maintainer: Guoyi Zhang + +_pkgname=rstan +_pkgver=2.21.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Interface to Stan' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bh + r-ggplot2 + r-gridextra + r-inline + r-loo + r-pkgbuild + r-rcpp + r-rcppeigen + r-rcppparallel + r-stanheaders +) +optdepends=( + r-bayesplot + r-bh + r-kernsmooth + r-knitr + r-matrix + r-parallel + r-rcppeigen + r-rmarkdown + r-rstantools + r-rstudioapi + r-runit + r-shinystan + r-v8 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rstan/lilac.py b/prepare/r-rstan/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rstan/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rstan/lilac.yaml b/prepare/r-rstan/lilac.yaml new file mode 100644 index 0000000000..5b662d72c8 --- /dev/null +++ b/prepare/r-rstan/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-ggplot2 +- r-gridextra +- r-inline +- r-loo +- r-pkgbuild +- r-rcpp +- r-rcppeigen +- r-rcppparallel +- r-stanheaders +update_on: +- regex: rstan_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rstan diff --git a/prepare/r-rstantools/PKGBUILD b/prepare/r-rstantools/PKGBUILD new file mode 100644 index 0000000000..b997645707 --- /dev/null +++ b/prepare/r-rstantools/PKGBUILD @@ -0,0 +1,41 @@ +# system requirements: pandoc, C++14 +# Maintainer: Guoyi Zhang + +_pkgname=rstantools +_pkgver=2.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Tools for Developing R Packages Interfacing with 'Stan'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-desc + r-rcpp + r-rcppparallel +) +optdepends=( + r-knitr + r-pkgbuild + r-pkgload + r-rmarkdown + r-roxygen2 + r-rstan + r-rstudioapi + r-testthat + r-usethis +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rstantools/lilac.py b/prepare/r-rstantools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rstantools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rstantools/lilac.yaml b/prepare/r-rstantools/lilac.yaml new file mode 100644 index 0000000000..f4c25261dd --- /dev/null +++ b/prepare/r-rstantools/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-desc +- r-rcpp +- r-rcppparallel +update_on: +- regex: rstantools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rstantools diff --git a/prepare/r-rstatix/PKGBUILD b/prepare/r-rstatix/PKGBUILD new file mode 100644 index 0000000000..15896b247e --- /dev/null +++ b/prepare/r-rstatix/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rstatix +_pkgver=0.7.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pipe-Friendly Framework for Basic Statistical Tests' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-broom + r-car + r-corrplot + r-dplyr + r-generics + r-magrittr + r-purrr + r-rlang + r-tibble + r-tidyr + r-tidyselect +) +optdepends=( + r-boot + r-coin + r-emmeans + r-ggpubr + r-graphics + r-knitr + r-rmarkdown + r-spelling + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rstatix/lilac.py b/prepare/r-rstatix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rstatix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rstatix/lilac.yaml b/prepare/r-rstatix/lilac.yaml new file mode 100644 index 0000000000..b01cb79ea5 --- /dev/null +++ b/prepare/r-rstatix/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-broom +- r-car +- r-corrplot +- r-dplyr +- r-generics +- r-magrittr +- r-purrr +- r-rlang +- r-tibble +- r-tidyr +- r-tidyselect +update_on: +- regex: rstatix_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rstatix diff --git a/prepare/r-rstudioapi/PKGBUILD b/prepare/r-rstudioapi/PKGBUILD new file mode 100644 index 0000000000..407da85ce0 --- /dev/null +++ b/prepare/r-rstudioapi/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rstudioapi +_pkgver=0.13 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Safely Access the RStudio API' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-clipr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rstudioapi/lilac.py b/prepare/r-rstudioapi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rstudioapi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rstudioapi/lilac.yaml b/prepare/r-rstudioapi/lilac.yaml new file mode 100644 index 0000000000..a670842711 --- /dev/null +++ b/prepare/r-rstudioapi/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: rstudioapi_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rstudioapi diff --git a/prepare/r-rsubread/PKGBUILD b/prepare/r-rsubread/PKGBUILD new file mode 100644 index 0000000000..c2cf58de65 --- /dev/null +++ b/prepare/r-rsubread/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rsubread +_pkgver=2.8.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mapping, quantification and variant analysis of sequencing data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rsubread/lilac.py b/prepare/r-rsubread/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rsubread/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rsubread/lilac.yaml b/prepare/r-rsubread/lilac.yaml new file mode 100644 index 0000000000..6d874ab4de --- /dev/null +++ b/prepare/r-rsubread/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Rsubread_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rsubread diff --git a/prepare/r-rsvd/PKGBUILD b/prepare/r-rsvd/PKGBUILD new file mode 100644 index 0000000000..9ea4392402 --- /dev/null +++ b/prepare/r-rsvd/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rsvd +_pkgver=1.0.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Randomized Singular Value Decomposition' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-ggplot2 + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rsvd/lilac.py b/prepare/r-rsvd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rsvd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rsvd/lilac.yaml b/prepare/r-rsvd/lilac.yaml new file mode 100644 index 0000000000..95fee74e79 --- /dev/null +++ b/prepare/r-rsvd/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: rsvd_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rsvd diff --git a/prepare/r-rsvg/PKGBUILD b/prepare/r-rsvg/PKGBUILD new file mode 100644 index 0000000000..93f39cee9b --- /dev/null +++ b/prepare/r-rsvg/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: librsvg2 +# Maintainer: Guoyi Zhang + +_pkgname=rsvg +_pkgver=2.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Render SVG Images into PDF, PNG, PostScript, or Bitmap Arrays' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-ggplot2 + r-knitr + r-magick + r-rmarkdown + r-spelling + r-svglite + r-webp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rsvg/lilac.py b/prepare/r-rsvg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rsvg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rsvg/lilac.yaml b/prepare/r-rsvg/lilac.yaml new file mode 100644 index 0000000000..29a00531d2 --- /dev/null +++ b/prepare/r-rsvg/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: rsvg_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rsvg diff --git a/prepare/r-rsvgtipsdevice/PKGBUILD b/prepare/r-rsvgtipsdevice/PKGBUILD new file mode 100644 index 0000000000..0ce6b5bfd0 --- /dev/null +++ b/prepare/r-rsvgtipsdevice/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RSVGTipsDevice +_pkgver=1.0-7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R SVG Graphics Device with Dynamic Tips and Hyperlinks' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://github.com/cran/${_pkgname}/archive/refs/tags/${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rsvgtipsdevice/lilac.py b/prepare/r-rsvgtipsdevice/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rsvgtipsdevice/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rsvgtipsdevice/lilac.yaml b/prepare/r-rsvgtipsdevice/lilac.yaml new file mode 100644 index 0000000000..7aab0d4132 --- /dev/null +++ b/prepare/r-rsvgtipsdevice/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: ([\d._-]+) + source: regex + url: https://github.com/cran/RSVGTipsDevice/tags diff --git a/prepare/r-rsvsim/PKGBUILD b/prepare/r-rsvsim/PKGBUILD new file mode 100644 index 0000000000..050ef4df01 --- /dev/null +++ b/prepare/r-rsvsim/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RSVSim +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RSVSim: an R/Bioconductor package for the simulation of structural variations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biostrings + r-genomicranges + r-iranges + r-shortread +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.hsapiens.ucsc.hg19.masked + r-mass + r-rtracklayer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rsvsim/lilac.py b/prepare/r-rsvsim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rsvsim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rsvsim/lilac.yaml b/prepare/r-rsvsim/lilac.yaml new file mode 100644 index 0000000000..e325bf4a3e --- /dev/null +++ b/prepare/r-rsvsim/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-genomicranges +- r-iranges +- r-shortread +update_on: +- regex: RSVSim_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RSVSim diff --git a/prepare/r-rsweep/PKGBUILD b/prepare/r-rsweep/PKGBUILD new file mode 100644 index 0000000000..a3d4212fb2 --- /dev/null +++ b/prepare/r-rsweep/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rSWeeP +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-pracma +) +optdepends=( + r-biocstyle + r-biostrings + r-knitr + r-methods + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rsweep/lilac.py b/prepare/r-rsweep/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rsweep/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rsweep/lilac.yaml b/prepare/r-rsweep/lilac.yaml new file mode 100644 index 0000000000..c8a896e1de --- /dev/null +++ b/prepare/r-rsweep/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-pracma +update_on: +- regex: rSWeeP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rSWeeP diff --git a/prepare/r-rtca/PKGBUILD b/prepare/r-rtca/PKGBUILD new file mode 100644 index 0000000000..910d84fa6e --- /dev/null +++ b/prepare/r-rtca/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RTCA +_pkgver=1.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Open-source toolkit to analyse data from xCELLigence System (RTCA)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-gtools + r-rcolorbrewer +) +optdepends=( + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rtca/lilac.py b/prepare/r-rtca/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rtca/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rtca/lilac.yaml b/prepare/r-rtca/lilac.yaml new file mode 100644 index 0000000000..4aca01ea1d --- /dev/null +++ b/prepare/r-rtca/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-gtools +- r-rcolorbrewer +update_on: +- regex: RTCA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RTCA diff --git a/prepare/r-rtcga/PKGBUILD b/prepare/r-rtcga/PKGBUILD new file mode 100644 index 0000000000..1779abcaa4 --- /dev/null +++ b/prepare/r-rtcga/PKGBUILD @@ -0,0 +1,61 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RTCGA +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The Cancer Genome Atlas Data Integration' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-data.table + r-dplyr + r-ggplot2 + r-ggthemes + r-knitr + r-purrr + r-rvest + r-scales + r-stringi + r-survminer + r-viridis + r-xml + r-xml2 +) +optdepends=( + r-biobase + r-devtools + r-genomicranges + r-iranges + r-magrittr + r-pander + r-rmarkdown + r-rtcga.clinical + r-rtcga.cnv + r-rtcga.methylation + r-rtcga.mirnaseq + r-rtcga.mrna + r-rtcga.mutations + r-rtcga.pancan12 + r-rtcga.rnaseq + r-rtcga.rppa + r-s4vectors + r-testthat + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rtcga/lilac.py b/prepare/r-rtcga/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rtcga/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rtcga/lilac.yaml b/prepare/r-rtcga/lilac.yaml new file mode 100644 index 0000000000..26201b176c --- /dev/null +++ b/prepare/r-rtcga/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-data.table +- r-dplyr +- r-ggplot2 +- r-ggthemes +- r-knitr +- r-purrr +- r-rvest +- r-scales +- r-stringi +- r-survminer +- r-viridis +- r-xml +- r-xml2 +update_on: +- regex: RTCGA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RTCGA diff --git a/prepare/r-rtcgatoolbox/PKGBUILD b/prepare/r-rtcgatoolbox/PKGBUILD new file mode 100644 index 0000000000..ee61284ca1 --- /dev/null +++ b/prepare/r-rtcgatoolbox/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RTCGAToolbox +_pkgver=2.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A new tool for exporting TCGA Firehose data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-biocgenerics + r-data.table + r-delayedarray + r-genomeinfodb + r-genomicranges + r-httr + r-limma + r-raggedexperiment + r-rcircos + r-rcurl + r-rjsonio + r-s4vectors + r-stringr + r-summarizedexperiment + r-tcgautils + r-xml +) +optdepends=( + r-biocstyle + r-homo.sapiens + r-knitr + r-readr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rtcgatoolbox/lilac.py b/prepare/r-rtcgatoolbox/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rtcgatoolbox/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rtcgatoolbox/lilac.yaml b/prepare/r-rtcgatoolbox/lilac.yaml new file mode 100644 index 0000000000..bfb4858b27 --- /dev/null +++ b/prepare/r-rtcgatoolbox/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-data.table +- r-delayedarray +- r-genomeinfodb +- r-genomicranges +- r-httr +- r-limma +- r-raggedexperiment +- r-rcircos +- r-rcurl +- r-rjsonio +- r-s4vectors +- r-stringr +- r-summarizedexperiment +- r-tcgautils +- r-xml +update_on: +- regex: RTCGAToolbox_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RTCGAToolbox diff --git a/prepare/r-rtensor/PKGBUILD b/prepare/r-rtensor/PKGBUILD new file mode 100644 index 0000000000..77d8ca0157 --- /dev/null +++ b/prepare/r-rtensor/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rTensor +_pkgver=1.4.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Tensor Analysis and Decomposition' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rtensor/lilac.py b/prepare/r-rtensor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rtensor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rtensor/lilac.yaml b/prepare/r-rtensor/lilac.yaml new file mode 100644 index 0000000000..512df092b4 --- /dev/null +++ b/prepare/r-rtensor/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: rTensor_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rTensor diff --git a/prepare/r-rtn/PKGBUILD b/prepare/r-rtn/PKGBUILD new file mode 100644 index 0000000000..667231a955 --- /dev/null +++ b/prepare/r-rtn/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RTN +_pkgver=2.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-car + r-data.table + r-igraph + r-iranges + r-limma + r-minet + r-mixtools + r-pheatmap + r-pwr + r-reder + r-s4vectors + r-snow + r-summarizedexperiment + r-viper +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rtn/lilac.py b/prepare/r-rtn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rtn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rtn/lilac.yaml b/prepare/r-rtn/lilac.yaml new file mode 100644 index 0000000000..59ef33cf05 --- /dev/null +++ b/prepare/r-rtn/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-car +- r-data.table +- r-igraph +- r-iranges +- r-limma +- r-minet +- r-mixtools +- r-pheatmap +- r-pwr +- r-reder +- r-s4vectors +- r-snow +- r-summarizedexperiment +- r-viper +update_on: +- regex: RTN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RTN diff --git a/prepare/r-rtnduals/PKGBUILD b/prepare/r-rtnduals/PKGBUILD new file mode 100644 index 0000000000..6b04e66887 --- /dev/null +++ b/prepare/r-rtnduals/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RTNduals +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Analysis of co-regulation and inference of 'dual regulons'" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-rtn +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rtnduals/lilac.py b/prepare/r-rtnduals/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rtnduals/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rtnduals/lilac.yaml b/prepare/r-rtnduals/lilac.yaml new file mode 100644 index 0000000000..7a6b7e4c9b --- /dev/null +++ b/prepare/r-rtnduals/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rtn +update_on: +- regex: RTNduals_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RTNduals diff --git a/prepare/r-rtnsurvival/PKGBUILD b/prepare/r-rtnsurvival/PKGBUILD new file mode 100644 index 0000000000..0a6426b167 --- /dev/null +++ b/prepare/r-rtnsurvival/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RTNsurvival +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Survival analysis using transcriptional networks inferred by the RTN package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-data.table + r-dunn.test + r-egg + r-ggplot2 + r-pheatmap + r-rcolorbrewer + r-rtn + r-rtnduals + r-scales +) +optdepends=( + r-biocgenerics + r-biocstyle + r-fletcher2013b + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rtnsurvival/lilac.py b/prepare/r-rtnsurvival/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rtnsurvival/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rtnsurvival/lilac.yaml b/prepare/r-rtnsurvival/lilac.yaml new file mode 100644 index 0000000000..cc512845d5 --- /dev/null +++ b/prepare/r-rtnsurvival/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-dunn.test +- r-egg +- r-ggplot2 +- r-pheatmap +- r-rcolorbrewer +- r-rtn +- r-rtnduals +- r-scales +update_on: +- regex: RTNsurvival_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RTNsurvival diff --git a/prepare/r-rtopper/PKGBUILD b/prepare/r-rtopper/PKGBUILD new file mode 100644 index 0000000000..68cc4ffead --- /dev/null +++ b/prepare/r-rtopper/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RTopper +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='This package is designed to perform Gene Set Analysis across multiple genomic platforms' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-limma + r-multtest +) +optdepends=( + r-go.db + r-keggrest + r-org.hs.eg.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rtopper/lilac.py b/prepare/r-rtopper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rtopper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rtopper/lilac.yaml b/prepare/r-rtopper/lilac.yaml new file mode 100644 index 0000000000..ec8aaea17d --- /dev/null +++ b/prepare/r-rtopper/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-limma +- r-multtest +update_on: +- regex: RTopper_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RTopper diff --git a/prepare/r-rtpca/PKGBUILD b/prepare/r-rtpca/PKGBUILD new file mode 100644 index 0000000000..6cee109a7a --- /dev/null +++ b/prepare/r-rtpca/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rtpca +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Thermal proximity co-aggregation with R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-dplyr + r-fdrtool + r-ggplot2 + r-proc + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat + r-tpp +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rtpca/lilac.py b/prepare/r-rtpca/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rtpca/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rtpca/lilac.yaml b/prepare/r-rtpca/lilac.yaml new file mode 100644 index 0000000000..404b1e1784 --- /dev/null +++ b/prepare/r-rtpca/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-dplyr +- r-fdrtool +- r-ggplot2 +- r-proc +- r-tibble +- r-tidyr +update_on: +- regex: Rtpca_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rtpca diff --git a/prepare/r-rtracklayer/PKGBUILD b/prepare/r-rtracklayer/PKGBUILD new file mode 100644 index 0000000000..eb482cab2f --- /dev/null +++ b/prepare/r-rtracklayer/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rtracklayer +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R interface to genome annotation files and the UCSC genome browser' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biocio + r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-rcurl + r-restfulr + r-rsamtools + r-s4vectors + r-xml + r-xvector + r-zlibbioc +) +optdepends=( + r-bsgenome + r-bsgenome.hsapiens.ucsc.hg19 + r-genefilter + r-genomicfeatures + r-hgu133plus2.db + r-humanstemcell + r-limma + r-microrna + r-org.hs.eg.db + r-runit + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rtracklayer/lilac.py b/prepare/r-rtracklayer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rtracklayer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rtracklayer/lilac.yaml b/prepare/r-rtracklayer/lilac.yaml new file mode 100644 index 0000000000..85c20e926b --- /dev/null +++ b/prepare/r-rtracklayer/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocio +- r-biostrings +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-rcurl +- r-restfulr +- r-rsamtools +- r-s4vectors +- r-xml +- r-xvector +- r-zlibbioc +update_on: +- regex: rtracklayer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rtracklayer diff --git a/prepare/r-rtreemix/PKGBUILD b/prepare/r-rtreemix/PKGBUILD new file mode 100644 index 0000000000..56e18ea37c --- /dev/null +++ b/prepare/r-rtreemix/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rtreemix +_pkgver=1.56.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Rtreemix: Mutagenetic trees mixture models.' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-graph + r-hmisc +) +optdepends=( + r-rgraphviz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rtreemix/lilac.py b/prepare/r-rtreemix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rtreemix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rtreemix/lilac.yaml b/prepare/r-rtreemix/lilac.yaml new file mode 100644 index 0000000000..47a402131e --- /dev/null +++ b/prepare/r-rtreemix/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-graph +- r-hmisc +update_on: +- regex: Rtreemix_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Rtreemix diff --git a/prepare/r-rtriangle/PKGBUILD b/prepare/r-rtriangle/PKGBUILD new file mode 100644 index 0000000000..9360bb5017 --- /dev/null +++ b/prepare/r-rtriangle/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RTriangle +_pkgver=1.6-0.10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Triangle - A 2D Quality Mesh Generator and Delaunay Triangulator' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('CCPL:by-nc-sa') +depends=( + r +) +optdepends=( + r-geometry + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rtriangle/lilac.py b/prepare/r-rtriangle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rtriangle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rtriangle/lilac.yaml b/prepare/r-rtriangle/lilac.yaml new file mode 100644 index 0000000000..7b3ee568d9 --- /dev/null +++ b/prepare/r-rtriangle/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RTriangle_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RTriangle diff --git a/prepare/r-rtrm/PKGBUILD b/prepare/r-rtrm/PKGBUILD new file mode 100644 index 0000000000..a6926fc5ba --- /dev/null +++ b/prepare/r-rtrm/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rTRM +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-dbi + r-igraph + r-rsqlite +) +optdepends=( + r-biocgenerics + r-biocstyle + r-biomart + r-biostrings + r-bsgenome.mmusculus.ucsc.mm8.masked + r-ggplot2 + r-graph + r-knitr + r-motifdb + r-org.hs.eg.db + r-org.mm.eg.db + r-pwmenrich + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rtrm/lilac.py b/prepare/r-rtrm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rtrm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rtrm/lilac.yaml b/prepare/r-rtrm/lilac.yaml new file mode 100644 index 0000000000..2df4cfbd1d --- /dev/null +++ b/prepare/r-rtrm/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-dbi +- r-igraph +- r-rsqlite +update_on: +- regex: rTRM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rTRM diff --git a/prepare/r-rtrmui/PKGBUILD b/prepare/r-rtrmui/PKGBUILD new file mode 100644 index 0000000000..102543d92d --- /dev/null +++ b/prepare/r-rtrmui/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rTRMui +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A shiny user interface for rTRM' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-motifdb + r-org.hs.eg.db + r-org.mm.eg.db + r-rtrm + r-shiny +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rtrmui/lilac.py b/prepare/r-rtrmui/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rtrmui/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rtrmui/lilac.yaml b/prepare/r-rtrmui/lilac.yaml new file mode 100644 index 0000000000..27c3dedd26 --- /dev/null +++ b/prepare/r-rtrmui/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-motifdb +- r-org.hs.eg.db +- r-org.mm.eg.db +- r-rtrm +- r-shiny +update_on: +- regex: rTRMui_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rTRMui diff --git a/prepare/r-rtsne/PKGBUILD b/prepare/r-rtsne/PKGBUILD new file mode 100644 index 0000000000..2059be3e9d --- /dev/null +++ b/prepare/r-rtsne/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rtsne +_pkgver=0.15 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('custom') +depends=( + r + r-rcpp +) +optdepends=( + r-irlba + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rtsne/lilac.py b/prepare/r-rtsne/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rtsne/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rtsne/lilac.yaml b/prepare/r-rtsne/lilac.yaml new file mode 100644 index 0000000000..aefbe1e54f --- /dev/null +++ b/prepare/r-rtsne/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: Rtsne_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rtsne diff --git a/prepare/r-rttf2pt1/PKGBUILD b/prepare/r-rttf2pt1/PKGBUILD new file mode 100644 index 0000000000..5497ac78b9 --- /dev/null +++ b/prepare/r-rttf2pt1/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rttf2pt1 +_pkgver=1.3.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'ttf2pt1' Program" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('custom') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rttf2pt1/lilac.py b/prepare/r-rttf2pt1/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rttf2pt1/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rttf2pt1/lilac.yaml b/prepare/r-rttf2pt1/lilac.yaml new file mode 100644 index 0000000000..e7a58aa2df --- /dev/null +++ b/prepare/r-rttf2pt1/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Rttf2pt1_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rttf2pt1 diff --git a/prepare/r-runibic/PKGBUILD b/prepare/r-runibic/PKGBUILD new file mode 100644 index 0000000000..7b695b4aaa --- /dev/null +++ b/prepare/r-runibic/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: C++11, GNU make +# Maintainer: Guoyi Zhang + +_pkgname=runibic +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='runibic: row-based biclustering algorithm for analysis of gene expression data in R' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biclust + r-rcpp + r-summarizedexperiment + r-testthat +) +optdepends=( + r-affy + r-airway + r-geoquery + r-knitr + r-qubic + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-runibic/lilac.py b/prepare/r-runibic/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-runibic/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-runibic/lilac.yaml b/prepare/r-runibic/lilac.yaml new file mode 100644 index 0000000000..7a805fb155 --- /dev/null +++ b/prepare/r-runibic/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biclust +- r-rcpp +- r-summarizedexperiment +- r-testthat +update_on: +- regex: runibic_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/runibic diff --git a/prepare/r-runit/PKGBUILD b/prepare/r-runit/PKGBUILD new file mode 100644 index 0000000000..7fb8cce9cf --- /dev/null +++ b/prepare/r-runit/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RUnit +_pkgver=0.4.32 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Unit Test Framework' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-xml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-runit/lilac.py b/prepare/r-runit/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-runit/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-runit/lilac.yaml b/prepare/r-runit/lilac.yaml new file mode 100644 index 0000000000..3bd52840be --- /dev/null +++ b/prepare/r-runit/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: RUnit_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RUnit diff --git a/prepare/r-ruv/PKGBUILD b/prepare/r-ruv/PKGBUILD new file mode 100644 index 0000000000..477eb7bd87 --- /dev/null +++ b/prepare/r-ruv/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ruv +_pkgver=0.9.7.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detect and Remove Unwanted Variation using Negative Controls' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-gridextra + r-scales +) +optdepends=( + r-colourpicker + r-shiny +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ruv/lilac.py b/prepare/r-ruv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ruv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ruv/lilac.yaml b/prepare/r-ruv/lilac.yaml new file mode 100644 index 0000000000..9a73ca02bb --- /dev/null +++ b/prepare/r-ruv/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gridextra +- r-scales +update_on: +- regex: ruv_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=ruv diff --git a/prepare/r-ruvcorr/PKGBUILD b/prepare/r-ruvcorr/PKGBUILD new file mode 100644 index 0000000000..6e6ff2b2ce --- /dev/null +++ b/prepare/r-ruvcorr/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RUVcorr +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Removal of unwanted variation for gene-gene correlations and related analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-bladderbatch + r-corrplot + r-gridextra + r-psych + r-reshape2 + r-snowfall +) +optdepends=( + r-hgu133a2.db + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ruvcorr/lilac.py b/prepare/r-ruvcorr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ruvcorr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ruvcorr/lilac.yaml b/prepare/r-ruvcorr/lilac.yaml new file mode 100644 index 0000000000..56ad82ee75 --- /dev/null +++ b/prepare/r-ruvcorr/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-bladderbatch +- r-corrplot +- r-gridextra +- r-psych +- r-reshape2 +- r-snowfall +update_on: +- regex: RUVcorr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RUVcorr diff --git a/prepare/r-ruvnormalize/PKGBUILD b/prepare/r-ruvnormalize/PKGBUILD new file mode 100644 index 0000000000..2f7036f547 --- /dev/null +++ b/prepare/r-ruvnormalize/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RUVnormalize +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RUV for normalization of expression array data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-ruvnormalizedata +) +optdepends=( + r-spams +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ruvnormalize/lilac.py b/prepare/r-ruvnormalize/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ruvnormalize/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ruvnormalize/lilac.yaml b/prepare/r-ruvnormalize/lilac.yaml new file mode 100644 index 0000000000..8841a5005e --- /dev/null +++ b/prepare/r-ruvnormalize/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-ruvnormalizedata +update_on: +- regex: RUVnormalize_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RUVnormalize diff --git a/prepare/r-ruvnormalizedata/PKGBUILD b/prepare/r-ruvnormalizedata/PKGBUILD new file mode 100644 index 0000000000..de6757ceb2 --- /dev/null +++ b/prepare/r-ruvnormalizedata/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RUVnormalizeData +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gender data for the RUVnormalize package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ruvnormalizedata/lilac.py b/prepare/r-ruvnormalizedata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ruvnormalizedata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ruvnormalizedata/lilac.yaml b/prepare/r-ruvnormalizedata/lilac.yaml new file mode 100644 index 0000000000..72d22356a2 --- /dev/null +++ b/prepare/r-ruvnormalizedata/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: RUVnormalizeData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RUVnormalizeData diff --git a/prepare/r-ruvseq/PKGBUILD b/prepare/r-ruvseq/PKGBUILD new file mode 100644 index 0000000000..dcee5a3ba9 --- /dev/null +++ b/prepare/r-ruvseq/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RUVSeq +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Remove Unwanted Variation from RNA-Seq Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-edaseq + r-edger +) +optdepends=( + r-biocstyle + r-deseq2 + r-knitr + r-rcolorbrewer + r-zebrafishrnaseq +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ruvseq/lilac.py b/prepare/r-ruvseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ruvseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ruvseq/lilac.yaml b/prepare/r-ruvseq/lilac.yaml new file mode 100644 index 0000000000..cf2e798bb4 --- /dev/null +++ b/prepare/r-ruvseq/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-edaseq +- r-edger +update_on: +- regex: RUVSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RUVSeq diff --git a/prepare/r-rversions/PKGBUILD b/prepare/r-rversions/PKGBUILD new file mode 100644 index 0000000000..afe2127480 --- /dev/null +++ b/prepare/r-rversions/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rversions +_pkgver=2.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Query 'R' Versions, Including 'r-release' and 'r-oldrel'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-curl + r-xml2 +) +optdepends=( + r-mockery + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rversions/lilac.py b/prepare/r-rversions/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rversions/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rversions/lilac.yaml b/prepare/r-rversions/lilac.yaml new file mode 100644 index 0000000000..8f06274874 --- /dev/null +++ b/prepare/r-rversions/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-xml2 +update_on: +- regex: rversions_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rversions diff --git a/prepare/r-rvest/PKGBUILD b/prepare/r-rvest/PKGBUILD new file mode 100644 index 0000000000..faee8b2385 --- /dev/null +++ b/prepare/r-rvest/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rvest +_pkgver=1.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Easily Harvest (Scrape) Web Pages' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-httr + r-lifecycle + r-magrittr + r-rlang + r-selectr + r-tibble + r-xml2 +) +optdepends=( + r-covr + r-glue + r-knitr + r-readr + r-repurrrsive + r-rmarkdown + r-spelling + r-stringi + r-testthat + r-webfakes +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rvest/lilac.py b/prepare/r-rvest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rvest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rvest/lilac.yaml b/prepare/r-rvest/lilac.yaml new file mode 100644 index 0000000000..0ba89e4ba6 --- /dev/null +++ b/prepare/r-rvest/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-httr +- r-lifecycle +- r-magrittr +- r-rlang +- r-selectr +- r-tibble +- r-xml2 +update_on: +- regex: rvest_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=rvest diff --git a/prepare/r-rvmmin/PKGBUILD b/prepare/r-rvmmin/PKGBUILD new file mode 100644 index 0000000000..83822e4744 --- /dev/null +++ b/prepare/r-rvmmin/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rvmmin +_pkgver=2018-4.17.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Variable Metric Nonlinear Function Minimization' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-optextras +) +optdepends=( + r-knitr + r-markdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rvmmin/lilac.py b/prepare/r-rvmmin/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rvmmin/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rvmmin/lilac.yaml b/prepare/r-rvmmin/lilac.yaml new file mode 100644 index 0000000000..9b8e0eadf5 --- /dev/null +++ b/prepare/r-rvmmin/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-optextras +update_on: +- regex: Rvmmin_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rvmmin diff --git a/prepare/r-rvs/PKGBUILD b/prepare/r-rvs/PKGBUILD new file mode 100644 index 0000000000..6ac33c4966 --- /dev/null +++ b/prepare/r-rvs/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=RVS +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Computes estimates of the probability of related individuals sharing a rare variant' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genlib + r-grain + r-kinship2 + r-snpstats +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rvs/lilac.py b/prepare/r-rvs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rvs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rvs/lilac.yaml b/prepare/r-rvs/lilac.yaml new file mode 100644 index 0000000000..f1cde36fa6 --- /dev/null +++ b/prepare/r-rvs/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genlib +- r-grain +- r-kinship2 +- r-snpstats +update_on: +- regex: RVS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/RVS diff --git a/prepare/r-rwave/PKGBUILD b/prepare/r-rwave/PKGBUILD new file mode 100644 index 0000000000..583694454f --- /dev/null +++ b/prepare/r-rwave/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Rwave +_pkgver=2.6-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Time-Frequency Analysis of 1-D Signals' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rwave/lilac.py b/prepare/r-rwave/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rwave/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rwave/lilac.yaml b/prepare/r-rwave/lilac.yaml new file mode 100644 index 0000000000..40479e1f8e --- /dev/null +++ b/prepare/r-rwave/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: Rwave_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Rwave diff --git a/prepare/r-rweka/PKGBUILD b/prepare/r-rweka/PKGBUILD new file mode 100644 index 0000000000..4a7431865d --- /dev/null +++ b/prepare/r-rweka/PKGBUILD @@ -0,0 +1,34 @@ +# system requirements: Java (>= 8) +# Maintainer: Guoyi Zhang + +_pkgname=RWeka +_pkgver=0.4-44 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R/Weka Interface' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rjava + r-rwekajars +) +optdepends=( + r-e1071 + r-mlbench + r-partykit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rweka/lilac.py b/prepare/r-rweka/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rweka/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rweka/lilac.yaml b/prepare/r-rweka/lilac.yaml new file mode 100644 index 0000000000..85ec758015 --- /dev/null +++ b/prepare/r-rweka/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rjava +- r-rwekajars +update_on: +- regex: RWeka_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RWeka diff --git a/prepare/r-rwekajars/PKGBUILD b/prepare/r-rwekajars/PKGBUILD new file mode 100644 index 0000000000..07550d2f80 --- /dev/null +++ b/prepare/r-rwekajars/PKGBUILD @@ -0,0 +1,28 @@ +# system requirements: Java (>= 8) +# Maintainer: Guoyi Zhang + +_pkgname=RWekajars +_pkgver=3.9.3-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R/Weka Interface Jars' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rjava +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rwekajars/lilac.py b/prepare/r-rwekajars/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rwekajars/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rwekajars/lilac.yaml b/prepare/r-rwekajars/lilac.yaml new file mode 100644 index 0000000000..d0ab3a4ed6 --- /dev/null +++ b/prepare/r-rwekajars/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rjava +update_on: +- regex: RWekajars_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=RWekajars diff --git a/prepare/r-rwikipathways/PKGBUILD b/prepare/r-rwikipathways/PKGBUILD new file mode 100644 index 0000000000..f8c1dcc9fd --- /dev/null +++ b/prepare/r-rwikipathways/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=rWikiPathways +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='rWikiPathways - R client library for the WikiPathways API' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-data.table + r-httr + r-rcurl + r-rjson + r-tidyr + r-xml +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-rwikipathways/lilac.py b/prepare/r-rwikipathways/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-rwikipathways/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-rwikipathways/lilac.yaml b/prepare/r-rwikipathways/lilac.yaml new file mode 100644 index 0000000000..50a0be789c --- /dev/null +++ b/prepare/r-rwikipathways/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-httr +- r-rcurl +- r-rjson +- r-tidyr +- r-xml +update_on: +- regex: rWikiPathways_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/rWikiPathways diff --git a/prepare/r-s2/PKGBUILD b/prepare/r-s2/PKGBUILD new file mode 100644 index 0000000000..171795776e --- /dev/null +++ b/prepare/r-s2/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: OpenSSL >= 1.0.1 +# Maintainer: Guoyi Zhang + +_pkgname=s2 +_pkgver=1.0.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Spherical Geometry Operators Using the S2 Geometry Library' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-rcpp + r-wk +) +optdepends=( + r-testthat + r-vctrs +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-s2/lilac.py b/prepare/r-s2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-s2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-s2/lilac.yaml b/prepare/r-s2/lilac.yaml new file mode 100644 index 0000000000..fb8ca1067d --- /dev/null +++ b/prepare/r-s2/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-wk +update_on: +- regex: s2_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=s2 diff --git a/prepare/r-s4vd/PKGBUILD b/prepare/r-s4vd/PKGBUILD new file mode 100644 index 0000000000..0a10dca438 --- /dev/null +++ b/prepare/r-s4vd/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=s4vd +_pkgver=1.1-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Biclustering via Sparse Singular Value Decomposition Incorporating Stability Selection' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-biclust + r-foreach + r-irlba +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-s4vd/lilac.py b/prepare/r-s4vd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-s4vd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-s4vd/lilac.yaml b/prepare/r-s4vd/lilac.yaml new file mode 100644 index 0000000000..92e40dcbd2 --- /dev/null +++ b/prepare/r-s4vd/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biclust +- r-foreach +- r-irlba +update_on: +- regex: s4vd_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=s4vd diff --git a/prepare/r-s4vectors/PKGBUILD b/prepare/r-s4vectors/PKGBUILD new file mode 100644 index 0000000000..217b2817e0 --- /dev/null +++ b/prepare/r-s4vectors/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=S4Vectors +_pkgver=0.32.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Foundation of vector-like and list-like containers in Bioconductor' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics +) +optdepends=( + r-biocstyle + r-data.table + r-delayedarray + r-genomicranges + r-graph + r-iranges + r-matrix + r-runit + r-shortread + r-summarizedexperiment +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-s4vectors/lilac.py b/prepare/r-s4vectors/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-s4vectors/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-s4vectors/lilac.yaml b/prepare/r-s4vectors/lilac.yaml new file mode 100644 index 0000000000..3345a0088e --- /dev/null +++ b/prepare/r-s4vectors/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +update_on: +- regex: S4Vectors_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/S4Vectors diff --git a/prepare/r-safe/PKGBUILD b/prepare/r-safe/PKGBUILD new file mode 100644 index 0000000000..87ea686b0f --- /dev/null +++ b/prepare/r-safe/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=safe +_pkgver=3.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Significance Analysis of Function and Expression' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biobase + r-sparsem +) +optdepends=( + r-breastcancerupp + r-dorng + r-foreach + r-go.db + r-gostats + r-hgu133a.db + r-pfam.db + r-reactome.db + r-rgraphviz + r-survival +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-safe/lilac.py b/prepare/r-safe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-safe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-safe/lilac.yaml b/prepare/r-safe/lilac.yaml new file mode 100644 index 0000000000..990ce8fca9 --- /dev/null +++ b/prepare/r-safe/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-sparsem +update_on: +- regex: safe_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/safe diff --git a/prepare/r-sagenhaft/PKGBUILD b/prepare/r-sagenhaft/PKGBUILD new file mode 100644 index 0000000000..8ae6619951 --- /dev/null +++ b/prepare/r-sagenhaft/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sagenhaft +_pkgver=1.64.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Collection of functions for reading and comparing SAGE libraries' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-sparsem +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sagenhaft/lilac.py b/prepare/r-sagenhaft/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sagenhaft/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sagenhaft/lilac.yaml b/prepare/r-sagenhaft/lilac.yaml new file mode 100644 index 0000000000..371c3e3e1d --- /dev/null +++ b/prepare/r-sagenhaft/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-sparsem +update_on: +- regex: sagenhaft_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sagenhaft diff --git a/prepare/r-saigegds/PKGBUILD b/prepare/r-saigegds/PKGBUILD new file mode 100644 index 0000000000..ab838e4c39 --- /dev/null +++ b/prepare/r-saigegds/PKGBUILD @@ -0,0 +1,43 @@ +# system requirements: C++11, GNU make +# Maintainer: Guoyi Zhang + +_pkgname=SAIGEgds +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-gdsfmt + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-seqarray + r-spatest +) +optdepends=( + r-biocgenerics + r-crayon + r-knitr + r-markdown + r-parallel + r-rmarkdown + r-runit + r-snprelate +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-saigegds/lilac.py b/prepare/r-saigegds/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-saigegds/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-saigegds/lilac.yaml b/prepare/r-saigegds/lilac.yaml new file mode 100644 index 0000000000..d70c4e5f81 --- /dev/null +++ b/prepare/r-saigegds/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gdsfmt +- r-rcpp +- r-rcpparmadillo +- r-rcppparallel +- r-seqarray +- r-spatest +update_on: +- regex: SAIGEgds_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SAIGEgds diff --git a/prepare/r-sampleclassifier/PKGBUILD b/prepare/r-sampleclassifier/PKGBUILD new file mode 100644 index 0000000000..16d5f37ca1 --- /dev/null +++ b/prepare/r-sampleclassifier/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sampleClassifier +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sample Classifier' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotate + r-e1071 + r-ggplot2 + r-mgfm + r-mgfr +) +optdepends=( + r-biocstyle + r-hgu133a.db + r-hgu133plus2.db + r-sampleclassifierdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sampleclassifier/lilac.py b/prepare/r-sampleclassifier/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sampleclassifier/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sampleclassifier/lilac.yaml b/prepare/r-sampleclassifier/lilac.yaml new file mode 100644 index 0000000000..668df08dae --- /dev/null +++ b/prepare/r-sampleclassifier/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-e1071 +- r-ggplot2 +- r-mgfm +- r-mgfr +update_on: +- regex: sampleClassifier_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sampleClassifier diff --git a/prepare/r-sampsurf/PKGBUILD b/prepare/r-sampsurf/PKGBUILD new file mode 100644 index 0000000000..831c84e8ff --- /dev/null +++ b/prepare/r-sampsurf/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sampSurf +_pkgver=0.7-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sampling Surface Simulation for Areal Sampling Methods' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-latticeextra + r-raster + r-rastervis + r-sp +) +optdepends=( + r-rgeos + r-rgl +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sampsurf/lilac.py b/prepare/r-sampsurf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sampsurf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sampsurf/lilac.yaml b/prepare/r-sampsurf/lilac.yaml new file mode 100644 index 0000000000..284a111d3d --- /dev/null +++ b/prepare/r-sampsurf/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-latticeextra +- r-raster +- r-rastervis +- r-sp +update_on: +- regex: sampSurf_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sampSurf diff --git a/prepare/r-samspectral/PKGBUILD b/prepare/r-samspectral/PKGBUILD new file mode 100644 index 0000000000..7b2bebe6f4 --- /dev/null +++ b/prepare/r-samspectral/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SamSPECTRAL +_pkgver=1.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identifies cell population in flow cytometry data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-samspectral/lilac.py b/prepare/r-samspectral/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-samspectral/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-samspectral/lilac.yaml b/prepare/r-samspectral/lilac.yaml new file mode 100644 index 0000000000..8f44d0a56c --- /dev/null +++ b/prepare/r-samspectral/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: SamSPECTRAL_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SamSPECTRAL diff --git a/prepare/r-sandwich/PKGBUILD b/prepare/r-sandwich/PKGBUILD new file mode 100644 index 0000000000..a1423837ac --- /dev/null +++ b/prepare/r-sandwich/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sandwich +_pkgver=3.0-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Robust Covariance Matrix Estimators' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-zoo +) +optdepends=( + r-aer + r-car + r-geepack + r-lattice + r-lmtest + r-mass + r-multiwayvcov + r-parallel + r-pcse + r-plm + r-pscl + r-scatterplot3d + r-stats4 + r-strucchange + r-survival +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sandwich/lilac.py b/prepare/r-sandwich/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sandwich/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sandwich/lilac.yaml b/prepare/r-sandwich/lilac.yaml new file mode 100644 index 0000000000..1ff9943963 --- /dev/null +++ b/prepare/r-sandwich/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-zoo +update_on: +- regex: sandwich_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sandwich diff --git a/prepare/r-sangeranalyser/PKGBUILD b/prepare/r-sangeranalyser/PKGBUILD new file mode 100644 index 0000000000..ef574413b6 --- /dev/null +++ b/prepare/r-sangeranalyser/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sangeranalyseR +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-biocstyle + r-biostrings + r-data.table + r-decipher + r-dt + r-excelr + r-ggdendro + r-gridextra + r-knitr + r-logger + r-openxlsx + r-phangorn + r-plotly + r-reshape2 + r-rmarkdown + r-sangerseqr + r-seqinr + r-shiny + r-shinycssloaders + r-shinydashboard + r-shinyjs + r-shinywidgets + r-stringr + r-zeallot +) +optdepends=( + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sangeranalyser/lilac.py b/prepare/r-sangeranalyser/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sangeranalyser/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sangeranalyser/lilac.yaml b/prepare/r-sangeranalyser/lilac.yaml new file mode 100644 index 0000000000..2dcd430a12 --- /dev/null +++ b/prepare/r-sangeranalyser/lilac.yaml @@ -0,0 +1,34 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-biocstyle +- r-biostrings +- r-data.table +- r-decipher +- r-dt +- r-excelr +- r-ggdendro +- r-gridextra +- r-knitr +- r-logger +- r-openxlsx +- r-phangorn +- r-plotly +- r-reshape2 +- r-rmarkdown +- r-sangerseqr +- r-seqinr +- r-shiny +- r-shinycssloaders +- r-shinydashboard +- r-shinyjs +- r-shinywidgets +- r-stringr +- r-zeallot +update_on: +- regex: sangeranalyseR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sangeranalyseR diff --git a/prepare/r-sangerseqr/PKGBUILD b/prepare/r-sangerseqr/PKGBUILD new file mode 100644 index 0000000000..01f3037af7 --- /dev/null +++ b/prepare/r-sangerseqr/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sangerseqR +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Sanger Sequencing Data in R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-shiny +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sangerseqr/lilac.py b/prepare/r-sangerseqr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sangerseqr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sangerseqr/lilac.yaml b/prepare/r-sangerseqr/lilac.yaml new file mode 100644 index 0000000000..182bb64db7 --- /dev/null +++ b/prepare/r-sangerseqr/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-shiny +update_on: +- regex: sangerseqR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sangerseqR diff --git a/prepare/r-santa/PKGBUILD b/prepare/r-santa/PKGBUILD new file mode 100644 index 0000000000..f4c0fe1c30 --- /dev/null +++ b/prepare/r-santa/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SANTA +_pkgver=2.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Spatial Analysis of Network Associations' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-igraph +) +optdepends=( + r-biocgenerics + r-bionet + r-dlbcl + r-formatr + r-knitr + r-markdown + r-msm + r-org.sc.sgd.db + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-santa/lilac.py b/prepare/r-santa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-santa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-santa/lilac.yaml b/prepare/r-santa/lilac.yaml new file mode 100644 index 0000000000..1b0e193f06 --- /dev/null +++ b/prepare/r-santa/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +update_on: +- regex: SANTA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SANTA diff --git a/prepare/r-sarks/PKGBUILD b/prepare/r-sarks/PKGBUILD new file mode 100644 index 0000000000..5930767eed --- /dev/null +++ b/prepare/r-sarks/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: Java (>= 1.8) +# Maintainer: Guoyi Zhang + +_pkgname=sarks +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-binom + r-biostrings + r-iranges + r-rjava +) +optdepends=( + r-biocgenerics + r-ggplot2 + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sarks/lilac.py b/prepare/r-sarks/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sarks/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sarks/lilac.yaml b/prepare/r-sarks/lilac.yaml new file mode 100644 index 0000000000..6124a137bb --- /dev/null +++ b/prepare/r-sarks/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-binom +- r-biostrings +- r-iranges +- r-rjava +update_on: +- regex: sarks_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sarks diff --git a/prepare/r-sass/PKGBUILD b/prepare/r-sass/PKGBUILD new file mode 100644 index 0000000000..aa69d27ab5 --- /dev/null +++ b/prepare/r-sass/PKGBUILD @@ -0,0 +1,41 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=sass +_pkgver=0.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Syntactically Awesome Style Sheets ('Sass')" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-fs + r-htmltools + r-r6 + r-rappdirs + r-rlang +) +optdepends=( + r-curl + r-knitr + r-rmarkdown + r-shiny + r-testthat + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sass/lilac.py b/prepare/r-sass/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sass/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sass/lilac.yaml b/prepare/r-sass/lilac.yaml new file mode 100644 index 0000000000..677008f935 --- /dev/null +++ b/prepare/r-sass/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fs +- r-htmltools +- r-r6 +- r-rappdirs +- r-rlang +update_on: +- regex: sass_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sass diff --git a/prepare/r-saturn/PKGBUILD b/prepare/r-saturn/PKGBUILD new file mode 100644 index 0000000000..a41042ee85 --- /dev/null +++ b/prepare/r-saturn/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=satuRn +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-ggplot2 + r-limma + r-locfdr + r-pbapply + r-summarizedexperiment +) +optdepends=( + r-annotationhub + r-biocstyle + r-covr + r-delayedarray + r-dexseq + r-edger + r-ensembldb + r-knitr + r-rmarkdown + r-stager + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-saturn/lilac.py b/prepare/r-saturn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-saturn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-saturn/lilac.yaml b/prepare/r-saturn/lilac.yaml new file mode 100644 index 0000000000..6e9ecdd8c1 --- /dev/null +++ b/prepare/r-saturn/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-ggplot2 +- r-limma +- r-locfdr +- r-pbapply +- r-summarizedexperiment +update_on: +- regex: satuRn_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/satuRn diff --git a/prepare/r-saver/PKGBUILD b/prepare/r-saver/PKGBUILD new file mode 100644 index 0000000000..b96b24c9c2 --- /dev/null +++ b/prepare/r-saver/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SAVER +_pkgver=1.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Single-Cell RNA-Seq Gene Expression Recovery' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-doparallel + r-foreach + r-glmnet + r-iterators +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-saver/lilac.py b/prepare/r-saver/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-saver/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-saver/lilac.yaml b/prepare/r-saver/lilac.yaml new file mode 100644 index 0000000000..8771d232d7 --- /dev/null +++ b/prepare/r-saver/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-foreach +- r-glmnet +- r-iterators +update_on: +- regex: SAVER_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=SAVER diff --git a/prepare/r-savr/PKGBUILD b/prepare/r-savr/PKGBUILD new file mode 100644 index 0000000000..897bc1cb10 --- /dev/null +++ b/prepare/r-savr/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=savR +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Parse and analyze Illumina SAV files' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-ggplot2 + r-gridextra + r-reshape2 + r-scales + r-xml +) +optdepends=( + r-cairo + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-savr/lilac.py b/prepare/r-savr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-savr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-savr/lilac.yaml b/prepare/r-savr/lilac.yaml new file mode 100644 index 0000000000..4726051382 --- /dev/null +++ b/prepare/r-savr/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gridextra +- r-reshape2 +- r-scales +- r-xml +update_on: +- regex: savR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/savR diff --git a/prepare/r-sbgnview.data/PKGBUILD b/prepare/r-sbgnview.data/PKGBUILD new file mode 100644 index 0000000000..9b7fc74a63 --- /dev/null +++ b/prepare/r-sbgnview.data/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SBGNview.data +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Supporting datasets for SBGNview package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-bookdown + r-knitr + r-rmarkdown +) +optdepends=( + r-summarizedexperiment +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sbgnview.data/lilac.py b/prepare/r-sbgnview.data/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sbgnview.data/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sbgnview.data/lilac.yaml b/prepare/r-sbgnview.data/lilac.yaml new file mode 100644 index 0000000000..cca3be1404 --- /dev/null +++ b/prepare/r-sbgnview.data/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bookdown +- r-knitr +- r-rmarkdown +update_on: +- regex: SBGNview.data_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SBGNview.data diff --git a/prepare/r-sbgnview/PKGBUILD b/prepare/r-sbgnview/PKGBUILD new file mode 100644 index 0000000000..ac46fee660 --- /dev/null +++ b/prepare/r-sbgnview/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SBGNview +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-annotationdbi + r-bookdown + r-httr + r-igraph + r-keggrest + r-knitr + r-pathview + r-rdpack + r-rmarkdown + r-rsvg + r-sbgnview.data + r-summarizedexperiment + r-xml2 +) +optdepends=( + r-gage + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sbgnview/lilac.py b/prepare/r-sbgnview/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sbgnview/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sbgnview/lilac.yaml b/prepare/r-sbgnview/lilac.yaml new file mode 100644 index 0000000000..3b0f50d1b6 --- /dev/null +++ b/prepare/r-sbgnview/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-bookdown +- r-httr +- r-igraph +- r-keggrest +- r-knitr +- r-pathview +- r-rdpack +- r-rmarkdown +- r-rsvg +- r-sbgnview.data +- r-summarizedexperiment +- r-xml2 +update_on: +- regex: SBGNview_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SBGNview diff --git a/prepare/r-sbmlr/PKGBUILD b/prepare/r-sbmlr/PKGBUILD new file mode 100644 index 0000000000..c266167ef5 --- /dev/null +++ b/prepare/r-sbmlr/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SBMLR +_pkgver=1.90.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SBML-R Interface and Analysis Tools' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-desolve + r-xml +) +optdepends=( + r-rsbml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sbmlr/lilac.py b/prepare/r-sbmlr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sbmlr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sbmlr/lilac.yaml b/prepare/r-sbmlr/lilac.yaml new file mode 100644 index 0000000000..ac0b90c589 --- /dev/null +++ b/prepare/r-sbmlr/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-desolve +- r-xml +update_on: +- regex: SBMLR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SBMLR diff --git a/prepare/r-sc3/PKGBUILD b/prepare/r-sc3/PKGBUILD new file mode 100644 index 0000000000..0f70b91488 --- /dev/null +++ b/prepare/r-sc3/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SC3 +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Single-Cell Consensus Clustering' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-doparallel + r-dorng + r-e1071 + r-foreach + r-ggplot2 + r-pheatmap + r-rcpp + r-rcpparmadillo + r-robustbase + r-rocr + r-rrcov + r-s4vectors + r-shiny + r-singlecellexperiment + r-summarizedexperiment + r-writexls +) +optdepends=( + r-knitr + r-mclust + r-rmarkdown + r-scater +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sc3/lilac.py b/prepare/r-sc3/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sc3/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sc3/lilac.yaml b/prepare/r-sc3/lilac.yaml new file mode 100644 index 0000000000..3930419a3d --- /dev/null +++ b/prepare/r-sc3/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-doparallel +- r-dorng +- r-e1071 +- r-foreach +- r-ggplot2 +- r-pheatmap +- r-rcpp +- r-rcpparmadillo +- r-robustbase +- r-rocr +- r-rrcov +- r-s4vectors +- r-shiny +- r-singlecellexperiment +- r-summarizedexperiment +- r-writexls +update_on: +- regex: SC3_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SC3 diff --git a/prepare/r-scale4c/PKGBUILD b/prepare/r-scale4c/PKGBUILD new file mode 100644 index 0000000000..6e2f0954ef --- /dev/null +++ b/prepare/r-scale4c/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Scale4C +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-genomicranges + r-iranges + r-smoothie + r-summarizedexperiment +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scale4c/lilac.py b/prepare/r-scale4c/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scale4c/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scale4c/lilac.yaml b/prepare/r-scale4c/lilac.yaml new file mode 100644 index 0000000000..12e69152b3 --- /dev/null +++ b/prepare/r-scale4c/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-iranges +- r-smoothie +- r-summarizedexperiment +update_on: +- regex: Scale4C_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Scale4C diff --git a/prepare/r-scaledmatrix/PKGBUILD b/prepare/r-scaledmatrix/PKGBUILD new file mode 100644 index 0000000000..9b9f13e62f --- /dev/null +++ b/prepare/r-scaledmatrix/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ScaledMatrix +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Creating a DelayedMatrix of Scaled and Centered Values' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-delayedarray + r-s4vectors +) +optdepends=( + r-biocsingular + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scaledmatrix/lilac.py b/prepare/r-scaledmatrix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scaledmatrix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scaledmatrix/lilac.yaml b/prepare/r-scaledmatrix/lilac.yaml new file mode 100644 index 0000000000..b9f1472725 --- /dev/null +++ b/prepare/r-scaledmatrix/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-delayedarray +- r-s4vectors +update_on: +- regex: ScaledMatrix_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ScaledMatrix diff --git a/prepare/r-scales/PKGBUILD b/prepare/r-scales/PKGBUILD new file mode 100644 index 0000000000..faa878ce08 --- /dev/null +++ b/prepare/r-scales/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scales +_pkgver=1.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Scale Functions for Visualization' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-farver + r-labeling + r-lifecycle + r-munsell + r-r6 + r-rcolorbrewer + r-viridislite +) +optdepends=( + r-bit64 + r-covr + r-dichromat + r-ggplot2 + r-hms + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scales/lilac.py b/prepare/r-scales/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scales/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scales/lilac.yaml b/prepare/r-scales/lilac.yaml new file mode 100644 index 0000000000..3cf4453818 --- /dev/null +++ b/prepare/r-scales/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-farver +- r-labeling +- r-lifecycle +- r-munsell +- r-r6 +- r-rcolorbrewer +- r-viridislite +update_on: +- regex: scales_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=scales diff --git a/prepare/r-scalign/PKGBUILD b/prepare/r-scalign/PKGBUILD new file mode 100644 index 0000000000..14377bc4c0 --- /dev/null +++ b/prepare/r-scalign/PKGBUILD @@ -0,0 +1,40 @@ +# system requirements: python (< 3.7), tensorflow +# Maintainer: Guoyi Zhang + +_pkgname=scAlign +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An alignment and integration method for single cell genomics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-fnn + r-ggplot2 + r-irlba + r-purrr + r-rtsne + r-seurat + r-singlecellexperiment + r-tensorflow +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scalign/lilac.py b/prepare/r-scalign/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scalign/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scalign/lilac.yaml b/prepare/r-scalign/lilac.yaml new file mode 100644 index 0000000000..72d4f56faa --- /dev/null +++ b/prepare/r-scalign/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fnn +- r-ggplot2 +- r-irlba +- r-purrr +- r-rtsne +- r-seurat +- r-singlecellexperiment +- r-tensorflow +update_on: +- regex: scAlign_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scAlign diff --git a/prepare/r-scam/PKGBUILD b/prepare/r-scam/PKGBUILD new file mode 100644 index 0000000000..37890843d4 --- /dev/null +++ b/prepare/r-scam/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scam +_pkgver=1.2-12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Shape Constrained Additive Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-nlme +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scam/lilac.py b/prepare/r-scam/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scam/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scam/lilac.yaml b/prepare/r-scam/lilac.yaml new file mode 100644 index 0000000000..876a4360c9 --- /dev/null +++ b/prepare/r-scam/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: scam_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=scam diff --git a/prepare/r-scan.upc/PKGBUILD b/prepare/r-scan.upc/PKGBUILD new file mode 100644 index 0000000000..26b6986243 --- /dev/null +++ b/prepare/r-scan.upc/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SCAN.UPC +_pkgver=2.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-affy + r-affyio + r-biobase + r-biostrings + r-foreach + r-geoquery + r-iranges + r-oligo + r-sva +) +optdepends=( + r-pd.hg.u95a +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scan.upc/lilac.py b/prepare/r-scan.upc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scan.upc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scan.upc/lilac.yaml b/prepare/r-scan.upc/lilac.yaml new file mode 100644 index 0000000000..7575da1530 --- /dev/null +++ b/prepare/r-scan.upc/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-affyio +- r-biobase +- r-biostrings +- r-foreach +- r-geoquery +- r-iranges +- r-oligo +- r-sva +update_on: +- regex: SCAN.UPC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SCAN.UPC diff --git a/prepare/r-scanmir/PKGBUILD b/prepare/r-scanmir/PKGBUILD new file mode 100644 index 0000000000..8abdaf8051 --- /dev/null +++ b/prepare/r-scanmir/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scanMiR +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='scanMiR' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-biostrings + r-data.table + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gridextra + r-iranges + r-s4vectors + r-seqlogo + r-stringi +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scanmir/lilac.py b/prepare/r-scanmir/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scanmir/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scanmir/lilac.yaml b/prepare/r-scanmir/lilac.yaml new file mode 100644 index 0000000000..e5b334504f --- /dev/null +++ b/prepare/r-scanmir/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-biostrings +- r-data.table +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-gridextra +- r-iranges +- r-s4vectors +- r-seqlogo +- r-stringi +update_on: +- regex: scanMiR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scanMiR diff --git a/prepare/r-scanmirapp/PKGBUILD b/prepare/r-scanmirapp/PKGBUILD new file mode 100644 index 0000000000..b4ce3d2fa3 --- /dev/null +++ b/prepare/r-scanmirapp/PKGBUILD @@ -0,0 +1,62 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scanMiRApp +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='scanMiR shiny application' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-annotationfilter + r-annotationhub + r-biocparallel + r-biostrings + r-data.table + r-digest + r-dt + r-ensembldb + r-fst + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-htmlwidgets + r-iranges + r-plotly + r-rintrojs + r-rtracklayer + r-s4vectors + r-scanmir + r-scanmirdata + r-shiny + r-shinycssloaders + r-shinydashboard + r-waiter +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg38 + r-bsgenome.mmusculus.ucsc.mm10 + r-bsgenome.rnorvegicus.ucsc.rn6 + r-knitr + r-rmarkdown + r-shinytest + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scanmirapp/lilac.py b/prepare/r-scanmirapp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scanmirapp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scanmirapp/lilac.yaml b/prepare/r-scanmirapp/lilac.yaml new file mode 100644 index 0000000000..0a00688c7c --- /dev/null +++ b/prepare/r-scanmirapp/lilac.yaml @@ -0,0 +1,35 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationfilter +- r-annotationhub +- r-biocparallel +- r-biostrings +- r-data.table +- r-digest +- r-dt +- r-ensembldb +- r-fst +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-htmlwidgets +- r-iranges +- r-plotly +- r-rintrojs +- r-rtracklayer +- r-s4vectors +- r-scanmir +- r-scanmirdata +- r-shiny +- r-shinycssloaders +- r-shinydashboard +- r-waiter +update_on: +- regex: scanMiRApp_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scanMiRApp diff --git a/prepare/r-scanmirdata/PKGBUILD b/prepare/r-scanmirdata/PKGBUILD new file mode 100644 index 0000000000..28f242fd4b --- /dev/null +++ b/prepare/r-scanmirdata/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scanMiRData +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='miRNA Affinity models for the scanMiR package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-scanmir +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scanmirdata/lilac.py b/prepare/r-scanmirdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scanmirdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scanmirdata/lilac.yaml b/prepare/r-scanmirdata/lilac.yaml new file mode 100644 index 0000000000..24667e9153 --- /dev/null +++ b/prepare/r-scanmirdata/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-scanmir +update_on: +- regex: scanMiRData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scanMiRData diff --git a/prepare/r-scannotatr/PKGBUILD b/prepare/r-scannotatr/PKGBUILD new file mode 100644 index 0000000000..b835d4740f --- /dev/null +++ b/prepare/r-scannotatr/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scAnnotatR +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pretrained learning models for cell type prediction on single cell RNA-sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationhub + r-ape + r-caret + r-data.tree + r-dplyr + r-e1071 + r-ggplot2 + r-kernlab + r-proc + r-rocr + r-seurat + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-knitr + r-rmarkdown + r-scrnaseq + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scannotatr/lilac.py b/prepare/r-scannotatr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scannotatr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scannotatr/lilac.yaml b/prepare/r-scannotatr/lilac.yaml new file mode 100644 index 0000000000..6ee0e1e074 --- /dev/null +++ b/prepare/r-scannotatr/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-ape +- r-caret +- r-data.tree +- r-dplyr +- r-e1071 +- r-ggplot2 +- r-kernlab +- r-proc +- r-rocr +- r-seurat +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: scAnnotatR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scAnnotatR diff --git a/prepare/r-scanvis/PKGBUILD b/prepare/r-scanvis/PKGBUILD new file mode 100644 index 0000000000..e5e27010e7 --- /dev/null +++ b/prepare/r-scanvis/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SCANVIS +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-iranges + r-plotrix + r-rcurl + r-rtracklayer +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scanvis/lilac.py b/prepare/r-scanvis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scanvis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scanvis/lilac.yaml b/prepare/r-scanvis/lilac.yaml new file mode 100644 index 0000000000..2982b6a030 --- /dev/null +++ b/prepare/r-scanvis/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-iranges +- r-plotrix +- r-rcurl +- r-rtracklayer +update_on: +- regex: SCANVIS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SCANVIS diff --git a/prepare/r-scarray/PKGBUILD b/prepare/r-scarray/PKGBUILD new file mode 100644 index 0000000000..c6151f386d --- /dev/null +++ b/prepare/r-scarray/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SCArray +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Large-scale single-cell RNA-seq data manipulation with GDS files' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-delayedarray + r-delayedmatrixstats + r-gdsfmt + r-iranges + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-knitr + r-markdown + r-matrix + r-rmarkdown + r-runit + r-scater + r-uwot +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scarray/lilac.py b/prepare/r-scarray/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scarray/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scarray/lilac.yaml b/prepare/r-scarray/lilac.yaml new file mode 100644 index 0000000000..4fecc730cf --- /dev/null +++ b/prepare/r-scarray/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-delayedarray +- r-delayedmatrixstats +- r-gdsfmt +- r-iranges +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: SCArray_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SCArray diff --git a/prepare/r-scate/PKGBUILD b/prepare/r-scate/PKGBUILD new file mode 100644 index 0000000000..d9c93679a0 --- /dev/null +++ b/prepare/r-scate/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SCATE +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SCATE: Single-cell ATAC-seq Signal Extraction and Enhancement' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-genomicalignments + r-genomicranges + r-mclust + r-preprocesscore + r-rtsne + r-scatedata + r-splines2 + r-xgboost +) +optdepends=( + r-ggplot2 + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scate/lilac.py b/prepare/r-scate/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scate/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scate/lilac.yaml b/prepare/r-scate/lilac.yaml new file mode 100644 index 0000000000..e86abcbce2 --- /dev/null +++ b/prepare/r-scate/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicalignments +- r-genomicranges +- r-mclust +- r-preprocesscore +- r-rtsne +- r-scatedata +- r-splines2 +- r-xgboost +update_on: +- regex: SCATE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SCATE diff --git a/prepare/r-scatedata/PKGBUILD b/prepare/r-scatedata/PKGBUILD new file mode 100644 index 0000000000..bce35cb80c --- /dev/null +++ b/prepare/r-scatedata/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SCATEData +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data for SCATE (Single-cell ATAC-seq Signal Extraction and Enhancement)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-experimenthub + r-genomicalignments + r-genomicranges +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scatedata/lilac.py b/prepare/r-scatedata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scatedata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scatedata/lilac.yaml b/prepare/r-scatedata/lilac.yaml new file mode 100644 index 0000000000..6af6cb55ed --- /dev/null +++ b/prepare/r-scatedata/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-experimenthub +- r-genomicalignments +- r-genomicranges +update_on: +- regex: SCATEData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SCATEData diff --git a/prepare/r-scater/PKGBUILD b/prepare/r-scater/PKGBUILD new file mode 100644 index 0000000000..e4f3330229 --- /dev/null +++ b/prepare/r-scater/PKGBUILD @@ -0,0 +1,61 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scater +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Single-Cell Analysis Toolkit for Gene Expression Data in R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-beachmat + r-biocgenerics + r-biocneighbors + r-biocparallel + r-biocsingular + r-delayedarray + r-delayedmatrixstats + r-ggbeeswarm + r-ggplot2 + r-ggrepel + r-gridextra + r-rcolorbrewer + r-rlang + r-rtsne + r-s4vectors + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-viridis +) +optdepends=( + r-biobase + r-biocstyle + r-biomart + r-cowplot + r-destiny + r-knitr + r-nmf + r-pheatmap + r-rmarkdown + r-robustbase + r-scrnaseq + r-snifter + r-testthat + r-uwot +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scater/lilac.py b/prepare/r-scater/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scater/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scater/lilac.yaml b/prepare/r-scater/lilac.yaml new file mode 100644 index 0000000000..32970bc74e --- /dev/null +++ b/prepare/r-scater/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beachmat +- r-biocgenerics +- r-biocneighbors +- r-biocparallel +- r-biocsingular +- r-delayedarray +- r-delayedmatrixstats +- r-ggbeeswarm +- r-ggplot2 +- r-ggrepel +- r-gridextra +- r-rcolorbrewer +- r-rlang +- r-rtsne +- r-s4vectors +- r-scuttle +- r-singlecellexperiment +- r-summarizedexperiment +- r-viridis +update_on: +- regex: scater_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scater diff --git a/prepare/r-scatterhatch/PKGBUILD b/prepare/r-scatterhatch/PKGBUILD new file mode 100644 index 0000000000..03b479a9ae --- /dev/null +++ b/prepare/r-scatterhatch/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scatterHatch +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Creates hatched patterns for scatterplots' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-ggplot2 + r-plyr + r-spatstat.geom +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scatterhatch/lilac.py b/prepare/r-scatterhatch/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scatterhatch/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scatterhatch/lilac.yaml b/prepare/r-scatterhatch/lilac.yaml new file mode 100644 index 0000000000..e2bc4671e3 --- /dev/null +++ b/prepare/r-scatterhatch/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-plyr +- r-spatstat.geom +update_on: +- regex: scatterHatch_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scatterHatch diff --git a/prepare/r-scattermore/PKGBUILD b/prepare/r-scattermore/PKGBUILD new file mode 100644 index 0000000000..93cd788083 --- /dev/null +++ b/prepare/r-scattermore/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scattermore +_pkgver=0.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Scatterplots with More Points' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-scales +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scattermore/lilac.py b/prepare/r-scattermore/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scattermore/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scattermore/lilac.yaml b/prepare/r-scattermore/lilac.yaml new file mode 100644 index 0000000000..c8e397fc30 --- /dev/null +++ b/prepare/r-scattermore/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-scales +update_on: +- regex: scattermore_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=scattermore diff --git a/prepare/r-scatterpie/PKGBUILD b/prepare/r-scatterpie/PKGBUILD new file mode 100644 index 0000000000..3e9abb51c1 --- /dev/null +++ b/prepare/r-scatterpie/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scatterpie +_pkgver=0.1.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Scatter Pie Plot' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ggforce + r-ggfun + r-ggplot2 + r-rlang + r-tidyr +) +optdepends=( + r-knitr + r-maps + r-prettydoc + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scatterpie/lilac.py b/prepare/r-scatterpie/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scatterpie/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scatterpie/lilac.yaml b/prepare/r-scatterpie/lilac.yaml new file mode 100644 index 0000000000..ddfdf72e38 --- /dev/null +++ b/prepare/r-scatterpie/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggforce +- r-ggfun +- r-ggplot2 +- r-rlang +- r-tidyr +update_on: +- regex: scatterpie_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=scatterpie diff --git a/prepare/r-scatterplot3d/PKGBUILD b/prepare/r-scatterplot3d/PKGBUILD new file mode 100644 index 0000000000..63045de724 --- /dev/null +++ b/prepare/r-scatterplot3d/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scatterplot3d +_pkgver=0.3-41 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='3D Scatter Plot' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scatterplot3d/lilac.py b/prepare/r-scatterplot3d/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scatterplot3d/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scatterplot3d/lilac.yaml b/prepare/r-scatterplot3d/lilac.yaml new file mode 100644 index 0000000000..a0ac7a8684 --- /dev/null +++ b/prepare/r-scatterplot3d/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: scatterplot3d_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=scatterplot3d diff --git a/prepare/r-scbfa/PKGBUILD b/prepare/r-scbfa/PKGBUILD new file mode 100644 index 0000000000..7c09a16126 --- /dev/null +++ b/prepare/r-scbfa/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scBFA +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-copula + r-deseq2 + r-ggplot2 + r-seurat + r-singlecellexperiment + r-summarizedexperiment + r-zinbwave +) +optdepends=( + r-knitr + r-rmarkdown + r-rtsne + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scbfa/lilac.py b/prepare/r-scbfa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scbfa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scbfa/lilac.yaml b/prepare/r-scbfa/lilac.yaml new file mode 100644 index 0000000000..f8cec69f7c --- /dev/null +++ b/prepare/r-scbfa/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-copula +- r-deseq2 +- r-ggplot2 +- r-seurat +- r-singlecellexperiment +- r-summarizedexperiment +- r-zinbwave +update_on: +- regex: scBFA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scBFA diff --git a/prepare/r-scbn/PKGBUILD b/prepare/r-scbn/PKGBUILD new file mode 100644 index 0000000000..1a955fd74c --- /dev/null +++ b/prepare/r-scbn/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SCBN +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A statistical normalization method and differential expression analysis for RNA-seq data between different species' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scbn/lilac.py b/prepare/r-scbn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scbn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scbn/lilac.yaml b/prepare/r-scbn/lilac.yaml new file mode 100644 index 0000000000..61547718d5 --- /dev/null +++ b/prepare/r-scbn/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: SCBN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SCBN diff --git a/prepare/r-sccb2/PKGBUILD b/prepare/r-sccb2/PKGBUILD new file mode 100644 index 0000000000..af029d05e3 --- /dev/null +++ b/prepare/r-sccb2/PKGBUILD @@ -0,0 +1,44 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=scCB2 +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-doparallel + r-dropletutils + r-edger + r-foreach + r-iterators + r-rhdf5 + r-seurat + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-beachmat + r-biocstyle + r-kernsmooth + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sccb2/lilac.py b/prepare/r-sccb2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sccb2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sccb2/lilac.yaml b/prepare/r-sccb2/lilac.yaml new file mode 100644 index 0000000000..8764c71549 --- /dev/null +++ b/prepare/r-sccb2/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-dropletutils +- r-edger +- r-foreach +- r-iterators +- r-rhdf5 +- r-seurat +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: scCB2_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scCB2 diff --git a/prepare/r-scclassifr/PKGBUILD b/prepare/r-scclassifr/PKGBUILD new file mode 100644 index 0000000000..aa4533148c --- /dev/null +++ b/prepare/r-scclassifr/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scClassifR +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pretrained learning models for cell type prediction on single cell RNA-sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-ape + r-caret + r-data.tree + r-dplyr + r-e1071 + r-ggplot2 + r-kernlab + r-proc + r-rocr + r-seurat + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-knitr + r-rmarkdown + r-scrnaseq + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scclassifr/lilac.py b/prepare/r-scclassifr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scclassifr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scclassifr/lilac.yaml b/prepare/r-scclassifr/lilac.yaml new file mode 100644 index 0000000000..163550b7a4 --- /dev/null +++ b/prepare/r-scclassifr/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-caret +- r-data.tree +- r-dplyr +- r-e1071 +- r-ggplot2 +- r-kernlab +- r-proc +- r-rocr +- r-seurat +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: scClassifR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scClassifR diff --git a/prepare/r-scclassify/PKGBUILD b/prepare/r-scclassify/PKGBUILD new file mode 100644 index 0000000000..599e79c4de --- /dev/null +++ b/prepare/r-scclassify/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scClassify +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='scClassify: single-cell Hierarchical Classification' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-cepo + r-diptest + r-ggplot2 + r-ggraph + r-hopach + r-igraph + r-limma + r-minpack.lm + r-mixtools + r-proxy + r-proxyc + r-s4vectors + r-statmod +) +optdepends=( + r-biocstyle + r-knitr + r-pkgdown + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scclassify/lilac.py b/prepare/r-scclassify/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scclassify/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scclassify/lilac.yaml b/prepare/r-scclassify/lilac.yaml new file mode 100644 index 0000000000..51f21b48ca --- /dev/null +++ b/prepare/r-scclassify/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-cepo +- r-diptest +- r-ggplot2 +- r-ggraph +- r-hopach +- r-igraph +- r-limma +- r-minpack.lm +- r-mixtools +- r-proxy +- r-proxyc +- r-s4vectors +- r-statmod +update_on: +- regex: scClassify_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scClassify diff --git a/prepare/r-scdataviz/PKGBUILD b/prepare/r-scdataviz/PKGBUILD new file mode 100644 index 0000000000..3f679b7d43 --- /dev/null +++ b/prepare/r-scdataviz/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scDataviz +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='scDataviz: single cell dataviz and downstream analyses' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-corrplot + r-flowcore + r-ggplot2 + r-ggrepel + r-matrixstats + r-rcolorbrewer + r-reshape2 + r-s4vectors + r-scales + r-seurat + r-singlecellexperiment + r-umap +) +optdepends=( + r-biocgenerics + r-cowplot + r-kableextra + r-knitr + r-pcatools + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scdataviz/lilac.py b/prepare/r-scdataviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scdataviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scdataviz/lilac.yaml b/prepare/r-scdataviz/lilac.yaml new file mode 100644 index 0000000000..e01dece1ca --- /dev/null +++ b/prepare/r-scdataviz/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-corrplot +- r-flowcore +- r-ggplot2 +- r-ggrepel +- r-matrixstats +- r-rcolorbrewer +- r-reshape2 +- r-s4vectors +- r-scales +- r-seurat +- r-singlecellexperiment +- r-umap +update_on: +- regex: scDataviz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scDataviz diff --git a/prepare/r-scdblfinder/PKGBUILD b/prepare/r-scdblfinder/PKGBUILD new file mode 100644 index 0000000000..f34a9e7f4a --- /dev/null +++ b/prepare/r-scdblfinder/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scDblFinder +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='scDblFinder' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocneighbors + r-biocparallel + r-biocsingular + r-bluster + r-delayedarray + r-igraph + r-s4vectors + r-scater + r-scran + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-xgboost +) +optdepends=( + r-biocstyle + r-circlize + r-complexheatmap + r-dplyr + r-ggplot2 + r-knitr + r-mass + r-mbkmeans + r-rmarkdown + r-scrnaseq + r-testthat + r-viridislite +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scdblfinder/lilac.py b/prepare/r-scdblfinder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scdblfinder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scdblfinder/lilac.yaml b/prepare/r-scdblfinder/lilac.yaml new file mode 100644 index 0000000000..2e417f1f1e --- /dev/null +++ b/prepare/r-scdblfinder/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocneighbors +- r-biocparallel +- r-biocsingular +- r-bluster +- r-delayedarray +- r-igraph +- r-s4vectors +- r-scater +- r-scran +- r-scuttle +- r-singlecellexperiment +- r-summarizedexperiment +- r-xgboost +update_on: +- regex: scDblFinder_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scDblFinder diff --git a/prepare/r-scdd/PKGBUILD b/prepare/r-scdd/PKGBUILD new file mode 100644 index 0000000000..ddb8cc01a8 --- /dev/null +++ b/prepare/r-scdd/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scDD +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-arm + r-biocparallel + r-ebseq + r-fields + r-ggplot2 + r-mclust + r-outliers + r-s4vectors + r-scran + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-gridextra + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scdd/lilac.py b/prepare/r-scdd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scdd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scdd/lilac.yaml b/prepare/r-scdd/lilac.yaml new file mode 100644 index 0000000000..287e2585ae --- /dev/null +++ b/prepare/r-scdd/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-arm +- r-biocparallel +- r-ebseq +- r-fields +- r-ggplot2 +- r-mclust +- r-outliers +- r-s4vectors +- r-scran +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: scDD_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scDD diff --git a/prepare/r-scde/PKGBUILD b/prepare/r-scde/PKGBUILD new file mode 100644 index 0000000000..06a0c39074 --- /dev/null +++ b/prepare/r-scde/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scde +_pkgver=2.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Single Cell Differential Expression' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-cairo + r-edger + r-extremes + r-flexmix + r-pcamethods + r-quantreg + r-rcolorbrewer + r-rcpp + r-rcpparmadillo + r-rjson + r-rmtstat + r-rook +) +optdepends=( + r-cba + r-fastcluster + r-go.db + r-knitr + r-org.hs.eg.db + r-rmarkdown + r-wgcna +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scde/lilac.py b/prepare/r-scde/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scde/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scde/lilac.yaml b/prepare/r-scde/lilac.yaml new file mode 100644 index 0000000000..22172d5017 --- /dev/null +++ b/prepare/r-scde/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-cairo +- r-edger +- r-extremes +- r-flexmix +- r-pcamethods +- r-quantreg +- r-rcolorbrewer +- r-rcpp +- r-rcpparmadillo +- r-rjson +- r-rmtstat +- r-rook +update_on: +- regex: scde_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scde diff --git a/prepare/r-scds/PKGBUILD b/prepare/r-scds/PKGBUILD new file mode 100644 index 0000000000..3350f0979a --- /dev/null +++ b/prepare/r-scds/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scds +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-proc + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-xgboost +) +optdepends=( + r-biocstyle + r-cowplot + r-knitr + r-rmarkdown + r-rsvd + r-rtsne + r-scater +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scds/lilac.py b/prepare/r-scds/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scds/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scds/lilac.yaml b/prepare/r-scds/lilac.yaml new file mode 100644 index 0000000000..8134080e5a --- /dev/null +++ b/prepare/r-scds/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-proc +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +- r-xgboost +update_on: +- regex: scds_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scds diff --git a/prepare/r-scfa/PKGBUILD b/prepare/r-scfa/PKGBUILD new file mode 100644 index 0000000000..494eef9f4e --- /dev/null +++ b/prepare/r-scfa/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SCFA +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SCFA: Subtyping via Consensus Factor Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biocparallel + r-clustercrit + r-glmnet + r-igraph + r-keras + r-matrixstats + r-psych + r-rhpcblasctl + r-tensorflow +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scfa/lilac.py b/prepare/r-scfa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scfa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scfa/lilac.yaml b/prepare/r-scfa/lilac.yaml new file mode 100644 index 0000000000..78d611839a --- /dev/null +++ b/prepare/r-scfa/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-clustercrit +- r-glmnet +- r-igraph +- r-keras +- r-matrixstats +- r-psych +- r-rhpcblasctl +- r-tensorflow +update_on: +- regex: SCFA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SCFA diff --git a/prepare/r-scfeaturefilter/PKGBUILD b/prepare/r-scfeaturefilter/PKGBUILD new file mode 100644 index 0000000000..c1c51594db --- /dev/null +++ b/prepare/r-scfeaturefilter/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scFeatureFilter +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A correlation-based method for quality filtering of single-cell RNAseq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-ggplot2 + r-magrittr + r-rlang + r-tibble +) +optdepends=( + r-biocstyle + r-cowplot + r-knitr + r-rmarkdown + r-scrnaseq + r-singlecellexperiment + r-summarizedexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scfeaturefilter/lilac.py b/prepare/r-scfeaturefilter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scfeaturefilter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scfeaturefilter/lilac.yaml b/prepare/r-scfeaturefilter/lilac.yaml new file mode 100644 index 0000000000..8537e0ff80 --- /dev/null +++ b/prepare/r-scfeaturefilter/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-magrittr +- r-rlang +- r-tibble +update_on: +- regex: scFeatureFilter_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scFeatureFilter diff --git a/prepare/r-scgps/PKGBUILD b/prepare/r-scgps/PKGBUILD new file mode 100644 index 0000000000..d455ea8206 --- /dev/null +++ b/prepare/r-scgps/PKGBUILD @@ -0,0 +1,62 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=scGPS +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-caret + r-deseq2 + r-dplyr + r-dynamictreecut + r-fastcluster + r-ggplot2 + r-glmnet + r-locfit + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocparallel + r-clusterprofiler + r-cowplot + r-dendextend + r-devtools + r-dose + r-e1071 + r-knitr + r-matrix + r-networkd3 + r-org.hs.eg.db + r-parallel + r-rcolorbrewer + r-reactomepa + r-reshape2 + r-rmarkdown + r-rtsne + r-testthat + r-wgcna + r-xlsx +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scgps/lilac.py b/prepare/r-scgps/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scgps/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scgps/lilac.yaml b/prepare/r-scgps/lilac.yaml new file mode 100644 index 0000000000..4c26ed15e3 --- /dev/null +++ b/prepare/r-scgps/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-caret +- r-deseq2 +- r-dplyr +- r-dynamictreecut +- r-fastcluster +- r-ggplot2 +- r-glmnet +- r-locfit +- r-rcpp +- r-rcpparmadillo +- r-rcppparallel +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: scGPS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scGPS diff --git a/prepare/r-schex/PKGBUILD b/prepare/r-schex/PKGBUILD new file mode 100644 index 0000000000..775153972b --- /dev/null +++ b/prepare/r-schex/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=schex +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Hexbin plots for single cell omics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-concaveman + r-dplyr + r-entropy + r-ggforce + r-ggplot2 + r-hexbin + r-scales + r-seurat + r-shiny + r-singlecellexperiment +) +optdepends=( + r-covr + r-ggrepel + r-igraph + r-isee + r-knitr + r-rmarkdown + r-scater + r-scran + r-shinydashboard + r-tenxpbmcdata + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-schex/lilac.py b/prepare/r-schex/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-schex/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-schex/lilac.yaml b/prepare/r-schex/lilac.yaml new file mode 100644 index 0000000000..77fce832c1 --- /dev/null +++ b/prepare/r-schex/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-concaveman +- r-dplyr +- r-entropy +- r-ggforce +- r-ggplot2 +- r-hexbin +- r-scales +- r-seurat +- r-shiny +- r-singlecellexperiment +update_on: +- regex: schex_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/schex diff --git a/prepare/r-schot/PKGBUILD b/prepare/r-schot/PKGBUILD new file mode 100644 index 0000000000..6b6c413bf5 --- /dev/null +++ b/prepare/r-schot/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scHOT +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='single-cell higher order testing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-ggforce + r-ggplot2 + r-igraph + r-iranges + r-reshape + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-deldir + r-knitr + r-markdown + r-matrixstats + r-rmarkdown + r-scales + r-scater + r-scattermore +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-schot/lilac.py b/prepare/r-schot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-schot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-schot/lilac.yaml b/prepare/r-schot/lilac.yaml new file mode 100644 index 0000000000..f91693c4b5 --- /dev/null +++ b/prepare/r-schot/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-ggforce +- r-ggplot2 +- r-igraph +- r-iranges +- r-reshape +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: scHOT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scHOT diff --git a/prepare/r-scico/PKGBUILD b/prepare/r-scico/PKGBUILD new file mode 100644 index 0000000000..3257eaf143 --- /dev/null +++ b/prepare/r-scico/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scico +_pkgver=1.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Colour Palettes Based on the Scientific Colour-Maps' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-scales +) +optdepends=( + r-covr + r-dplyr + r-ggplot2 + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scico/lilac.py b/prepare/r-scico/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scico/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scico/lilac.yaml b/prepare/r-scico/lilac.yaml new file mode 100644 index 0000000000..bba4b900a3 --- /dev/null +++ b/prepare/r-scico/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-scales +update_on: +- regex: scico_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=scico diff --git a/prepare/r-scisi/PKGBUILD b/prepare/r-scisi/PKGBUILD new file mode 100644 index 0000000000..491ed8bf72 --- /dev/null +++ b/prepare/r-scisi/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ScISI +_pkgver=1.65.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='In Silico Interactome' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-annotate + r-annotationdbi + r-apcomplex + r-go.db + r-org.sc.sgd.db + r-rpsixml +) +optdepends=( + r-ppidata + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scisi/lilac.py b/prepare/r-scisi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scisi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scisi/lilac.yaml b/prepare/r-scisi/lilac.yaml new file mode 100644 index 0000000000..954c419ebc --- /dev/null +++ b/prepare/r-scisi/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-apcomplex +- r-go.db +- r-org.sc.sgd.db +- r-rpsixml +update_on: +- regex: ScISI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ScISI diff --git a/prepare/r-scmageck/PKGBUILD b/prepare/r-scmageck/PKGBUILD new file mode 100644 index 0000000000..49d7124f3b --- /dev/null +++ b/prepare/r-scmageck/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scMAGeCK +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-ggplot2 + r-seurat +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scmageck/lilac.py b/prepare/r-scmageck/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scmageck/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scmageck/lilac.yaml b/prepare/r-scmageck/lilac.yaml new file mode 100644 index 0000000000..a623ac5fe3 --- /dev/null +++ b/prepare/r-scmageck/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-seurat +update_on: +- regex: scMAGeCK_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scMAGeCK diff --git a/prepare/r-scmap/PKGBUILD b/prepare/r-scmap/PKGBUILD new file mode 100644 index 0000000000..190648c47f --- /dev/null +++ b/prepare/r-scmap/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scmap +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A tool for unsupervised projection of single cell RNA-seq data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-dplyr + r-e1071 + r-ggplot2 + r-googlevis + r-matrixstats + r-proxy + r-randomforest + r-rcpp + r-rcpparmadillo + r-reshape2 + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scmap/lilac.py b/prepare/r-scmap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scmap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scmap/lilac.yaml b/prepare/r-scmap/lilac.yaml new file mode 100644 index 0000000000..db0ccb4378 --- /dev/null +++ b/prepare/r-scmap/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-dplyr +- r-e1071 +- r-ggplot2 +- r-googlevis +- r-matrixstats +- r-proxy +- r-randomforest +- r-rcpp +- r-rcpparmadillo +- r-reshape2 +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: scmap_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scmap diff --git a/prepare/r-scmerge/PKGBUILD b/prepare/r-scmerge/PKGBUILD new file mode 100644 index 0000000000..afab8fed74 --- /dev/null +++ b/prepare/r-scmerge/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scMerge +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='scMerge: Merging multiple batches of scRNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-biocsingular + r-delayedarray + r-delayedmatrixstats + r-distr + r-igraph + r-m3drop + r-pdist + r-proxy + r-ruv + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-badger + r-biocstyle + r-covr + r-hdf5array + r-knitr + r-matrix + r-rmarkdown + r-scales + r-scater + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scmerge/lilac.py b/prepare/r-scmerge/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scmerge/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scmerge/lilac.yaml b/prepare/r-scmerge/lilac.yaml new file mode 100644 index 0000000000..d65542db5b --- /dev/null +++ b/prepare/r-scmerge/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-biocsingular +- r-delayedarray +- r-delayedmatrixstats +- r-distr +- r-igraph +- r-m3drop +- r-pdist +- r-proxy +- r-ruv +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: scMerge_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scMerge diff --git a/prepare/r-scmeth/PKGBUILD b/prepare/r-scmeth/PKGBUILD new file mode 100644 index 0000000000..0da76757ed --- /dev/null +++ b/prepare/r-scmeth/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scmeth +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions to conduct quality control analysis in methylation data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationhub + r-annotatr + r-biostrings + r-bsgenome + r-bsseq + r-delayedarray + r-dt + r-genomeinfodb + r-genomicranges + r-hdf5array + r-knitr + r-reshape2 + r-rmarkdown + r-summarizedexperiment +) +optdepends=( + r-biobase + r-biocgenerics + r-bsgenome.hsapiens.ncbi.grch38 + r-bsgenome.mmusculus.ucsc.mm10 + r-ggplot2 + r-ggthemes + r-org.hs.eg.db + r-txdb.hsapiens.ucsc.hg38.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scmeth/lilac.py b/prepare/r-scmeth/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scmeth/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scmeth/lilac.yaml b/prepare/r-scmeth/lilac.yaml new file mode 100644 index 0000000000..173f855fea --- /dev/null +++ b/prepare/r-scmeth/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-annotatr +- r-biostrings +- r-bsgenome +- r-bsseq +- r-delayedarray +- r-dt +- r-genomeinfodb +- r-genomicranges +- r-hdf5array +- r-knitr +- r-reshape2 +- r-rmarkdown +- r-summarizedexperiment +update_on: +- regex: scmeth_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scmeth diff --git a/prepare/r-scnorm/PKGBUILD b/prepare/r-scnorm/PKGBUILD new file mode 100644 index 0000000000..cc95a4c56e --- /dev/null +++ b/prepare/r-scnorm/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SCnorm +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Normalization of single cell RNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-data.table + r-forcats + r-ggplot2 + r-moments + r-quantreg + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-devtools + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scnorm/lilac.py b/prepare/r-scnorm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scnorm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scnorm/lilac.yaml b/prepare/r-scnorm/lilac.yaml new file mode 100644 index 0000000000..e0c45d1e4e --- /dev/null +++ b/prepare/r-scnorm/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-data.table +- r-forcats +- r-ggplot2 +- r-moments +- r-quantreg +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: SCnorm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SCnorm diff --git a/prepare/r-scone/PKGBUILD b/prepare/r-scone/PKGBUILD new file mode 100644 index 0000000000..e846e297ef --- /dev/null +++ b/prepare/r-scone/PKGBUILD @@ -0,0 +1,67 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scone +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Single Cell Overview of Normalized Expression data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-aroma.light + r-biocparallel + r-compositions + r-diptest + r-edger + r-fpc + r-gplots + r-hexbin + r-limma + r-matrixgenerics + r-matrixstats + r-mixtools + r-rarpack + r-rcolorbrewer + r-rhdf5 + r-ruvseq + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-batchjobs + r-biocstyle + r-doparallel + r-dt + r-ggplot2 + r-kableextra + r-knitr + r-mclust + r-miniui + r-nmf + r-plotly + r-reshape2 + r-rmarkdown + r-scater + r-scran + r-scrnaseq + r-shiny + r-splatter + r-tenxpbmcdata + r-testthat + r-visnetwork +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scone/lilac.py b/prepare/r-scone/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scone/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scone/lilac.yaml b/prepare/r-scone/lilac.yaml new file mode 100644 index 0000000000..81376794d0 --- /dev/null +++ b/prepare/r-scone/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aroma.light +- r-biocparallel +- r-compositions +- r-diptest +- r-edger +- r-fpc +- r-gplots +- r-hexbin +- r-limma +- r-matrixgenerics +- r-matrixstats +- r-mixtools +- r-rarpack +- r-rcolorbrewer +- r-rhdf5 +- r-ruvseq +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: scone_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scone diff --git a/prepare/r-sconify/PKGBUILD b/prepare/r-sconify/PKGBUILD new file mode 100644 index 0000000000..6e2563c499 --- /dev/null +++ b/prepare/r-sconify/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Sconify +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A toolkit for performing KNN-based statistics for flow and mass cytometry data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-dplyr + r-flowcore + r-fnn + r-ggplot2 + r-magrittr + r-readr + r-rtsne + r-tibble +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sconify/lilac.py b/prepare/r-sconify/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sconify/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sconify/lilac.yaml b/prepare/r-sconify/lilac.yaml new file mode 100644 index 0000000000..e266ce8b7a --- /dev/null +++ b/prepare/r-sconify/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-flowcore +- r-fnn +- r-ggplot2 +- r-magrittr +- r-readr +- r-rtsne +- r-tibble +update_on: +- regex: Sconify_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Sconify diff --git a/prepare/r-scope/PKGBUILD b/prepare/r-scope/PKGBUILD new file mode 100644 index 0000000000..016f6c8b5b --- /dev/null +++ b/prepare/r-scope/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SCOPE +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A normalization and copy number estimation method for single-cell DNA sequencing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-bsgenome + r-bsgenome.hsapiens.ucsc.hg19 + r-desctools + r-dnacopy + r-doparallel + r-foreach + r-genomeinfodb + r-genomicranges + r-gplots + r-iranges + r-rcolorbrewer + r-rsamtools + r-s4vectors +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg38 + r-bsgenome.mmusculus.ucsc.mm10 + r-knitr + r-rmarkdown + r-testthat + r-wgsmapp +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scope/lilac.py b/prepare/r-scope/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scope/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scope/lilac.yaml b/prepare/r-scope/lilac.yaml new file mode 100644 index 0000000000..d6dd5a8718 --- /dev/null +++ b/prepare/r-scope/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-bsgenome.hsapiens.ucsc.hg19 +- r-desctools +- r-dnacopy +- r-doparallel +- r-foreach +- r-genomeinfodb +- r-genomicranges +- r-gplots +- r-iranges +- r-rcolorbrewer +- r-rsamtools +- r-s4vectors +update_on: +- regex: SCOPE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SCOPE diff --git a/prepare/r-scoreinvhap/PKGBUILD b/prepare/r-scoreinvhap/PKGBUILD new file mode 100644 index 0000000000..745fb20c9f --- /dev/null +++ b/prepare/r-scoreinvhap/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scoreInvHap +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Get inversion status in predefined regions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-biocparallel + r-biostrings + r-genomicranges + r-snpstats + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scoreinvhap/lilac.py b/prepare/r-scoreinvhap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scoreinvhap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scoreinvhap/lilac.yaml b/prepare/r-scoreinvhap/lilac.yaml new file mode 100644 index 0000000000..45fce3986a --- /dev/null +++ b/prepare/r-scoreinvhap/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-biostrings +- r-genomicranges +- r-snpstats +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: scoreInvHap_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scoreInvHap diff --git a/prepare/r-scp/PKGBUILD b/prepare/r-scp/PKGBUILD new file mode 100644 index 0000000000..55e1ca4064 --- /dev/null +++ b/prepare/r-scp/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scp +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mass Spectrometry-Based Single-Cell Proteomics Data Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-dplyr + r-magrittr + r-matrixstats + r-mscoreutils + r-multiassayexperiment + r-qfeatures + r-rlang + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-ggplot2 + r-impute + r-knitr + r-patchwork + r-preprocesscore + r-rmarkdown + r-scater + r-sva + r-testthat + r-uwot + r-vsn +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scp/lilac.py b/prepare/r-scp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scp/lilac.yaml b/prepare/r-scp/lilac.yaml new file mode 100644 index 0000000000..d1dd5adb45 --- /dev/null +++ b/prepare/r-scp/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-magrittr +- r-matrixstats +- r-mscoreutils +- r-multiassayexperiment +- r-qfeatures +- r-rlang +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: scp_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scp diff --git a/prepare/r-scpca/PKGBUILD b/prepare/r-scpca/PKGBUILD new file mode 100644 index 0000000000..a098316433 --- /dev/null +++ b/prepare/r-scpca/PKGBUILD @@ -0,0 +1,58 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scPCA +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sparse Contrastive Principal Component Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-assertthat + r-biocparallel + r-coop + r-delayedarray + r-dplyr + r-elasticnet + r-kernlab + r-matrixgenerics + r-matrixstats + r-origami + r-purrr + r-rdpack + r-rspectra + r-scaledmatrix + r-sparsepca + r-stringr + r-tibble +) +optdepends=( + r-biocstyle + r-covr + r-delayedmatrixstats + r-ggplot2 + r-ggpubr + r-knitr + r-microbenchmark + r-rmarkdown + r-singlecellexperiment + r-sparsematrixstats + r-splatter + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scpca/lilac.py b/prepare/r-scpca/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scpca/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scpca/lilac.yaml b/prepare/r-scpca/lilac.yaml new file mode 100644 index 0000000000..1ec4d9a930 --- /dev/null +++ b/prepare/r-scpca/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biocparallel +- r-coop +- r-delayedarray +- r-dplyr +- r-elasticnet +- r-kernlab +- r-matrixgenerics +- r-matrixstats +- r-origami +- r-purrr +- r-rdpack +- r-rspectra +- r-scaledmatrix +- r-sparsepca +- r-stringr +- r-tibble +update_on: +- regex: scPCA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scPCA diff --git a/prepare/r-scpipe/PKGBUILD b/prepare/r-scpipe/PKGBUILD new file mode 100644 index 0000000000..14bc9de8c7 --- /dev/null +++ b/prepare/r-scpipe/PKGBUILD @@ -0,0 +1,60 @@ +# system requirements: C++11, GNU make +# Maintainer: Guoyi Zhang + +_pkgname=scPipe +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='pipeline for single cell RNA-seq data analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocgenerics + r-biomart + r-dplyr + r-genomicranges + r-ggally + r-ggplot2 + r-glue + r-hash + r-magrittr + r-mclust + r-org.hs.eg.db + r-org.mm.eg.db + r-rcpp + r-reshape + r-rhtslib + r-rlang + r-robustbase + r-rtracklayer + r-s4vectors + r-scales + r-scater + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-testthat + r-zlibbioc +) +optdepends=( + r-knitr + r-rmarkdown + r-rsubread + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scpipe/lilac.py b/prepare/r-scpipe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scpipe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scpipe/lilac.yaml b/prepare/r-scpipe/lilac.yaml new file mode 100644 index 0000000000..fe2bbfd69b --- /dev/null +++ b/prepare/r-scpipe/lilac.yaml @@ -0,0 +1,36 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-biomart +- r-dplyr +- r-genomicranges +- r-ggally +- r-ggplot2 +- r-glue +- r-hash +- r-magrittr +- r-mclust +- r-org.hs.eg.db +- r-org.mm.eg.db +- r-rcpp +- r-reshape +- r-rhtslib +- r-rlang +- r-robustbase +- r-rtracklayer +- r-s4vectors +- r-scales +- r-scater +- r-singlecellexperiment +- r-stringr +- r-summarizedexperiment +- r-testthat +- r-zlibbioc +update_on: +- regex: scPipe_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scPipe diff --git a/prepare/r-scran/PKGBUILD b/prepare/r-scran/PKGBUILD new file mode 100644 index 0000000000..3018f4b772 --- /dev/null +++ b/prepare/r-scran/PKGBUILD @@ -0,0 +1,62 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=scran +_pkgver=1.22.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methods for Single-Cell RNA-Seq Data Analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-beachmat + r-bh + r-biocgenerics + r-biocparallel + r-biocsingular + r-bluster + r-delayedarray + r-delayedmatrixstats + r-dqrng + r-edger + r-igraph + r-limma + r-metapod + r-rcpp + r-s4vectors + r-scuttle + r-singlecellexperiment + r-statmod + r-summarizedexperiment +) +optdepends=( + r-biobase + r-biocstyle + r-deseq2 + r-dynamictreecut + r-hdf5array + r-knitr + r-monocle + r-pheatmap + r-residualmatrix + r-rmarkdown + r-scaledmatrix + r-scater + r-scrnaseq + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scran/lilac.py b/prepare/r-scran/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scran/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scran/lilac.yaml b/prepare/r-scran/lilac.yaml new file mode 100644 index 0000000000..c15ace092b --- /dev/null +++ b/prepare/r-scran/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beachmat +- r-bh +- r-biocgenerics +- r-biocparallel +- r-biocsingular +- r-bluster +- r-delayedarray +- r-delayedmatrixstats +- r-dqrng +- r-edger +- r-igraph +- r-limma +- r-metapod +- r-rcpp +- r-s4vectors +- r-scuttle +- r-singlecellexperiment +- r-statmod +- r-summarizedexperiment +update_on: +- regex: scran_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scran diff --git a/prepare/r-screclassify/PKGBUILD b/prepare/r-screclassify/PKGBUILD new file mode 100644 index 0000000000..a6b3cba50c --- /dev/null +++ b/prepare/r-screclassify/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scReClassify +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='scReClassify: post hoc cell type classification of single-cell RNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-e1071 + r-randomforest + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-dplyr + r-dt + r-knitr + r-mclust + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-screclassify/lilac.py b/prepare/r-screclassify/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-screclassify/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-screclassify/lilac.yaml b/prepare/r-screclassify/lilac.yaml new file mode 100644 index 0000000000..720134a2fb --- /dev/null +++ b/prepare/r-screclassify/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-e1071 +- r-randomforest +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: scReClassify_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scReClassify diff --git a/prepare/r-screcover/PKGBUILD b/prepare/r-screcover/PKGBUILD new file mode 100644 index 0000000000..943f96b513 --- /dev/null +++ b/prepare/r-screcover/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scRecover +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='scRecover for imputation of single-cell RNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bbmle + r-biocparallel + r-doparallel + r-foreach + r-gamlss + r-kernlab + r-penalized + r-preseqr + r-pscl + r-rmagic + r-rsvd + r-saver +) +optdepends=( + r-knitr + r-rmarkdown + r-singlecellexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-screcover/lilac.py b/prepare/r-screcover/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-screcover/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-screcover/lilac.yaml b/prepare/r-screcover/lilac.yaml new file mode 100644 index 0000000000..2249da7205 --- /dev/null +++ b/prepare/r-screcover/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bbmle +- r-biocparallel +- r-doparallel +- r-foreach +- r-gamlss +- r-kernlab +- r-penalized +- r-preseqr +- r-pscl +- r-rmagic +- r-rsvd +- r-saver +update_on: +- regex: scRecover_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scRecover diff --git a/prepare/r-screpertoire/PKGBUILD b/prepare/r-screpertoire/PKGBUILD new file mode 100644 index 0000000000..9d030b6b3a --- /dev/null +++ b/prepare/r-screpertoire/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scRepertoire +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A toolkit for single-cell immune receptor profiling' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Apache') +depends=( + r + r-doparallel + r-dplyr + r-ggalluvial + r-ggplot2 + r-igraph + r-plyr + r-powertcr + r-reshape2 + r-rlang + r-seuratobject + r-stringdist + r-stringr + r-summarizedexperiment + r-vegan +) +optdepends=( + r-biocstyle + r-circlize + r-knitr + r-rmarkdown + r-scales + r-scater + r-seurat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-screpertoire/lilac.py b/prepare/r-screpertoire/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-screpertoire/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-screpertoire/lilac.yaml b/prepare/r-screpertoire/lilac.yaml new file mode 100644 index 0000000000..3b1b56fbcd --- /dev/null +++ b/prepare/r-screpertoire/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-dplyr +- r-ggalluvial +- r-ggplot2 +- r-igraph +- r-plyr +- r-powertcr +- r-reshape2 +- r-rlang +- r-seuratobject +- r-stringdist +- r-stringr +- r-summarizedexperiment +- r-vegan +update_on: +- regex: scRepertoire_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scRepertoire diff --git a/prepare/r-scrime/PKGBUILD b/prepare/r-scrime/PKGBUILD new file mode 100644 index 0000000000..e9f8fe2e8e --- /dev/null +++ b/prepare/r-scrime/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scrime +_pkgver=1.3.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of High-Dimensional Categorical Data Such as SNP Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-dbi + r-mass + r-oligoclasses + r-rsqlite +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scrime/lilac.py b/prepare/r-scrime/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scrime/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scrime/lilac.yaml b/prepare/r-scrime/lilac.yaml new file mode 100644 index 0000000000..5f2d4cbc52 --- /dev/null +++ b/prepare/r-scrime/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: scrime_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=scrime diff --git a/prepare/r-scrnaseq/PKGBUILD b/prepare/r-scrnaseq/PKGBUILD new file mode 100644 index 0000000000..a927245449 --- /dev/null +++ b/prepare/r-scrnaseq/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scRNAseq +_pkgver=2.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Collection of Public Single-Cell RNA-Seq Datasets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CC0') +depends=( + r + r-annotationdbi + r-annotationhub + r-biocgenerics + r-ensembldb + r-experimenthub + r-genomicfeatures + r-genomicranges + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocfilecache + r-biocstyle + r-knitr + r-rappdirs + r-rmarkdown + r-testthat + r-tools +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scrnaseq/lilac.py b/prepare/r-scrnaseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scrnaseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scrnaseq/lilac.yaml b/prepare/r-scrnaseq/lilac.yaml new file mode 100644 index 0000000000..dbe406b320 --- /dev/null +++ b/prepare/r-scrnaseq/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-biocgenerics +- r-ensembldb +- r-experimenthub +- r-genomicfeatures +- r-genomicranges +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: scRNAseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scRNAseq diff --git a/prepare/r-scruff/PKGBUILD b/prepare/r-scruff/PKGBUILD new file mode 100644 index 0000000000..080bbe86f5 --- /dev/null +++ b/prepare/r-scruff/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scruff +_pkgver=1.12.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Single Cell RNA-Seq UMI Filtering Facilitator (scruff)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-biocgenerics + r-biocparallel + r-biostrings + r-data.table + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggbio + r-ggplot2 + r-ggthemes + r-plyr + r-rsamtools + r-rsubread + r-rtracklayer + r-s4vectors + r-scales + r-shortread + r-singlecellexperiment + r-stringdist + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scruff/lilac.py b/prepare/r-scruff/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scruff/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scruff/lilac.yaml b/prepare/r-scruff/lilac.yaml new file mode 100644 index 0000000000..5b0dca3060 --- /dev/null +++ b/prepare/r-scruff/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-data.table +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggbio +- r-ggplot2 +- r-ggthemes +- r-plyr +- r-rsamtools +- r-rsubread +- r-rtracklayer +- r-s4vectors +- r-scales +- r-shortread +- r-singlecellexperiment +- r-stringdist +- r-summarizedexperiment +update_on: +- regex: scruff_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scruff diff --git a/prepare/r-scry/PKGBUILD b/prepare/r-scry/PKGBUILD new file mode 100644 index 0000000000..113a795d3f --- /dev/null +++ b/prepare/r-scry/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scry +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Small-Count Analysis Methods for High-Dimensional Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocsingular + r-delayedarray + r-glmpca + r-hdf5array + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocgenerics + r-covr + r-duoclustering2018 + r-ggplot2 + r-knitr + r-markdown + r-rmarkdown + r-tenxpbmcdata + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scry/lilac.py b/prepare/r-scry/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scry/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scry/lilac.yaml b/prepare/r-scry/lilac.yaml new file mode 100644 index 0000000000..9738fcf968 --- /dev/null +++ b/prepare/r-scry/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocsingular +- r-delayedarray +- r-glmpca +- r-hdf5array +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: scry_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scry diff --git a/prepare/r-scshapes/PKGBUILD b/prepare/r-scshapes/PKGBUILD new file mode 100644 index 0000000000..6bcd780119 --- /dev/null +++ b/prepare/r-scshapes/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scShapes +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Statistical Framework for Modeling and Identifying Differential Distributions in Single-cell RNA-sequencing Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-dgof + r-emdbook + r-magrittr + r-pscl + r-vgam +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scshapes/lilac.py b/prepare/r-scshapes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scshapes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scshapes/lilac.yaml b/prepare/r-scshapes/lilac.yaml new file mode 100644 index 0000000000..d527889d95 --- /dev/null +++ b/prepare/r-scshapes/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-dgof +- r-emdbook +- r-magrittr +- r-pscl +- r-vgam +update_on: +- regex: scShapes_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scShapes diff --git a/prepare/r-sctensor/PKGBUILD b/prepare/r-sctensor/PKGBUILD new file mode 100644 index 0000000000..5219dd0a0a --- /dev/null +++ b/prepare/r-sctensor/PKGBUILD @@ -0,0 +1,65 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scTensor +_pkgver=2.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-abind + r-annotationdbi + r-annotationhub + r-biocmanager + r-biocstyle + r-category + r-cctensor + r-checkmate + r-crayon + r-dose + r-ggplot2 + r-gostats + r-heatmaply + r-igraph + r-knitr + r-meshdbi + r-meshr + r-nntensor + r-outliers + r-plotly + r-plotrix + r-reactome.db + r-reactomepa + r-rmarkdown + r-rsqlite + r-rtensor + r-s4vectors + r-schex + r-singlecellexperiment + r-summarizedexperiment + r-tagcloud + r-visnetwork +) +optdepends=( + r-homo.sapiens + r-lrbasedbi + r-sctgif + r-seurat + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sctensor/lilac.py b/prepare/r-sctensor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sctensor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sctensor/lilac.yaml b/prepare/r-sctensor/lilac.yaml new file mode 100644 index 0000000000..7bde0c9dc3 --- /dev/null +++ b/prepare/r-sctensor/lilac.yaml @@ -0,0 +1,41 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-annotationdbi +- r-annotationhub +- r-biocmanager +- r-biocstyle +- r-category +- r-cctensor +- r-checkmate +- r-crayon +- r-dose +- r-ggplot2 +- r-gostats +- r-heatmaply +- r-igraph +- r-knitr +- r-meshdbi +- r-meshr +- r-nntensor +- r-outliers +- r-plotly +- r-plotrix +- r-reactome.db +- r-reactomepa +- r-rmarkdown +- r-rsqlite +- r-rtensor +- r-s4vectors +- r-schex +- r-singlecellexperiment +- r-summarizedexperiment +- r-tagcloud +- r-visnetwork +update_on: +- regex: scTensor_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scTensor diff --git a/prepare/r-sctgif/PKGBUILD b/prepare/r-sctgif/PKGBUILD new file mode 100644 index 0000000000..321c71d67e --- /dev/null +++ b/prepare/r-sctgif/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scTGIF +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cell type annotation for unannotated single-cell RNA-Seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocstyle + r-ggplot2 + r-gseabase + r-igraph + r-knitr + r-msigdbr + r-nntensor + r-plotly + r-rcolorbrewer + r-rcpp + r-rmarkdown + r-s4vectors + r-scales + r-schex + r-singlecellexperiment + r-summarizedexperiment + r-tagcloud + r-tibble +) +optdepends=( + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sctgif/lilac.py b/prepare/r-sctgif/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sctgif/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sctgif/lilac.yaml b/prepare/r-sctgif/lilac.yaml new file mode 100644 index 0000000000..623b82e6cd --- /dev/null +++ b/prepare/r-sctgif/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocstyle +- r-ggplot2 +- r-gseabase +- r-igraph +- r-knitr +- r-msigdbr +- r-nntensor +- r-plotly +- r-rcolorbrewer +- r-rcpp +- r-rmarkdown +- r-s4vectors +- r-scales +- r-schex +- r-singlecellexperiment +- r-summarizedexperiment +- r-tagcloud +- r-tibble +update_on: +- regex: scTGIF_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scTGIF diff --git a/prepare/r-scthi/PKGBUILD b/prepare/r-scthi/PKGBUILD new file mode 100644 index 0000000000..6b045ff0b6 --- /dev/null +++ b/prepare/r-scthi/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scTHI +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Indentification of significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-rtsne +) +optdepends=( + r-knitr + r-rmarkdown + r-scthi.data +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scthi/lilac.py b/prepare/r-scthi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scthi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scthi/lilac.yaml b/prepare/r-scthi/lilac.yaml new file mode 100644 index 0000000000..361d144f80 --- /dev/null +++ b/prepare/r-scthi/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-rtsne +update_on: +- regex: scTHI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scTHI diff --git a/prepare/r-sctransform/PKGBUILD b/prepare/r-sctransform/PKGBUILD new file mode 100644 index 0000000000..5b979073d3 --- /dev/null +++ b/prepare/r-sctransform/PKGBUILD @@ -0,0 +1,41 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=sctransform +_pkgver=0.3.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Variance Stabilizing Transformations for Single Cell UMI Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-future + r-future.apply + r-ggplot2 + r-gridextra + r-matrixstats + r-rcpp + r-rcpparmadillo + r-reshape2 +) +optdepends=( + r-glmgampoi + r-irlba + r-knitr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sctransform/lilac.py b/prepare/r-sctransform/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sctransform/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sctransform/lilac.yaml b/prepare/r-sctransform/lilac.yaml new file mode 100644 index 0000000000..04d99b14e4 --- /dev/null +++ b/prepare/r-sctransform/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-future +- r-future.apply +- r-ggplot2 +- r-gridextra +- r-matrixstats +- r-rcpp +- r-rcpparmadillo +- r-reshape2 +update_on: +- regex: sctransform_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sctransform diff --git a/prepare/r-sctreeviz/PKGBUILD b/prepare/r-sctreeviz/PKGBUILD new file mode 100644 index 0000000000..fa0bcc5cbb --- /dev/null +++ b/prepare/r-sctreeviz/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=scTreeViz +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-clustree + r-data.table + r-digest + r-epivizr + r-epivizrdata + r-epivizrserver + r-ggplot2 + r-ggraph + r-httr + r-igraph + r-rtsne + r-s4vectors + r-scater + r-scran + r-seurat + r-singlecellexperiment + r-summarizedexperiment + r-sys +) +optdepends=( + r-biocstyle + r-epivizrstandalone + r-genomeinfodb + r-knitr + r-metagenomeseq + r-msd16s + r-rmarkdown + r-sc3 + r-scrnaseq + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sctreeviz/lilac.py b/prepare/r-sctreeviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sctreeviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sctreeviz/lilac.yaml b/prepare/r-sctreeviz/lilac.yaml new file mode 100644 index 0000000000..0d8ec06ab3 --- /dev/null +++ b/prepare/r-sctreeviz/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clustree +- r-data.table +- r-digest +- r-epivizr +- r-epivizrdata +- r-epivizrserver +- r-ggplot2 +- r-ggraph +- r-httr +- r-igraph +- r-rtsne +- r-s4vectors +- r-scater +- r-scran +- r-seurat +- r-singlecellexperiment +- r-summarizedexperiment +- r-sys +update_on: +- regex: scTreeViz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scTreeViz diff --git a/prepare/r-scuttle/PKGBUILD b/prepare/r-scuttle/PKGBUILD new file mode 100644 index 0000000000..85e7952190 --- /dev/null +++ b/prepare/r-scuttle/PKGBUILD @@ -0,0 +1,45 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=scuttle +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Single-Cell RNA-Seq Analysis Utilities' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-beachmat + r-biocgenerics + r-biocparallel + r-delayedarray + r-delayedmatrixstats + r-genomicranges + r-rcpp + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-scran + r-scrnaseq + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-scuttle/lilac.py b/prepare/r-scuttle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-scuttle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-scuttle/lilac.yaml b/prepare/r-scuttle/lilac.yaml new file mode 100644 index 0000000000..54b8bfed5a --- /dev/null +++ b/prepare/r-scuttle/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beachmat +- r-biocgenerics +- r-biocparallel +- r-delayedarray +- r-delayedmatrixstats +- r-genomicranges +- r-rcpp +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: scuttle_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/scuttle diff --git a/prepare/r-sdams/PKGBUILD b/prepare/r-sdams/PKGBUILD new file mode 100644 index 0000000000..4a33bb5c14 --- /dev/null +++ b/prepare/r-sdams/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SDAMS +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-qvalue + r-summarizedexperiment + r-trust +) +optdepends=( + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sdams/lilac.py b/prepare/r-sdams/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sdams/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sdams/lilac.yaml b/prepare/r-sdams/lilac.yaml new file mode 100644 index 0000000000..510f46e1c4 --- /dev/null +++ b/prepare/r-sdams/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-qvalue +- r-summarizedexperiment +- r-trust +update_on: +- regex: SDAMS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SDAMS diff --git a/prepare/r-sechm/PKGBUILD b/prepare/r-sechm/PKGBUILD new file mode 100644 index 0000000000..f7c0513555 --- /dev/null +++ b/prepare/r-sechm/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sechm +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='sechm: Complex Heatmaps from a SummarizedExperiment' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-circlize + r-complexheatmap + r-randomcolor + r-s4vectors + r-seriation + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sechm/lilac.py b/prepare/r-sechm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sechm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sechm/lilac.yaml b/prepare/r-sechm/lilac.yaml new file mode 100644 index 0000000000..6d7567ea88 --- /dev/null +++ b/prepare/r-sechm/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circlize +- r-complexheatmap +- r-randomcolor +- r-s4vectors +- r-seriation +- r-summarizedexperiment +update_on: +- regex: sechm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sechm diff --git a/prepare/r-segmented/PKGBUILD b/prepare/r-segmented/PKGBUILD new file mode 100644 index 0000000000..613f1d1b0e --- /dev/null +++ b/prepare/r-segmented/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=segmented +_pkgver=1.3-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Regression Models with Break-Points / Change-Points Estimation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-segmented/lilac.py b/prepare/r-segmented/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-segmented/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-segmented/lilac.yaml b/prepare/r-segmented/lilac.yaml new file mode 100644 index 0000000000..c0b5a5ce97 --- /dev/null +++ b/prepare/r-segmented/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: segmented_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=segmented diff --git a/prepare/r-segmenter/PKGBUILD b/prepare/r-segmenter/PKGBUILD new file mode 100644 index 0000000000..0a32c264c5 --- /dev/null +++ b/prepare/r-segmenter/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=segmenter +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Perform Chromatin Segmentation Analysis in R by Calling ChromHMM' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bamsignals + r-chipseeker + r-chromhmmdata + r-complexheatmap + r-genomicranges + r-iranges + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-gviz + r-knitr + r-rmarkdown + r-testthat + r-txdb.hsapiens.ucsc.hg18.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-segmenter/lilac.py b/prepare/r-segmenter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-segmenter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-segmenter/lilac.yaml b/prepare/r-segmenter/lilac.yaml new file mode 100644 index 0000000000..c6188f9f03 --- /dev/null +++ b/prepare/r-segmenter/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bamsignals +- r-chipseeker +- r-chromhmmdata +- r-complexheatmap +- r-genomicranges +- r-iranges +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: segmenter_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/segmenter diff --git a/prepare/r-segmentseq/PKGBUILD b/prepare/r-segmentseq/PKGBUILD new file mode 100644 index 0000000000..45b49d089a --- /dev/null +++ b/prepare/r-segmentseq/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=segmentSeq +_pkgver=2.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methods for identifying small RNA loci from high-throughput sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-bayseq + r-genomeinfodb + r-genomicranges + r-iranges + r-rsamtools + r-s4vectors + r-shortread +) +optdepends=( + r-biocgenerics + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-segmentseq/lilac.py b/prepare/r-segmentseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-segmentseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-segmentseq/lilac.yaml b/prepare/r-segmentseq/lilac.yaml new file mode 100644 index 0000000000..fecf4efe6e --- /dev/null +++ b/prepare/r-segmentseq/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-bayseq +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rsamtools +- r-s4vectors +- r-shortread +update_on: +- regex: segmentSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/segmentSeq diff --git a/prepare/r-selectksigs/PKGBUILD b/prepare/r-selectksigs/PKGBUILD new file mode 100644 index 0000000000..72a1756ee6 --- /dev/null +++ b/prepare/r-selectksigs/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=selectKSigs +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Selecting the number of mutational signatures using a perplexity-based measure and cross-validation' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-gtools + r-hilda + r-magrittr + r-rcpp +) +optdepends=( + r-biocstyle + r-dplyr + r-ggplot2 + r-knitr + r-rmarkdown + r-testthat + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-selectksigs/lilac.py b/prepare/r-selectksigs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-selectksigs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-selectksigs/lilac.yaml b/prepare/r-selectksigs/lilac.yaml new file mode 100644 index 0000000000..55e3318e6c --- /dev/null +++ b/prepare/r-selectksigs/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gtools +- r-hilda +- r-magrittr +- r-rcpp +update_on: +- regex: selectKSigs_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/selectKSigs diff --git a/prepare/r-selectr/PKGBUILD b/prepare/r-selectr/PKGBUILD new file mode 100644 index 0000000000..d69687ab04 --- /dev/null +++ b/prepare/r-selectr/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=selectr +_pkgver=0.4-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Translate CSS Selectors to XPath Expressions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-r6 + r-stringr +) +optdepends=( + r-testthat + r-xml + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENCE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-selectr/lilac.py b/prepare/r-selectr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-selectr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-selectr/lilac.yaml b/prepare/r-selectr/lilac.yaml new file mode 100644 index 0000000000..fc8002959b --- /dev/null +++ b/prepare/r-selectr/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-r6 +- r-stringr +update_on: +- regex: selectr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=selectr diff --git a/prepare/r-selex/PKGBUILD b/prepare/r-selex/PKGBUILD new file mode 100644 index 0000000000..ddc50232b6 --- /dev/null +++ b/prepare/r-selex/PKGBUILD @@ -0,0 +1,29 @@ +# system requirements: Java (>= 1.5) +# Maintainer: Guoyi Zhang + +_pkgname=SELEX +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for analyzing SELEX-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-rjava +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-selex/lilac.py b/prepare/r-selex/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-selex/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-selex/lilac.yaml b/prepare/r-selex/lilac.yaml new file mode 100644 index 0000000000..8b3bbebaf5 --- /dev/null +++ b/prepare/r-selex/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-rjava +update_on: +- regex: SELEX_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SELEX diff --git a/prepare/r-semdist/PKGBUILD b/prepare/r-semdist/PKGBUILD new file mode 100644 index 0000000000..be9a76c354 --- /dev/null +++ b/prepare/r-semdist/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SemDist +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Information Accretion-based Function Predictor Evaluation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotate + r-annotationdbi + r-go.db +) +optdepends=( + r-gosemsim +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-semdist/lilac.py b/prepare/r-semdist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-semdist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-semdist/lilac.yaml b/prepare/r-semdist/lilac.yaml new file mode 100644 index 0000000000..c536500a68 --- /dev/null +++ b/prepare/r-semdist/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-go.db +update_on: +- regex: SemDist_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SemDist diff --git a/prepare/r-semisup/PKGBUILD b/prepare/r-semisup/PKGBUILD new file mode 100644 index 0000000000..fe31de819c --- /dev/null +++ b/prepare/r-semisup/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=semisup +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Semi-Supervised Mixture Model' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-vgam +) +optdepends=( + r-knitr + r-summarizedexperiment + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-semisup/lilac.py b/prepare/r-semisup/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-semisup/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-semisup/lilac.yaml b/prepare/r-semisup/lilac.yaml new file mode 100644 index 0000000000..fb8b454ccd --- /dev/null +++ b/prepare/r-semisup/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-vgam +update_on: +- regex: semisup_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/semisup diff --git a/prepare/r-sendmailr/PKGBUILD b/prepare/r-sendmailr/PKGBUILD new file mode 100644 index 0000000000..e4637fac67 --- /dev/null +++ b/prepare/r-sendmailr/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sendmailR +_pkgver=1.2-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='send email using R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-base64enc +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sendmailr/lilac.py b/prepare/r-sendmailr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sendmailr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sendmailr/lilac.yaml b/prepare/r-sendmailr/lilac.yaml new file mode 100644 index 0000000000..c5ddc7e38f --- /dev/null +++ b/prepare/r-sendmailr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +update_on: +- regex: sendmailR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sendmailR diff --git a/prepare/r-sepira/PKGBUILD b/prepare/r-sepira/PKGBUILD new file mode 100644 index 0000000000..1f4f4a62af --- /dev/null +++ b/prepare/r-sepira/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SEPIRA +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Systems EPigenomics Inference of Regulatory Activity' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-corpcor + r-limma +) +optdepends=( + r-igraph + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sepira/lilac.py b/prepare/r-sepira/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sepira/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sepira/lilac.yaml b/prepare/r-sepira/lilac.yaml new file mode 100644 index 0000000000..3d1ce3bb19 --- /dev/null +++ b/prepare/r-sepira/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-corpcor +- r-limma +update_on: +- regex: SEPIRA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SEPIRA diff --git a/prepare/r-seq2pathway.data/PKGBUILD b/prepare/r-seq2pathway.data/PKGBUILD new file mode 100644 index 0000000000..3bc7767ae9 --- /dev/null +++ b/prepare/r-seq2pathway.data/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=seq2pathway.data +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='data set for R package seq2pathway' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seq2pathway.data/lilac.py b/prepare/r-seq2pathway.data/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seq2pathway.data/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seq2pathway.data/lilac.yaml b/prepare/r-seq2pathway.data/lilac.yaml new file mode 100644 index 0000000000..80555be9a8 --- /dev/null +++ b/prepare/r-seq2pathway.data/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: seq2pathway.data_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/seq2pathway.data diff --git a/prepare/r-seq2pathway/PKGBUILD b/prepare/r-seq2pathway/PKGBUILD new file mode 100644 index 0000000000..5e07db09b5 --- /dev/null +++ b/prepare/r-seq2pathway/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=seq2pathway +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-genomicranges + r-gsa + r-seq2pathway.data + r-wgcna +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seq2pathway/lilac.py b/prepare/r-seq2pathway/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seq2pathway/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seq2pathway/lilac.yaml b/prepare/r-seq2pathway/lilac.yaml new file mode 100644 index 0000000000..db2c5e953e --- /dev/null +++ b/prepare/r-seq2pathway/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-genomicranges +- r-gsa +- r-seq2pathway.data +- r-wgcna +update_on: +- regex: seq2pathway_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/seq2pathway diff --git a/prepare/r-seqarray/PKGBUILD b/prepare/r-seqarray/PKGBUILD new file mode 100644 index 0000000000..b11e0891d1 --- /dev/null +++ b/prepare/r-seqarray/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SeqArray +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data management of large-scale whole-genome sequence variant calls' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-gdsfmt + r-genomeinfodb + r-genomicranges + r-iranges + r-s4vectors +) +optdepends=( + r-biobase + r-biocgenerics + r-biocparallel + r-crayon + r-digest + r-knitr + r-markdown + r-rcpp + r-rmarkdown + r-rsamtools + r-runit + r-snprelate + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seqarray/lilac.py b/prepare/r-seqarray/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seqarray/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seqarray/lilac.yaml b/prepare/r-seqarray/lilac.yaml new file mode 100644 index 0000000000..4e7031f901 --- /dev/null +++ b/prepare/r-seqarray/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-gdsfmt +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-s4vectors +update_on: +- regex: SeqArray_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SeqArray diff --git a/prepare/r-seqbias/PKGBUILD b/prepare/r-seqbias/PKGBUILD new file mode 100644 index 0000000000..5ec34747e6 --- /dev/null +++ b/prepare/r-seqbias/PKGBUILD @@ -0,0 +1,34 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=seqbias +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimation of per-position bias in high-throughput sequencing data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biostrings + r-genomicranges + r-rhtslib +) +optdepends=( + r-ggplot2 + r-rsamtools +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seqbias/lilac.py b/prepare/r-seqbias/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seqbias/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seqbias/lilac.yaml b/prepare/r-seqbias/lilac.yaml new file mode 100644 index 0000000000..6562a5eb05 --- /dev/null +++ b/prepare/r-seqbias/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-genomicranges +- r-rhtslib +update_on: +- regex: seqbias_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/seqbias diff --git a/prepare/r-seqcat/PKGBUILD b/prepare/r-seqcat/PKGBUILD new file mode 100644 index 0000000000..991e59d257 --- /dev/null +++ b/prepare/r-seqcat/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=seqCAT +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='High Throughput Sequencing Cell Authentication Toolkit' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-rlang + r-rtracklayer + r-s4vectors + r-scales + r-summarizedexperiment + r-tidyr + r-variantannotation +) +optdepends=( + r-biocmanager + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENCE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seqcat/lilac.py b/prepare/r-seqcat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seqcat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seqcat/lilac.yaml b/prepare/r-seqcat/lilac.yaml new file mode 100644 index 0000000000..c24debbfe1 --- /dev/null +++ b/prepare/r-seqcat/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-rlang +- r-rtracklayer +- r-s4vectors +- r-scales +- r-summarizedexperiment +- r-tidyr +- r-variantannotation +update_on: +- regex: seqCAT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/seqCAT diff --git a/prepare/r-seqcna.annot/PKGBUILD b/prepare/r-seqcna.annot/PKGBUILD new file mode 100644 index 0000000000..65e53054aa --- /dev/null +++ b/prepare/r-seqcna.annot/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=seqCNA.annot +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation for the copy number analysis of deep sequencing cancer data with seqCNA' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seqcna.annot/lilac.py b/prepare/r-seqcna.annot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seqcna.annot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seqcna.annot/lilac.yaml b/prepare/r-seqcna.annot/lilac.yaml new file mode 100644 index 0000000000..a445469d24 --- /dev/null +++ b/prepare/r-seqcna.annot/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: seqCNA.annot_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/seqCNA.annot diff --git a/prepare/r-seqcna/PKGBUILD b/prepare/r-seqcna/PKGBUILD new file mode 100644 index 0000000000..2621627a63 --- /dev/null +++ b/prepare/r-seqcna/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: samtools +# Maintainer: Guoyi Zhang + +_pkgname=seqCNA +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Copy number analysis of high-throughput sequencing cancer data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-adehabitatlt + r-dosnow + r-glad + r-seqcna.annot +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seqcna/lilac.py b/prepare/r-seqcna/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seqcna/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seqcna/lilac.yaml b/prepare/r-seqcna/lilac.yaml new file mode 100644 index 0000000000..4240be0c9f --- /dev/null +++ b/prepare/r-seqcna/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-adehabitatlt +- r-dosnow +- r-glad +- r-seqcna.annot +update_on: +- regex: seqCNA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/seqCNA diff --git a/prepare/r-seqcombo/PKGBUILD b/prepare/r-seqcombo/PKGBUILD new file mode 100644 index 0000000000..d95c83cdcb --- /dev/null +++ b/prepare/r-seqcombo/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=seqcombo +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization Tool for Sequence Recombination and Reassortment' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-cowplot + r-dplyr + r-ggplot2 + r-igraph + r-magrittr + r-yulab.utils +) +optdepends=( + r-emojifont + r-knitr + r-prettydoc + r-rmarkdown + r-tibble +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seqcombo/lilac.py b/prepare/r-seqcombo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seqcombo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seqcombo/lilac.yaml b/prepare/r-seqcombo/lilac.yaml new file mode 100644 index 0000000000..c1bda0be3d --- /dev/null +++ b/prepare/r-seqcombo/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-cowplot +- r-dplyr +- r-ggplot2 +- r-igraph +- r-magrittr +- r-yulab.utils +update_on: +- regex: seqcombo_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/seqcombo diff --git a/prepare/r-seqgate/PKGBUILD b/prepare/r-seqgate/PKGBUILD new file mode 100644 index 0000000000..143b68c3a4 --- /dev/null +++ b/prepare/r-seqgate/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SeqGate +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Filtering of Lowly Expressed Features' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocmanager + r-genomicranges + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-edger + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seqgate/lilac.py b/prepare/r-seqgate/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seqgate/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seqgate/lilac.yaml b/prepare/r-seqgate/lilac.yaml new file mode 100644 index 0000000000..a51ac29346 --- /dev/null +++ b/prepare/r-seqgate/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocmanager +- r-genomicranges +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: SeqGate_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SeqGate diff --git a/prepare/r-seqgsea/PKGBUILD b/prepare/r-seqgsea/PKGBUILD new file mode 100644 index 0000000000..969535d9c7 --- /dev/null +++ b/prepare/r-seqgsea/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SeqGSEA +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biomart + r-deseq2 + r-doparallel +) +optdepends=( + r-genomicranges +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seqgsea/lilac.py b/prepare/r-seqgsea/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seqgsea/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seqgsea/lilac.yaml b/prepare/r-seqgsea/lilac.yaml new file mode 100644 index 0000000000..ac2f0bc3c8 --- /dev/null +++ b/prepare/r-seqgsea/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biomart +- r-deseq2 +- r-doparallel +update_on: +- regex: SeqGSEA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SeqGSEA diff --git a/prepare/r-seqinr/PKGBUILD b/prepare/r-seqinr/PKGBUILD new file mode 100644 index 0000000000..7600ec840d --- /dev/null +++ b/prepare/r-seqinr/PKGBUILD @@ -0,0 +1,29 @@ +# system requirements: zlib headers and library. +# Maintainer: Guoyi Zhang + +_pkgname=seqinr +_pkgver=4.2-8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Biological Sequences Retrieval and Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ade4 + r-segmented +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seqinr/lilac.py b/prepare/r-seqinr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seqinr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seqinr/lilac.yaml b/prepare/r-seqinr/lilac.yaml new file mode 100644 index 0000000000..d1d04d9556 --- /dev/null +++ b/prepare/r-seqinr/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ade4 +- r-segmented +update_on: +- regex: seqinr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=seqinr diff --git a/prepare/r-seqlogo/PKGBUILD b/prepare/r-seqlogo/PKGBUILD new file mode 100644 index 0000000000..ff46038f35 --- /dev/null +++ b/prepare/r-seqlogo/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=seqLogo +_pkgver=1.60.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sequence logos for DNA sequence alignments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seqlogo/lilac.py b/prepare/r-seqlogo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seqlogo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seqlogo/lilac.yaml b/prepare/r-seqlogo/lilac.yaml new file mode 100644 index 0000000000..9d7ab34657 --- /dev/null +++ b/prepare/r-seqlogo/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: seqLogo_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/seqLogo diff --git a/prepare/r-seqmagick/PKGBUILD b/prepare/r-seqmagick/PKGBUILD new file mode 100644 index 0000000000..35a3849d2b --- /dev/null +++ b/prepare/r-seqmagick/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=seqmagick +_pkgver=0.1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sequence Manipulation Utilities' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biostrings + r-magrittr +) +optdepends=( + r-downloader + r-genomicalignments + r-genomicranges + r-iranges + r-knitr + r-muscle + r-prettydoc + r-rmarkdown + r-rsamtools +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seqmagick/lilac.py b/prepare/r-seqmagick/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seqmagick/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seqmagick/lilac.yaml b/prepare/r-seqmagick/lilac.yaml new file mode 100644 index 0000000000..af6e44a885 --- /dev/null +++ b/prepare/r-seqmagick/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-magrittr +update_on: +- regex: seqmagick_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=seqmagick diff --git a/prepare/r-seqminer/PKGBUILD b/prepare/r-seqminer/PKGBUILD new file mode 100644 index 0000000000..38d3997a2e --- /dev/null +++ b/prepare/r-seqminer/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: C++11, zlib headers and libraries, GNU make,optionally also bzip2 and POSIX-compliant regex functions. +# Maintainer: Guoyi Zhang + +_pkgname=seqminer +_pkgver=8.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-skat + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seqminer/lilac.py b/prepare/r-seqminer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seqminer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seqminer/lilac.yaml b/prepare/r-seqminer/lilac.yaml new file mode 100644 index 0000000000..5800bd698d --- /dev/null +++ b/prepare/r-seqminer/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: seqminer_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=seqminer diff --git a/prepare/r-seqpattern/PKGBUILD b/prepare/r-seqpattern/PKGBUILD new file mode 100644 index 0000000000..1ae4a168a7 --- /dev/null +++ b/prepare/r-seqpattern/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=seqPattern +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-genomicranges + r-iranges + r-plotrix +) +optdepends=( + r-biocgenerics + r-biocstyle + r-bsgenome.drerio.ucsc.danrer7 + r-cager + r-parallel + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seqpattern/lilac.py b/prepare/r-seqpattern/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seqpattern/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seqpattern/lilac.yaml b/prepare/r-seqpattern/lilac.yaml new file mode 100644 index 0000000000..61662bbff5 --- /dev/null +++ b/prepare/r-seqpattern/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-genomicranges +- r-iranges +- r-plotrix +update_on: +- regex: seqPattern_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/seqPattern diff --git a/prepare/r-seqsetvis/PKGBUILD b/prepare/r-seqsetvis/PKGBUILD new file mode 100644 index 0000000000..cb41abf31a --- /dev/null +++ b/prepare/r-seqsetvis/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=seqsetvis +_pkgver=1.14.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Set Based Visualizations for Next-Gen Sequencing Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-data.table + r-eulerr + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-ggplotify + r-iranges + r-limma + r-pbapply + r-pbmcapply + r-png + r-rcolorbrewer + r-rsamtools + r-rtracklayer + r-s4vectors + r-upsetr +) +optdepends=( + r-biocfilecache + r-biocmanager + r-biocstyle + r-chippeakanno + r-covr + r-cowplot + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seqsetvis/lilac.py b/prepare/r-seqsetvis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seqsetvis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seqsetvis/lilac.yaml b/prepare/r-seqsetvis/lilac.yaml new file mode 100644 index 0000000000..b5875d3852 --- /dev/null +++ b/prepare/r-seqsetvis/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-eulerr +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-ggplotify +- r-iranges +- r-limma +- r-pbapply +- r-pbmcapply +- r-png +- r-rcolorbrewer +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-upsetr +update_on: +- regex: seqsetvis_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/seqsetvis diff --git a/prepare/r-seqsqc/PKGBUILD b/prepare/r-seqsqc/PKGBUILD new file mode 100644 index 0000000000..4b837f3924 --- /dev/null +++ b/prepare/r-seqsqc/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SeqSQC +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A bioconductor package for sample quality check with next generation sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-e1071 + r-experimenthub + r-gdsfmt + r-genomicranges + r-ggally + r-ggplot2 + r-iranges + r-rbokeh + r-rcolorbrewer + r-reshape2 + r-rmarkdown + r-s4vectors + r-snprelate +) +optdepends=( + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seqsqc/lilac.py b/prepare/r-seqsqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seqsqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seqsqc/lilac.yaml b/prepare/r-seqsqc/lilac.yaml new file mode 100644 index 0000000000..9b0a073222 --- /dev/null +++ b/prepare/r-seqsqc/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-e1071 +- r-experimenthub +- r-gdsfmt +- r-genomicranges +- r-ggally +- r-ggplot2 +- r-iranges +- r-rbokeh +- r-rcolorbrewer +- r-reshape2 +- r-rmarkdown +- r-s4vectors +- r-snprelate +update_on: +- regex: SeqSQC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SeqSQC diff --git a/prepare/r-seqtools/PKGBUILD b/prepare/r-seqtools/PKGBUILD new file mode 100644 index 0000000000..fa6eca7675 --- /dev/null +++ b/prepare/r-seqtools/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=seqTools +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of nucleotide, sequence and quality content on fastq files' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-zlibbioc +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seqtools/lilac.py b/prepare/r-seqtools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seqtools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seqtools/lilac.yaml b/prepare/r-seqtools/lilac.yaml new file mode 100644 index 0000000000..f659e5ef97 --- /dev/null +++ b/prepare/r-seqtools/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-zlibbioc +update_on: +- regex: seqTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/seqTools diff --git a/prepare/r-seqvartools/PKGBUILD b/prepare/r-seqvartools/PKGBUILD new file mode 100644 index 0000000000..8a4ae0142d --- /dev/null +++ b/prepare/r-seqvartools/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SeqVarTools +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for variant data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-data.table + r-gdsfmt + r-genomicranges + r-gwasexacthw + r-iranges + r-logistf + r-s4vectors + r-seqarray +) +optdepends=( + r-biocstyle + r-runit + r-stringr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seqvartools/lilac.py b/prepare/r-seqvartools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seqvartools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seqvartools/lilac.yaml b/prepare/r-seqvartools/lilac.yaml new file mode 100644 index 0000000000..b4e41954f2 --- /dev/null +++ b/prepare/r-seqvartools/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-data.table +- r-gdsfmt +- r-genomicranges +- r-gwasexacthw +- r-iranges +- r-logistf +- r-s4vectors +- r-seqarray +update_on: +- regex: SeqVarTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SeqVarTools diff --git a/prepare/r-seriation/PKGBUILD b/prepare/r-seriation/PKGBUILD new file mode 100644 index 0000000000..c3e007c866 --- /dev/null +++ b/prepare/r-seriation/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=seriation +_pkgver=1.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Infrastructure for Ordering Objects Using Seriation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-colorspace + r-gclus + r-qap + r-registry + r-tsp +) +optdepends=( + r-dbscan + r-dendextend + r-dendser + r-ga + r-ggplot2 + r-rtsne + r-scales + r-testthat + r-umap +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seriation/lilac.py b/prepare/r-seriation/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seriation/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seriation/lilac.yaml b/prepare/r-seriation/lilac.yaml new file mode 100644 index 0000000000..b53a8b0233 --- /dev/null +++ b/prepare/r-seriation/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colorspace +- r-gclus +- r-qap +- r-registry +- r-tsp +update_on: +- regex: seriation_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=seriation diff --git a/prepare/r-servr/PKGBUILD b/prepare/r-servr/PKGBUILD new file mode 100644 index 0000000000..38980013fe --- /dev/null +++ b/prepare/r-servr/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=servr +_pkgver=0.24 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Simple HTTP Server to Serve Static Files or Dynamic Documents' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-httpuv + r-jsonlite + r-mime + r-xfun +) +optdepends=( + r-knitr + r-later + r-rmarkdown + r-rstudioapi + r-tools +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-servr/lilac.py b/prepare/r-servr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-servr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-servr/lilac.yaml b/prepare/r-servr/lilac.yaml new file mode 100644 index 0000000000..39e8b8f000 --- /dev/null +++ b/prepare/r-servr/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-httpuv +- r-jsonlite +- r-mime +- r-xfun +update_on: +- regex: servr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=servr diff --git a/prepare/r-sesame/PKGBUILD b/prepare/r-sesame/PKGBUILD new file mode 100644 index 0000000000..10dd49b26c --- /dev/null +++ b/prepare/r-sesame/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sesame +_pkgver=1.12.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SEnsible Step-wise Analysis of DNA MEthylation BeadChips' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocparallel + r-dnacopy + r-e1071 + r-fgsea + r-genomicranges + r-ggplot2 + r-ggrepel + r-illuminaio + r-iranges + r-matrixstats + r-preprocesscore + r-randomforest + r-reshape2 + r-s4vectors + r-sesamedata + r-stringr + r-summarizedexperiment + r-tibble + r-wheatmap +) +optdepends=( + r-biocstyle + r-dplyr + r-flowsorted.blood.450k + r-flowsorted.cordbloodnorway.450k + r-hdf5array + r-illuminahumanmethylation450kmanifest + r-knitr + r-minfi + r-rmarkdown + r-scales + r-testthat + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sesame/lilac.py b/prepare/r-sesame/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sesame/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sesame/lilac.yaml b/prepare/r-sesame/lilac.yaml new file mode 100644 index 0000000000..719ddca8d6 --- /dev/null +++ b/prepare/r-sesame/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-dnacopy +- r-e1071 +- r-fgsea +- r-genomicranges +- r-ggplot2 +- r-ggrepel +- r-illuminaio +- r-iranges +- r-matrixstats +- r-preprocesscore +- r-randomforest +- r-reshape2 +- r-s4vectors +- r-sesamedata +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-wheatmap +update_on: +- regex: sesame_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sesame diff --git a/prepare/r-sesamedata/PKGBUILD b/prepare/r-sesamedata/PKGBUILD new file mode 100644 index 0000000000..fbb5b068be --- /dev/null +++ b/prepare/r-sesamedata/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sesameData +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Supporting Data for SeSAMe Package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationhub + r-curl + r-experimenthub + r-rmarkdown +) +optdepends=( + r-biocgenerics + r-genomicranges + r-knitr + r-sesame + r-testthat +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sesamedata/lilac.py b/prepare/r-sesamedata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sesamedata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sesamedata/lilac.yaml b/prepare/r-sesamedata/lilac.yaml new file mode 100644 index 0000000000..a7d9fa6fa0 --- /dev/null +++ b/prepare/r-sesamedata/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-curl +- r-experimenthub +- r-rmarkdown +update_on: +- regex: sesameData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sesameData diff --git a/prepare/r-sessioninfo/PKGBUILD b/prepare/r-sessioninfo/PKGBUILD new file mode 100644 index 0000000000..75fb9660cb --- /dev/null +++ b/prepare/r-sessioninfo/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sessioninfo +_pkgver=1.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Session Information' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-cli +) +optdepends=( + r-callr + r-covr + r-mockery + r-reticulate + r-rmarkdown + r-testthat + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sessioninfo/lilac.py b/prepare/r-sessioninfo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sessioninfo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sessioninfo/lilac.yaml b/prepare/r-sessioninfo/lilac.yaml new file mode 100644 index 0000000000..6c4a3d8717 --- /dev/null +++ b/prepare/r-sessioninfo/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cli +update_on: +- regex: sessioninfo_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sessioninfo diff --git a/prepare/r-setools/PKGBUILD b/prepare/r-setools/PKGBUILD new file mode 100644 index 0000000000..93432cfa66 --- /dev/null +++ b/prepare/r-setools/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SEtools +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SEtools: tools for working with SummarizedExperiment' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-circlize + r-complexheatmap + r-data.table + r-deseq2 + r-edger + r-openxlsx + r-randomcolor + r-s4vectors + r-seriation + r-summarizedexperiment + r-sva +) +optdepends=( + r-biocstyle + r-ggplot2 + r-knitr + r-pheatmap + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-setools/lilac.py b/prepare/r-setools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-setools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-setools/lilac.yaml b/prepare/r-setools/lilac.yaml new file mode 100644 index 0000000000..fc86f581b7 --- /dev/null +++ b/prepare/r-setools/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-circlize +- r-complexheatmap +- r-data.table +- r-deseq2 +- r-edger +- r-openxlsx +- r-randomcolor +- r-s4vectors +- r-seriation +- r-summarizedexperiment +- r-sva +update_on: +- regex: SEtools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SEtools diff --git a/prepare/r-setrng/PKGBUILD b/prepare/r-setrng/PKGBUILD new file mode 100644 index 0000000000..49c9ce8fc4 --- /dev/null +++ b/prepare/r-setrng/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=setRNG +_pkgver=2013.9-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Set (Normal) Random Number Generator and Seed' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-setrng/lilac.py b/prepare/r-setrng/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-setrng/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-setrng/lilac.yaml b/prepare/r-setrng/lilac.yaml new file mode 100644 index 0000000000..78cdb37a59 --- /dev/null +++ b/prepare/r-setrng/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: setRNG_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=setRNG diff --git a/prepare/r-sets/PKGBUILD b/prepare/r-sets/PKGBUILD new file mode 100644 index 0000000000..058e3a987e --- /dev/null +++ b/prepare/r-sets/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sets +_pkgver=1.0-20 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sets, Generalized Sets, Customizable Sets and Intervals' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-proxy +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sets/lilac.py b/prepare/r-sets/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sets/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sets/lilac.yaml b/prepare/r-sets/lilac.yaml new file mode 100644 index 0000000000..85a8c7540d --- /dev/null +++ b/prepare/r-sets/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: sets_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sets diff --git a/prepare/r-settings/PKGBUILD b/prepare/r-settings/PKGBUILD new file mode 100644 index 0000000000..b959315667 --- /dev/null +++ b/prepare/r-settings/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=settings +_pkgver=0.2.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Software Option Settings Manager for R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-settings/lilac.py b/prepare/r-settings/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-settings/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-settings/lilac.yaml b/prepare/r-settings/lilac.yaml new file mode 100644 index 0000000000..0a8aae7ab4 --- /dev/null +++ b/prepare/r-settings/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: settings_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=settings diff --git a/prepare/r-seurat/PKGBUILD b/prepare/r-seurat/PKGBUILD new file mode 100644 index 0000000000..ef57f5c43c --- /dev/null +++ b/prepare/r-seurat/PKGBUILD @@ -0,0 +1,91 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Seurat +_pkgver=4.0.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Single Cell Genomics' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-cowplot + r-fitdistrplus + r-future + r-future.apply + r-ggplot2 + r-ggrepel + r-ggridges + r-httr + r-ica + r-igraph + r-irlba + r-jsonlite + r-leiden + r-lmtest + r-matrixstats + r-miniui + r-patchwork + r-pbapply + r-plotly + r-png + r-rann + r-rcolorbrewer + r-rcpp + r-rcppannoy + r-rcppeigen + r-rcppprogress + r-reticulate + r-rlang + r-rocr + r-rtsne + r-scales + r-scattermore + r-sctransform + r-seuratobject + r-shiny + r-spatstat.core + r-spatstat.geom + r-tibble + r-uwot +) +optdepends=( + r-ape + r-biobase + r-biocgenerics + r-deseq2 + r-enrichr + r-genomeinfodb + r-genomicranges + r-ggrastr + r-hdf5r + r-iranges + r-limma + r-mast + r-metap + r-mixtools + r-monocle + r-rfast2 + r-rsvd + r-rtracklayer + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-testthat + r-vgam +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seurat/lilac.py b/prepare/r-seurat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seurat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seurat/lilac.yaml b/prepare/r-seurat/lilac.yaml new file mode 100644 index 0000000000..e8c76aaab1 --- /dev/null +++ b/prepare/r-seurat/lilac.yaml @@ -0,0 +1,48 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cowplot +- r-fitdistrplus +- r-future +- r-future.apply +- r-ggplot2 +- r-ggrepel +- r-ggridges +- r-httr +- r-ica +- r-igraph +- r-irlba +- r-jsonlite +- r-leiden +- r-lmtest +- r-matrixstats +- r-miniui +- r-patchwork +- r-pbapply +- r-plotly +- r-png +- r-rann +- r-rcolorbrewer +- r-rcpp +- r-rcppannoy +- r-rcppeigen +- r-rcppprogress +- r-reticulate +- r-rlang +- r-rocr +- r-rtsne +- r-scales +- r-scattermore +- r-sctransform +- r-seuratobject +- r-shiny +- r-spatstat.core +- r-spatstat.geom +- r-tibble +- r-uwot +update_on: +- regex: Seurat_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=Seurat diff --git a/prepare/r-seuratobject/PKGBUILD b/prepare/r-seuratobject/PKGBUILD new file mode 100644 index 0000000000..b5264b53e7 --- /dev/null +++ b/prepare/r-seuratobject/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SeuratObject +_pkgver=4.0.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data Structures for Single Cell Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-rcpp + r-rcppeigen + r-rlang +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-seuratobject/lilac.py b/prepare/r-seuratobject/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-seuratobject/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-seuratobject/lilac.yaml b/prepare/r-seuratobject/lilac.yaml new file mode 100644 index 0000000000..c695661001 --- /dev/null +++ b/prepare/r-seuratobject/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcppeigen +- r-rlang +update_on: +- regex: SeuratObject_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=SeuratObject diff --git a/prepare/r-sevenbridges/PKGBUILD b/prepare/r-sevenbridges/PKGBUILD new file mode 100644 index 0000000000..178aad546c --- /dev/null +++ b/prepare/r-sevenbridges/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sevenbridges +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Apache') +depends=( + r + r-curl + r-data.table + r-docopt + r-httr + r-jsonlite + r-objectproperties + r-s4vectors + r-stringr + r-uuid + r-yaml +) +optdepends=( + r-knitr + r-readr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sevenbridges/lilac.py b/prepare/r-sevenbridges/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sevenbridges/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sevenbridges/lilac.yaml b/prepare/r-sevenbridges/lilac.yaml new file mode 100644 index 0000000000..032cecaf82 --- /dev/null +++ b/prepare/r-sevenbridges/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-data.table +- r-docopt +- r-httr +- r-jsonlite +- r-objectproperties +- r-s4vectors +- r-stringr +- r-uuid +- r-yaml +update_on: +- regex: sevenbridges_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sevenbridges diff --git a/prepare/r-sevenc/PKGBUILD b/prepare/r-sevenc/PKGBUILD new file mode 100644 index 0000000000..5e6ba4c282 --- /dev/null +++ b/prepare/r-sevenc/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sevenC +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-data.table + r-genomeinfodb + r-genomicranges + r-interactionset + r-iranges + r-purrr + r-readr + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocstyle + r-covr + r-genomicinteractions + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sevenc/lilac.py b/prepare/r-sevenc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sevenc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sevenc/lilac.yaml b/prepare/r-sevenc/lilac.yaml new file mode 100644 index 0000000000..1701698d7d --- /dev/null +++ b/prepare/r-sevenc/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-data.table +- r-genomeinfodb +- r-genomicranges +- r-interactionset +- r-iranges +- r-purrr +- r-readr +- r-rtracklayer +- r-s4vectors +update_on: +- regex: sevenC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sevenC diff --git a/prepare/r-sf/PKGBUILD b/prepare/r-sf/PKGBUILD new file mode 100644 index 0000000000..8133712fe4 --- /dev/null +++ b/prepare/r-sf/PKGBUILD @@ -0,0 +1,71 @@ +# system requirements: C++11, GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>=4.8.0), sqlite3 +# Maintainer: Guoyi Zhang + +_pkgname=sf +_pkgver=1.0-5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Simple Features for R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-classint + r-dbi + r-magrittr + r-rcpp + r-s2 + r-units +) +optdepends=( + r-blob + r-covr + r-dplyr + r-ggplot2 + r-knitr + r-lwgeom + r-maps + r-mapview + r-matrix + r-microbenchmark + r-odbc + r-pillar + r-pool + r-raster + r-rgdal + r-rgeos + r-rlang + r-rmarkdown + r-rpostgres + r-rpostgresql + r-rsqlite + r-sp + r-spatstat + r-spatstat.core + r-spatstat.geom + r-spatstat.linnet + r-spatstat.utils + r-stars + r-terra + r-testthat + r-tibble + r-tidyr + r-tidyselect + r-tmap + r-vctrs + r-wk +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sf/lilac.py b/prepare/r-sf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sf/lilac.yaml b/prepare/r-sf/lilac.yaml new file mode 100644 index 0000000000..b1b4474e0d --- /dev/null +++ b/prepare/r-sf/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-classint +- r-dbi +- r-magrittr +- r-rcpp +- r-s2 +- r-units +update_on: +- regex: sf_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sf diff --git a/prepare/r-sfsmisc/PKGBUILD b/prepare/r-sfsmisc/PKGBUILD new file mode 100644 index 0000000000..1d019f5f48 --- /dev/null +++ b/prepare/r-sfsmisc/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sfsmisc +_pkgver=1.1-12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities from Seminar fuer Statistik ETH Zurich' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sfsmisc/lilac.py b/prepare/r-sfsmisc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sfsmisc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sfsmisc/lilac.yaml b/prepare/r-sfsmisc/lilac.yaml new file mode 100644 index 0000000000..e0563204ff --- /dev/null +++ b/prepare/r-sfsmisc/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: sfsmisc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sfsmisc diff --git a/prepare/r-sgeostat/PKGBUILD b/prepare/r-sgeostat/PKGBUILD new file mode 100644 index 0000000000..c48651e12c --- /dev/null +++ b/prepare/r-sgeostat/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sgeostat +_pkgver=1.0-27 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Object-Oriented Framework for Geostatistical Modeling in S+' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sgeostat/lilac.py b/prepare/r-sgeostat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sgeostat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sgeostat/lilac.yaml b/prepare/r-sgeostat/lilac.yaml new file mode 100644 index 0000000000..0fb6f89ffb --- /dev/null +++ b/prepare/r-sgeostat/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: sgeostat_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sgeostat diff --git a/prepare/r-sgseq/PKGBUILD b/prepare/r-sgseq/PKGBUILD new file mode 100644 index 0000000000..569da63492 --- /dev/null +++ b/prepare/r-sgseq/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SGSeq +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Splice event prediction and quantification from RNA-seq data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biocgenerics + r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-igraph + r-iranges + r-rsamtools + r-rtracklayer + r-runit + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-knitr + r-rmarkdown + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sgseq/lilac.py b/prepare/r-sgseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sgseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sgseq/lilac.yaml b/prepare/r-sgseq/lilac.yaml new file mode 100644 index 0000000000..d6c2aa3b78 --- /dev/null +++ b/prepare/r-sgseq/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-biostrings +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-igraph +- r-iranges +- r-rsamtools +- r-rtracklayer +- r-runit +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: SGSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SGSeq diff --git a/prepare/r-shades/PKGBUILD b/prepare/r-shades/PKGBUILD new file mode 100644 index 0000000000..c0ed4fa156 --- /dev/null +++ b/prepare/r-shades/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shades +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Simple Colour Manipulation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +optdepends=( + r-colorspace + r-covr + r-ggplot2 + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENCE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shades/lilac.py b/prepare/r-shades/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shades/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shades/lilac.yaml b/prepare/r-shades/lilac.yaml new file mode 100644 index 0000000000..824a847d77 --- /dev/null +++ b/prepare/r-shades/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: shades_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shades diff --git a/prepare/r-shadowtext/PKGBUILD b/prepare/r-shadowtext/PKGBUILD new file mode 100644 index 0000000000..b367d6fbc4 --- /dev/null +++ b/prepare/r-shadowtext/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shadowtext +_pkgver=0.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Shadow Text Grob and Layer' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ggplot2 + r-scales +) +optdepends=( + r-knitr + r-prettydoc + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shadowtext/lilac.py b/prepare/r-shadowtext/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shadowtext/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shadowtext/lilac.yaml b/prepare/r-shadowtext/lilac.yaml new file mode 100644 index 0000000000..fd320b61f7 --- /dev/null +++ b/prepare/r-shadowtext/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-scales +update_on: +- regex: shadowtext_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shadowtext diff --git a/prepare/r-shape/PKGBUILD b/prepare/r-shape/PKGBUILD new file mode 100644 index 0000000000..e594b14c67 --- /dev/null +++ b/prepare/r-shape/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shape +_pkgver=1.4.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for Plotting Graphical Shapes, Colors' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shape/lilac.py b/prepare/r-shape/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shape/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shape/lilac.yaml b/prepare/r-shape/lilac.yaml new file mode 100644 index 0000000000..84798e53cf --- /dev/null +++ b/prepare/r-shape/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: shape_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shape diff --git a/prepare/r-sharedobject/PKGBUILD b/prepare/r-sharedobject/PKGBUILD new file mode 100644 index 0000000000..4cb44a1fb5 --- /dev/null +++ b/prepare/r-sharedobject/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: GNU make, C++11 +# Maintainer: Guoyi Zhang + +_pkgname=SharedObject +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sharing R objects across multiple R processes without memory duplication' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bh + r-biocgenerics + r-rcpp +) +optdepends=( + r-biocstyle + r-knitr + r-parallel + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sharedobject/lilac.py b/prepare/r-sharedobject/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sharedobject/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sharedobject/lilac.yaml b/prepare/r-sharedobject/lilac.yaml new file mode 100644 index 0000000000..9888a06a17 --- /dev/null +++ b/prepare/r-sharedobject/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-biocgenerics +- r-rcpp +update_on: +- regex: SharedObject_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SharedObject diff --git a/prepare/r-shiny/PKGBUILD b/prepare/r-shiny/PKGBUILD new file mode 100644 index 0000000000..9992037480 --- /dev/null +++ b/prepare/r-shiny/PKGBUILD @@ -0,0 +1,64 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shiny +_pkgver=1.7.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Web Application Framework for R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bslib + r-cachem + r-commonmark + r-crayon + r-ellipsis + r-fastmap + r-fontawesome + r-glue + r-htmltools + r-httpuv + r-jsonlite + r-later + r-lifecycle + r-mime + r-promises + r-r6 + r-rlang + r-sourcetools + r-withr + r-xtable +) +optdepends=( + r-cairo + r-datasets + r-dygraphs + r-future + r-ggplot2 + r-knitr + r-magrittr + r-markdown + r-ragg + r-reactlog + r-rmarkdown + r-sass + r-shinytest + r-showtext + r-testthat + r-yaml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shiny/lilac.py b/prepare/r-shiny/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shiny/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shiny/lilac.yaml b/prepare/r-shiny/lilac.yaml new file mode 100644 index 0000000000..40114f733d --- /dev/null +++ b/prepare/r-shiny/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bslib +- r-cachem +- r-commonmark +- r-crayon +- r-ellipsis +- r-fastmap +- r-fontawesome +- r-glue +- r-htmltools +- r-httpuv +- r-jsonlite +- r-later +- r-lifecycle +- r-mime +- r-promises +- r-r6 +- r-rlang +- r-sourcetools +- r-withr +- r-xtable +update_on: +- regex: shiny_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shiny diff --git a/prepare/r-shinyace/PKGBUILD b/prepare/r-shinyace/PKGBUILD new file mode 100644 index 0000000000..5d8906c6ed --- /dev/null +++ b/prepare/r-shinyace/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinyAce +_pkgver=0.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Ace Editor Bindings for Shiny' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-jsonlite + r-shiny +) +optdepends=( + r-dplyr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinyace/lilac.py b/prepare/r-shinyace/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinyace/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinyace/lilac.yaml b/prepare/r-shinyace/lilac.yaml new file mode 100644 index 0000000000..6191013372 --- /dev/null +++ b/prepare/r-shinyace/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-jsonlite +- r-shiny +update_on: +- regex: shinyAce_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinyAce diff --git a/prepare/r-shinyalert/PKGBUILD b/prepare/r-shinyalert/PKGBUILD new file mode 100644 index 0000000000..4307a8e0c7 --- /dev/null +++ b/prepare/r-shinyalert/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinyalert +_pkgver=3.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Easily Create Pretty Popup Messages (Modals) in 'Shiny'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmltools + r-knitr + r-shiny + r-uuid +) +optdepends=( + r-colourpicker + r-shinydisconnect +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinyalert/lilac.py b/prepare/r-shinyalert/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinyalert/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinyalert/lilac.yaml b/prepare/r-shinyalert/lilac.yaml new file mode 100644 index 0000000000..fe9e143e99 --- /dev/null +++ b/prepare/r-shinyalert/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-knitr +- r-shiny +- r-uuid +update_on: +- regex: shinyalert_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinyalert diff --git a/prepare/r-shinybs/PKGBUILD b/prepare/r-shinybs/PKGBUILD new file mode 100644 index 0000000000..67c9169a32 --- /dev/null +++ b/prepare/r-shinybs/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinyBS +_pkgver=0.61 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Twitter Bootstrap Components for Shiny' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-htmltools + r-shiny +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinybs/lilac.py b/prepare/r-shinybs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinybs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinybs/lilac.yaml b/prepare/r-shinybs/lilac.yaml new file mode 100644 index 0000000000..1120748ca3 --- /dev/null +++ b/prepare/r-shinybs/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-shiny +update_on: +- regex: shinyBS_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinyBS diff --git a/prepare/r-shinybusy/PKGBUILD b/prepare/r-shinybusy/PKGBUILD new file mode 100644 index 0000000000..bd8189624a --- /dev/null +++ b/prepare/r-shinybusy/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinybusy +_pkgver=0.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Busy Indicator for 'Shiny' Applications" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-htmltools + r-htmlwidgets + r-jsonlite + r-shiny +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinybusy/lilac.py b/prepare/r-shinybusy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinybusy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinybusy/lilac.yaml b/prepare/r-shinybusy/lilac.yaml new file mode 100644 index 0000000000..c4496aff65 --- /dev/null +++ b/prepare/r-shinybusy/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-htmlwidgets +- r-jsonlite +- r-shiny +update_on: +- regex: shinybusy_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinybusy diff --git a/prepare/r-shinycssloaders/PKGBUILD b/prepare/r-shinycssloaders/PKGBUILD new file mode 100644 index 0000000000..7fd98d94c0 --- /dev/null +++ b/prepare/r-shinycssloaders/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinycssloaders +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Add Loading Animations to a 'shiny' Output While It's Recalculating" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-digest + r-glue + r-shiny +) +optdepends=( + r-shinydisconnect + r-shinyjs +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinycssloaders/lilac.py b/prepare/r-shinycssloaders/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinycssloaders/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinycssloaders/lilac.yaml b/prepare/r-shinycssloaders/lilac.yaml new file mode 100644 index 0000000000..6c0154283f --- /dev/null +++ b/prepare/r-shinycssloaders/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-glue +- r-shiny +update_on: +- regex: shinycssloaders_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinycssloaders diff --git a/prepare/r-shinycustomloader/PKGBUILD b/prepare/r-shinycustomloader/PKGBUILD new file mode 100644 index 0000000000..92f93435e5 --- /dev/null +++ b/prepare/r-shinycustomloader/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinycustomloader +_pkgver=0.9.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Custom Loader for Shiny Outputs' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-glue + r-shiny +) +optdepends=( + r-shinycssloaders +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinycustomloader/lilac.py b/prepare/r-shinycustomloader/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinycustomloader/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinycustomloader/lilac.yaml b/prepare/r-shinycustomloader/lilac.yaml new file mode 100644 index 0000000000..ca123776b0 --- /dev/null +++ b/prepare/r-shinycustomloader/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-glue +- r-shiny +update_on: +- regex: shinycustomloader_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinycustomloader diff --git a/prepare/r-shinydashboard/PKGBUILD b/prepare/r-shinydashboard/PKGBUILD new file mode 100644 index 0000000000..6a59ff7d9c --- /dev/null +++ b/prepare/r-shinydashboard/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinydashboard +_pkgver=0.7.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Create Dashboards with 'Shiny'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-htmltools + r-promises + r-shiny +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinydashboard/lilac.py b/prepare/r-shinydashboard/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinydashboard/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinydashboard/lilac.yaml b/prepare/r-shinydashboard/lilac.yaml new file mode 100644 index 0000000000..bd7ad3c580 --- /dev/null +++ b/prepare/r-shinydashboard/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-promises +- r-shiny +update_on: +- regex: shinydashboard_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinydashboard diff --git a/prepare/r-shinydashboardplus/PKGBUILD b/prepare/r-shinydashboardplus/PKGBUILD new file mode 100644 index 0000000000..6773518213 --- /dev/null +++ b/prepare/r-shinydashboardplus/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinydashboardPlus +_pkgver=2.0.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Add More 'AdminLTE2' Components to 'shinydashboard'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-fresh + r-htmltools + r-lifecycle + r-shiny + r-shinydashboard + r-waiter +) +optdepends=( + r-jsonlite + r-knitr + r-rmarkdown + r-shinyace + r-shinyeffects + r-shinyjqui + r-shinywidgets + r-styler +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinydashboardplus/lilac.py b/prepare/r-shinydashboardplus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinydashboardplus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinydashboardplus/lilac.yaml b/prepare/r-shinydashboardplus/lilac.yaml new file mode 100644 index 0000000000..b80829e7be --- /dev/null +++ b/prepare/r-shinydashboardplus/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fresh +- r-htmltools +- r-lifecycle +- r-shiny +- r-shinydashboard +- r-waiter +update_on: +- regex: shinydashboardPlus_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinydashboardPlus diff --git a/prepare/r-shinyepico/PKGBUILD b/prepare/r-shinyepico/PKGBUILD new file mode 100644 index 0000000000..edd2967e03 --- /dev/null +++ b/prepare/r-shinyepico/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinyepico +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ShinyÉPICo' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-data.table + r-doparallel + r-dplyr + r-dt + r-foreach + r-genomicranges + r-ggplot2 + r-gplots + r-heatmaply + r-limma + r-minfi + r-plotly + r-reshape2 + r-rlang + r-rmarkdown + r-rtracklayer + r-shiny + r-shinycssloaders + r-shinyjs + r-shinythemes + r-shinywidgets + r-statmod + r-tidyr + r-zip +) +optdepends=( + r-illuminahumanmethylation450kanno.ilmn12.hg19 + r-illuminahumanmethylation450kmanifest + r-illuminahumanmethylationepicanno.ilm10b4.hg19 + r-illuminahumanmethylationepicmanifest + r-knitr + r-mcsea + r-minfidata + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinyepico/lilac.py b/prepare/r-shinyepico/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinyepico/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinyepico/lilac.yaml b/prepare/r-shinyepico/lilac.yaml new file mode 100644 index 0000000000..587ac196d1 --- /dev/null +++ b/prepare/r-shinyepico/lilac.yaml @@ -0,0 +1,33 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-doparallel +- r-dplyr +- r-dt +- r-foreach +- r-genomicranges +- r-ggplot2 +- r-gplots +- r-heatmaply +- r-limma +- r-minfi +- r-plotly +- r-reshape2 +- r-rlang +- r-rmarkdown +- r-rtracklayer +- r-shiny +- r-shinycssloaders +- r-shinyjs +- r-shinythemes +- r-shinywidgets +- r-statmod +- r-tidyr +- r-zip +update_on: +- regex: shinyepico_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/shinyepico diff --git a/prepare/r-shinyfeedback/PKGBUILD b/prepare/r-shinyfeedback/PKGBUILD new file mode 100644 index 0000000000..67e5486261 --- /dev/null +++ b/prepare/r-shinyfeedback/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinyFeedback +_pkgver=0.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Display User Feedback in Shiny Apps' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-fontawesome + r-htmltools + r-jsonlite + r-shiny +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinyfeedback/lilac.py b/prepare/r-shinyfeedback/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinyfeedback/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinyfeedback/lilac.yaml b/prepare/r-shinyfeedback/lilac.yaml new file mode 100644 index 0000000000..ec68522041 --- /dev/null +++ b/prepare/r-shinyfeedback/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fontawesome +- r-htmltools +- r-jsonlite +- r-shiny +update_on: +- regex: shinyFeedback_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinyFeedback diff --git a/prepare/r-shinyfiles/PKGBUILD b/prepare/r-shinyfiles/PKGBUILD new file mode 100644 index 0000000000..adf473df9c --- /dev/null +++ b/prepare/r-shinyfiles/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinyFiles +_pkgver=0.9.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Server-Side File System Viewer for Shiny' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-fs + r-htmltools + r-jsonlite + r-shiny + r-tibble +) +optdepends=( + r-covr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinyfiles/lilac.py b/prepare/r-shinyfiles/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinyfiles/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinyfiles/lilac.yaml b/prepare/r-shinyfiles/lilac.yaml new file mode 100644 index 0000000000..182cca8e2d --- /dev/null +++ b/prepare/r-shinyfiles/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fs +- r-htmltools +- r-jsonlite +- r-shiny +- r-tibble +update_on: +- regex: shinyFiles_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinyFiles diff --git a/prepare/r-shinyheatmaply/PKGBUILD b/prepare/r-shinyheatmaply/PKGBUILD new file mode 100644 index 0000000000..521196af14 --- /dev/null +++ b/prepare/r-shinyheatmaply/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinyHeatmaply +_pkgver=0.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Deploy 'heatmaply' using 'shiny'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-heatmaply + r-htmltools + r-plotly + r-readxl + r-rmarkdown + r-shiny + r-xtable +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinyheatmaply/lilac.py b/prepare/r-shinyheatmaply/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinyheatmaply/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinyheatmaply/lilac.yaml b/prepare/r-shinyheatmaply/lilac.yaml new file mode 100644 index 0000000000..72049c0d66 --- /dev/null +++ b/prepare/r-shinyheatmaply/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-heatmaply +- r-htmltools +- r-plotly +- r-readxl +- r-rmarkdown +- r-shiny +- r-xtable +update_on: +- regex: shinyHeatmaply_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinyHeatmaply diff --git a/prepare/r-shinyhelper/PKGBUILD b/prepare/r-shinyhelper/PKGBUILD new file mode 100644 index 0000000000..d5fac6f581 --- /dev/null +++ b/prepare/r-shinyhelper/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinyhelper +_pkgver=0.3.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Easily Add Markdown Help Files to 'shiny' App Elements" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-markdown + r-shiny +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinyhelper/lilac.py b/prepare/r-shinyhelper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinyhelper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinyhelper/lilac.yaml b/prepare/r-shinyhelper/lilac.yaml new file mode 100644 index 0000000000..2fb471463a --- /dev/null +++ b/prepare/r-shinyhelper/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-markdown +- r-shiny +update_on: +- regex: shinyhelper_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinyhelper diff --git a/prepare/r-shinyjqui/PKGBUILD b/prepare/r-shinyjqui/PKGBUILD new file mode 100644 index 0000000000..cb5148b2d9 --- /dev/null +++ b/prepare/r-shinyjqui/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinyjqui +_pkgver=0.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'jQuery UI' Interactions and Effects for Shiny" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmltools + r-htmlwidgets + r-jsonlite + r-shiny +) +optdepends=( + r-ggplot2 + r-highcharter + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinyjqui/lilac.py b/prepare/r-shinyjqui/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinyjqui/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinyjqui/lilac.yaml b/prepare/r-shinyjqui/lilac.yaml new file mode 100644 index 0000000000..ab321d9d1d --- /dev/null +++ b/prepare/r-shinyjqui/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-htmlwidgets +- r-jsonlite +- r-shiny +update_on: +- regex: shinyjqui_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinyjqui diff --git a/prepare/r-shinyjs/PKGBUILD b/prepare/r-shinyjs/PKGBUILD new file mode 100644 index 0000000000..060fd340de --- /dev/null +++ b/prepare/r-shinyjs/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinyjs +_pkgver=2.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Easily Improve the User Experience of Your Shiny Apps in Seconds' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-digest + r-jsonlite + r-shiny +) +optdepends=( + r-htmltools + r-knitr + r-rmarkdown + r-shinyace + r-shinydisconnect + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinyjs/lilac.py b/prepare/r-shinyjs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinyjs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinyjs/lilac.yaml b/prepare/r-shinyjs/lilac.yaml new file mode 100644 index 0000000000..1735e061be --- /dev/null +++ b/prepare/r-shinyjs/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +- r-jsonlite +- r-shiny +update_on: +- regex: shinyjs_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinyjs diff --git a/prepare/r-shinymatrix/PKGBUILD b/prepare/r-shinymatrix/PKGBUILD new file mode 100644 index 0000000000..da02a3399b --- /dev/null +++ b/prepare/r-shinymatrix/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinyMatrix +_pkgver=0.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Shiny Matrix Input Field' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-jsonlite + r-shiny +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinymatrix/lilac.py b/prepare/r-shinymatrix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinymatrix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinymatrix/lilac.yaml b/prepare/r-shinymatrix/lilac.yaml new file mode 100644 index 0000000000..b33785677f --- /dev/null +++ b/prepare/r-shinymatrix/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-jsonlite +- r-shiny +update_on: +- regex: shinyMatrix_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinyMatrix diff --git a/prepare/r-shinymethyl/PKGBUILD b/prepare/r-shinymethyl/PKGBUILD new file mode 100644 index 0000000000..601546ddd1 --- /dev/null +++ b/prepare/r-shinymethyl/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinyMethyl +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive visualization for Illumina methylation arrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-illuminahumanmethylation450kmanifest + r-matrixstats + r-minfi + r-rcolorbrewer + r-shiny +) +optdepends=( + r-biocstyle + r-digest + r-knitr + r-minfidata + r-runit + r-shinymethyldata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinymethyl/lilac.py b/prepare/r-shinymethyl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinymethyl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinymethyl/lilac.yaml b/prepare/r-shinymethyl/lilac.yaml new file mode 100644 index 0000000000..474ec31d60 --- /dev/null +++ b/prepare/r-shinymethyl/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-illuminahumanmethylation450kmanifest +- r-matrixstats +- r-minfi +- r-rcolorbrewer +- r-shiny +update_on: +- regex: shinyMethyl_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/shinyMethyl diff --git a/prepare/r-shinypanel/PKGBUILD b/prepare/r-shinypanel/PKGBUILD new file mode 100644 index 0000000000..9279a63cc6 --- /dev/null +++ b/prepare/r-shinypanel/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinypanel +_pkgver=0.1.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Shiny Control Panel' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmltools + r-jsonlite + r-shiny + r-shinybs + r-shinyjs +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinypanel/lilac.py b/prepare/r-shinypanel/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinypanel/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinypanel/lilac.yaml b/prepare/r-shinypanel/lilac.yaml new file mode 100644 index 0000000000..d776b2f744 --- /dev/null +++ b/prepare/r-shinypanel/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-jsonlite +- r-shiny +- r-shinybs +- r-shinyjs +update_on: +- regex: shinypanel_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinypanel diff --git a/prepare/r-shinyscreenshot/PKGBUILD b/prepare/r-shinyscreenshot/PKGBUILD new file mode 100644 index 0000000000..8978b639ae --- /dev/null +++ b/prepare/r-shinyscreenshot/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinyscreenshot +_pkgver=0.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Capture Screenshots of Entire Pages or Parts of Pages in 'Shiny'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-base64enc + r-jsonlite + r-shiny + r-uuid +) +optdepends=( + r-timevis +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinyscreenshot/lilac.py b/prepare/r-shinyscreenshot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinyscreenshot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinyscreenshot/lilac.yaml b/prepare/r-shinyscreenshot/lilac.yaml new file mode 100644 index 0000000000..f841a0d110 --- /dev/null +++ b/prepare/r-shinyscreenshot/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-jsonlite +- r-shiny +- r-uuid +update_on: +- regex: shinyscreenshot_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinyscreenshot diff --git a/prepare/r-shinythemes/PKGBUILD b/prepare/r-shinythemes/PKGBUILD new file mode 100644 index 0000000000..b92c119ba0 --- /dev/null +++ b/prepare/r-shinythemes/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinythemes +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Themes for Shiny' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-shiny +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinythemes/lilac.py b/prepare/r-shinythemes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinythemes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinythemes/lilac.yaml b/prepare/r-shinythemes/lilac.yaml new file mode 100644 index 0000000000..a1769e4705 --- /dev/null +++ b/prepare/r-shinythemes/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-shiny +update_on: +- regex: shinythemes_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinythemes diff --git a/prepare/r-shinytoastr/PKGBUILD b/prepare/r-shinytoastr/PKGBUILD new file mode 100644 index 0000000000..7c1cd0571d --- /dev/null +++ b/prepare/r-shinytoastr/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinytoastr +_pkgver=2.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Notifications from 'Shiny'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-shiny +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinytoastr/lilac.py b/prepare/r-shinytoastr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinytoastr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinytoastr/lilac.yaml b/prepare/r-shinytoastr/lilac.yaml new file mode 100644 index 0000000000..ded7c7feb5 --- /dev/null +++ b/prepare/r-shinytoastr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-shiny +update_on: +- regex: shinytoastr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinytoastr diff --git a/prepare/r-shinytree/PKGBUILD b/prepare/r-shinytree/PKGBUILD new file mode 100644 index 0000000000..d6771fe697 --- /dev/null +++ b/prepare/r-shinytree/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinyTree +_pkgver=0.2.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='jsTree Bindings for Shiny' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmlwidgets + r-jsonlite + r-promises + r-shiny + r-stringr +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinytree/lilac.py b/prepare/r-shinytree/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinytree/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinytree/lilac.yaml b/prepare/r-shinytree/lilac.yaml new file mode 100644 index 0000000000..f525edc939 --- /dev/null +++ b/prepare/r-shinytree/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmlwidgets +- r-jsonlite +- r-promises +- r-shiny +- r-stringr +update_on: +- regex: shinyTree_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinyTree diff --git a/prepare/r-shinywidgets/PKGBUILD b/prepare/r-shinywidgets/PKGBUILD new file mode 100644 index 0000000000..d08dc548b9 --- /dev/null +++ b/prepare/r-shinywidgets/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=shinyWidgets +_pkgver=0.6.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Custom Inputs Widgets for Shiny' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bslib + r-htmltools + r-jsonlite + r-sass + r-shiny +) +optdepends=( + r-argondash + r-argonr + r-bs4dash + r-covr + r-dt + r-ggplot2 + r-scales + r-shinydashboard + r-shinydashboardplus + r-tablerdash + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shinywidgets/lilac.py b/prepare/r-shinywidgets/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shinywidgets/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shinywidgets/lilac.yaml b/prepare/r-shinywidgets/lilac.yaml new file mode 100644 index 0000000000..92d04a332d --- /dev/null +++ b/prepare/r-shinywidgets/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bslib +- r-htmltools +- r-jsonlite +- r-sass +- r-shiny +update_on: +- regex: shinyWidgets_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=shinyWidgets diff --git a/prepare/r-shortread/PKGBUILD b/prepare/r-shortread/PKGBUILD new file mode 100644 index 0000000000..911cba01bb --- /dev/null +++ b/prepare/r-shortread/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ShortRead +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='FASTQ input and manipulation' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-hwriter + r-iranges + r-latticeextra + r-rhtslib + r-rsamtools + r-s4vectors + r-xvector + r-zlibbioc +) +optdepends=( + r-biocstyle + r-biomart + r-genomicfeatures + r-runit + r-yeastnagalakshmi +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-shortread/lilac.py b/prepare/r-shortread/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-shortread/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-shortread/lilac.yaml b/prepare/r-shortread/lilac.yaml new file mode 100644 index 0000000000..af278fe960 --- /dev/null +++ b/prepare/r-shortread/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-hwriter +- r-iranges +- r-latticeextra +- r-rhtslib +- r-rsamtools +- r-s4vectors +- r-xvector +- r-zlibbioc +update_on: +- regex: ShortRead_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ShortRead diff --git a/prepare/r-siamcat/PKGBUILD b/prepare/r-siamcat/PKGBUILD new file mode 100644 index 0000000000..4228220e5e --- /dev/null +++ b/prepare/r-siamcat/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SIAMCAT +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Inference of Associations between Microbial Communities And host phenoTypes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-beanplot + r-corrplot + r-glmnet + r-gridbase + r-gridextra + r-infotheo + r-liblinear + r-matrixstats + r-mlr + r-paramhelpers + r-phyloseq + r-proc + r-progress + r-prroc + r-rcolorbrewer + r-scales + r-stringr +) +optdepends=( + r-biocstyle + r-ggpubr + r-knitr + r-optparse + r-rmarkdown + r-testthat + r-tidyverse +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-siamcat/lilac.py b/prepare/r-siamcat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-siamcat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-siamcat/lilac.yaml b/prepare/r-siamcat/lilac.yaml new file mode 100644 index 0000000000..2387b70284 --- /dev/null +++ b/prepare/r-siamcat/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beanplot +- r-corrplot +- r-glmnet +- r-gridbase +- r-gridextra +- r-infotheo +- r-liblinear +- r-matrixstats +- r-mlr +- r-paramhelpers +- r-phyloseq +- r-proc +- r-progress +- r-prroc +- r-rcolorbrewer +- r-scales +- r-stringr +update_on: +- regex: SIAMCAT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SIAMCAT diff --git a/prepare/r-sictools/PKGBUILD b/prepare/r-sictools/PKGBUILD new file mode 100644 index 0000000000..effbe275ab --- /dev/null +++ b/prepare/r-sictools/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SICtools +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Find SNV/Indel differences between two bam files with near relationship' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-doparallel + r-genomicranges + r-iranges + r-matrixstats + r-plyr + r-rsamtools + r-stringr +) +optdepends=( + r-biocgenerics + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sictools/lilac.py b/prepare/r-sictools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sictools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sictools/lilac.yaml b/prepare/r-sictools/lilac.yaml new file mode 100644 index 0000000000..fceda6e128 --- /dev/null +++ b/prepare/r-sictools/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-doparallel +- r-genomicranges +- r-iranges +- r-matrixstats +- r-plyr +- r-rsamtools +- r-stringr +update_on: +- regex: SICtools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SICtools diff --git a/prepare/r-sift.hsapiens.dbsnp137/PKGBUILD b/prepare/r-sift.hsapiens.dbsnp137/PKGBUILD new file mode 100644 index 0000000000..ffafe57dcc --- /dev/null +++ b/prepare/r-sift.hsapiens.dbsnp137/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SIFT.Hsapiens.dbSNP137 +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PROVEAN/SIFT Predictions for Homo sapiens dbSNP build 137' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-rsqlite + r-variantannotation +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sift.hsapiens.dbsnp137/lilac.py b/prepare/r-sift.hsapiens.dbsnp137/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sift.hsapiens.dbsnp137/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sift.hsapiens.dbsnp137/lilac.yaml b/prepare/r-sift.hsapiens.dbsnp137/lilac.yaml new file mode 100644 index 0000000000..b119c780ac --- /dev/null +++ b/prepare/r-sift.hsapiens.dbsnp137/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-rsqlite +- r-variantannotation +update_on: +- regex: SIFT.Hsapiens.dbSNP137_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SIFT.Hsapiens.dbSNP137 diff --git a/prepare/r-sigcheck/PKGBUILD b/prepare/r-sigcheck/PKGBUILD new file mode 100644 index 0000000000..70b356a058 --- /dev/null +++ b/prepare/r-sigcheck/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SigCheck +_pkgver=2.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocparallel + r-e1071 + r-mlinterfaces +) +optdepends=( + r-biocstyle + r-breastcancernki + r-qusage +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sigcheck/lilac.py b/prepare/r-sigcheck/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sigcheck/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sigcheck/lilac.yaml b/prepare/r-sigcheck/lilac.yaml new file mode 100644 index 0000000000..cb06afcf54 --- /dev/null +++ b/prepare/r-sigcheck/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocparallel +- r-e1071 +- r-mlinterfaces +update_on: +- regex: SigCheck_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SigCheck diff --git a/prepare/r-sigclust/PKGBUILD b/prepare/r-sigclust/PKGBUILD new file mode 100644 index 0000000000..84e813ff54 --- /dev/null +++ b/prepare/r-sigclust/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sigclust +_pkgver=1.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Significance of Clustering' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sigclust/lilac.py b/prepare/r-sigclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sigclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sigclust/lilac.yaml b/prepare/r-sigclust/lilac.yaml new file mode 100644 index 0000000000..1a1c0dd935 --- /dev/null +++ b/prepare/r-sigclust/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: sigclust_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sigclust diff --git a/prepare/r-sigfeature/PKGBUILD b/prepare/r-sigfeature/PKGBUILD new file mode 100644 index 0000000000..e794e14603 --- /dev/null +++ b/prepare/r-sigfeature/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sigFeature +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='sigFeature: Significant feature selection using SVM-RFE & t-statistic' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-biocviews + r-e1071 + r-openxlsx + r-pheatmap + r-rcolorbrewer + r-sparsem + r-summarizedexperiment +) +optdepends=( + r-biocgenerics + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sigfeature/lilac.py b/prepare/r-sigfeature/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sigfeature/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sigfeature/lilac.yaml b/prepare/r-sigfeature/lilac.yaml new file mode 100644 index 0000000000..b0533815b4 --- /dev/null +++ b/prepare/r-sigfeature/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-biocviews +- r-e1071 +- r-openxlsx +- r-pheatmap +- r-rcolorbrewer +- r-sparsem +- r-summarizedexperiment +update_on: +- regex: sigFeature_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sigFeature diff --git a/prepare/r-sigfuge/PKGBUILD b/prepare/r-sigfuge/PKGBUILD new file mode 100644 index 0000000000..64e9c47f37 --- /dev/null +++ b/prepare/r-sigfuge/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SigFuge +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SigFuge' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicranges + r-ggplot2 + r-matlab + r-reshape + r-sigclust +) +optdepends=( + r-biocstyle + r-org.hs.eg.db + r-prebsdata + r-rsamtools + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sigfuge/lilac.py b/prepare/r-sigfuge/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sigfuge/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sigfuge/lilac.yaml b/prepare/r-sigfuge/lilac.yaml new file mode 100644 index 0000000000..fd9f410b0d --- /dev/null +++ b/prepare/r-sigfuge/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-ggplot2 +- r-matlab +- r-reshape +- r-sigclust +update_on: +- regex: SigFuge_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SigFuge diff --git a/prepare/r-siggenes/PKGBUILD b/prepare/r-siggenes/PKGBUILD new file mode 100644 index 0000000000..0e22e28fb7 --- /dev/null +++ b/prepare/r-siggenes/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=siggenes +_pkgver=1.68.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Multiple Testing using SAM and Efron's Empirical Bayes Approaches" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-multtest + r-scrime +) +optdepends=( + r-affy + r-annotate + r-genefilter + r-kernsmooth +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-siggenes/lilac.py b/prepare/r-siggenes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-siggenes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-siggenes/lilac.yaml b/prepare/r-siggenes/lilac.yaml new file mode 100644 index 0000000000..18f93acdbb --- /dev/null +++ b/prepare/r-siggenes/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-multtest +- r-scrime +update_on: +- regex: siggenes_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/siggenes diff --git a/prepare/r-sights/PKGBUILD b/prepare/r-sights/PKGBUILD new file mode 100644 index 0000000000..215249b1a9 --- /dev/null +++ b/prepare/r-sights/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sights +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistics and dIagnostic Graphs for HTS' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-qvalue + r-reshape2 +) +optdepends=( + r-ggthemes + r-gridextra + r-knitr + r-rmarkdown + r-testthat + r-xlsx +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sights/lilac.py b/prepare/r-sights/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sights/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sights/lilac.yaml b/prepare/r-sights/lilac.yaml new file mode 100644 index 0000000000..a4870bf8fc --- /dev/null +++ b/prepare/r-sights/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-qvalue +- r-reshape2 +update_on: +- regex: sights_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sights diff --git a/prepare/r-signal/PKGBUILD b/prepare/r-signal/PKGBUILD new file mode 100644 index 0000000000..1dd6e4b8ce --- /dev/null +++ b/prepare/r-signal/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=signal +_pkgver=0.7-7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Signal Processing' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-matlab + r-pracma +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-signal/lilac.py b/prepare/r-signal/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-signal/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-signal/lilac.yaml b/prepare/r-signal/lilac.yaml new file mode 100644 index 0000000000..fb9c7da2b7 --- /dev/null +++ b/prepare/r-signal/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: signal_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=signal diff --git a/prepare/r-signaturesearch/PKGBUILD b/prepare/r-signaturesearch/PKGBUILD new file mode 100644 index 0000000000..e3adc2ea5e --- /dev/null +++ b/prepare/r-signaturesearch/PKGBUILD @@ -0,0 +1,61 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=signatureSearch +_pkgver=1.8.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Environment for Gene Expression Searching Combined with Functional Enrichment Analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biocgenerics + r-biocparallel + r-clusterprofiler + r-data.table + r-delayedarray + r-dose + r-dplyr + r-experimenthub + r-fastmatch + r-fgsea + r-ggplot2 + r-gseabase + r-hdf5array + r-magrittr + r-qvalue + r-rcpp + r-reactome.db + r-readr + r-reshape2 + r-rhdf5 + r-rsqlite + r-scales + r-summarizedexperiment + r-visnetwork +) +optdepends=( + r-biocstyle + r-dt + r-knitr + r-org.hs.eg.db + r-rmarkdown + r-signaturesearchdata + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-signaturesearch/lilac.py b/prepare/r-signaturesearch/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-signaturesearch/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-signaturesearch/lilac.yaml b/prepare/r-signaturesearch/lilac.yaml new file mode 100644 index 0000000000..5aca921cee --- /dev/null +++ b/prepare/r-signaturesearch/lilac.yaml @@ -0,0 +1,34 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-biocparallel +- r-clusterprofiler +- r-data.table +- r-delayedarray +- r-dose +- r-dplyr +- r-experimenthub +- r-fastmatch +- r-fgsea +- r-ggplot2 +- r-gseabase +- r-hdf5array +- r-magrittr +- r-qvalue +- r-rcpp +- r-reactome.db +- r-readr +- r-reshape2 +- r-rhdf5 +- r-rsqlite +- r-scales +- r-summarizedexperiment +- r-visnetwork +update_on: +- regex: signatureSearch_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/signatureSearch diff --git a/prepare/r-signer/PKGBUILD b/prepare/r-signer/PKGBUILD new file mode 100644 index 0000000000..49649679fb --- /dev/null +++ b/prepare/r-signer/PKGBUILD @@ -0,0 +1,43 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=signeR +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Empirical Bayesian approach to mutational signature discovery' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-genomeinfodb + r-genomicranges + r-iranges + r-nloptr + r-nmf + r-pmcmrplus + r-rcpp + r-rcpparmadillo + r-variantannotation +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg19 + r-knitr + r-rtracklayer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-signer/lilac.py b/prepare/r-signer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-signer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-signer/lilac.yaml b/prepare/r-signer/lilac.yaml new file mode 100644 index 0000000000..97b2b83a66 --- /dev/null +++ b/prepare/r-signer/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-nloptr +- r-nmf +- r-pmcmrplus +- r-rcpp +- r-rcpparmadillo +- r-variantannotation +update_on: +- regex: signeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/signeR diff --git a/prepare/r-sigpathway/PKGBUILD b/prepare/r-sigpathway/PKGBUILD new file mode 100644 index 0000000000..e40ca1d1a8 --- /dev/null +++ b/prepare/r-sigpathway/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sigPathway +_pkgver=1.62.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Pathway Analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-annotationdbi + r-hgu133a.db + r-xml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sigpathway/lilac.py b/prepare/r-sigpathway/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sigpathway/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sigpathway/lilac.yaml b/prepare/r-sigpathway/lilac.yaml new file mode 100644 index 0000000000..2592ead86e --- /dev/null +++ b/prepare/r-sigpathway/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: sigPathway_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sigPathway diff --git a/prepare/r-sigspack/PKGBUILD b/prepare/r-sigspack/PKGBUILD new file mode 100644 index 0000000000..9fb688bc94 --- /dev/null +++ b/prepare/r-sigspack/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SigsPack +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Mutational Signature Estimation for Single Samples' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-quadprog + r-biobase + r-bsgenome + r-variantannotation + r-biostrings + r-genomeinfodb + r-genomicranges + r-rtracklayer + r-summarizedexperiment +) +makedepends=( + git + tar +) +optdepends=( + r-iranges + r-bsgenome.hsapines.ucsc.hg19 + r-biocstyle + r-knitr + r-rmarkdown +) +source=("git+https://git.bioconductor.org/packages/${_pkgname}.git") +sha256sums=('SKIP') + +build() { + tar -zcvf ${_pkgname}.tar.gz ${_pkgname} + R CMD INSTALL ${_pkgname}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: + diff --git a/prepare/r-sigspack/lilac.py b/prepare/r-sigspack/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sigspack/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sigspack/lilac.yaml b/prepare/r-sigspack/lilac.yaml new file mode 100644 index 0000000000..ca8ade3522 --- /dev/null +++ b/prepare/r-sigspack/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-quadprog +- r-biobase +- r-bsgenome +- r-variantannotation +- r-biostrings +- r-genomeinfodb +- r-genomicranges +- r-rtracklayer +- r-summarizedexperiment +update_on: +- regex: Version(\d+.\d+.\d+) + source: regex + url: https://bioconductor.org/packages/SigsPack + diff --git a/prepare/r-sigsquared/PKGBUILD b/prepare/r-sigsquared/PKGBUILD new file mode 100644 index 0000000000..a3442f0d77 --- /dev/null +++ b/prepare/r-sigsquared/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sigsquared +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Gene signature generation for functionally validated signaling pathways' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sigsquared/lilac.py b/prepare/r-sigsquared/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sigsquared/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sigsquared/lilac.yaml b/prepare/r-sigsquared/lilac.yaml new file mode 100644 index 0000000000..08920f414d --- /dev/null +++ b/prepare/r-sigsquared/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: sigsquared_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sigsquared diff --git a/prepare/r-sim/PKGBUILD b/prepare/r-sim/PKGBUILD new file mode 100644 index 0000000000..6a60b5ca0a --- /dev/null +++ b/prepare/r-sim/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SIM +_pkgver=1.64.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Integrated Analysis on two human genomic datasets' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-globaltest + r-quantreg + r-quantsmooth +) +optdepends=( + r-biomart + r-rcolorbrewer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sim/lilac.py b/prepare/r-sim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sim/lilac.yaml b/prepare/r-sim/lilac.yaml new file mode 100644 index 0000000000..05f9d69449 --- /dev/null +++ b/prepare/r-sim/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-globaltest +- r-quantreg +- r-quantsmooth +update_on: +- regex: SIM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SIM diff --git a/prepare/r-simat/PKGBUILD b/prepare/r-simat/PKGBUILD new file mode 100644 index 0000000000..b6ac19aad7 --- /dev/null +++ b/prepare/r-simat/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SIMAT +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GC-SIM-MS data processing and alaysis tool' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-mzr + r-rcpp + r-reshape2 +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-simat/lilac.py b/prepare/r-simat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-simat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-simat/lilac.yaml b/prepare/r-simat/lilac.yaml new file mode 100644 index 0000000000..df2be73c29 --- /dev/null +++ b/prepare/r-simat/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-mzr +- r-rcpp +- r-reshape2 +update_on: +- regex: SIMAT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SIMAT diff --git a/prepare/r-simbindprofiles/PKGBUILD b/prepare/r-simbindprofiles/PKGBUILD new file mode 100644 index 0000000000..583e8c3c3d --- /dev/null +++ b/prepare/r-simbindprofiles/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SimBindProfiles +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Similar Binding Profiles' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-limma + r-mclust + r-ringo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-simbindprofiles/lilac.py b/prepare/r-simbindprofiles/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-simbindprofiles/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-simbindprofiles/lilac.yaml b/prepare/r-simbindprofiles/lilac.yaml new file mode 100644 index 0000000000..4ae3a00ae0 --- /dev/null +++ b/prepare/r-simbindprofiles/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-limma +- r-mclust +- r-ringo +update_on: +- regex: SimBindProfiles_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SimBindProfiles diff --git a/prepare/r-simd/PKGBUILD b/prepare/r-simd/PKGBUILD new file mode 100644 index 0000000000..946038c9aa --- /dev/null +++ b/prepare/r-simd/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SIMD +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-edger + r-methylmnm + r-statmod +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-simd/lilac.py b/prepare/r-simd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-simd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-simd/lilac.yaml b/prepare/r-simd/lilac.yaml new file mode 100644 index 0000000000..f6aab1e00a --- /dev/null +++ b/prepare/r-simd/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-edger +- r-methylmnm +- r-statmod +update_on: +- regex: SIMD_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SIMD diff --git a/prepare/r-simffpe/PKGBUILD b/prepare/r-simffpe/PKGBUILD new file mode 100644 index 0000000000..16109cc900 --- /dev/null +++ b/prepare/r-simffpe/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SimFFPE +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='NGS Read Simulator for FFPE Tissue' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biostrings + r-doparallel + r-dplyr + r-foreach + r-genomicranges + r-iranges + r-rsamtools + r-truncnorm +) +optdepends=( + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-simffpe/lilac.py b/prepare/r-simffpe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-simffpe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-simffpe/lilac.yaml b/prepare/r-simffpe/lilac.yaml new file mode 100644 index 0000000000..b798e341ec --- /dev/null +++ b/prepare/r-simffpe/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-doparallel +- r-dplyr +- r-foreach +- r-genomicranges +- r-iranges +- r-rsamtools +- r-truncnorm +update_on: +- regex: SimFFPE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SimFFPE diff --git a/prepare/r-similarpeak/PKGBUILD b/prepare/r-similarpeak/PKGBUILD new file mode 100644 index 0000000000..1322ecc6cb --- /dev/null +++ b/prepare/r-similarpeak/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=similaRpeak +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Metrics to estimate a level of similarity between two ChIP-Seq profiles' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-r6 +) +optdepends=( + r-biocgenerics + r-biocstyle + r-genomicalignments + r-knitr + r-rmarkdown + r-rsamtools + r-rtracklayer + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-similarpeak/lilac.py b/prepare/r-similarpeak/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-similarpeak/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-similarpeak/lilac.yaml b/prepare/r-similarpeak/lilac.yaml new file mode 100644 index 0000000000..4131b756e4 --- /dev/null +++ b/prepare/r-similarpeak/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-r6 +update_on: +- regex: similaRpeak_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/similaRpeak diff --git a/prepare/r-simlr/PKGBUILD b/prepare/r-simlr/PKGBUILD new file mode 100644 index 0000000000..7a880c54f0 --- /dev/null +++ b/prepare/r-simlr/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SIMLR +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-pracma + r-rcpp + r-rcppannoy + r-rspectra +) +optdepends=( + r-biocgenerics + r-biocstyle + r-igraph + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-simlr/lilac.py b/prepare/r-simlr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-simlr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-simlr/lilac.yaml b/prepare/r-simlr/lilac.yaml new file mode 100644 index 0000000000..0ba70e0e07 --- /dev/null +++ b/prepare/r-simlr/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-pracma +- r-rcpp +- r-rcppannoy +- r-rspectra +update_on: +- regex: SIMLR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SIMLR diff --git a/prepare/r-simpintlists/PKGBUILD b/prepare/r-simpintlists/PKGBUILD new file mode 100644 index 0000000000..3c6f2ce79a --- /dev/null +++ b/prepare/r-simpintlists/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=simpIntLists +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The package contains BioGRID interactions for various organisms in a simple format' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-simpintlists/lilac.py b/prepare/r-simpintlists/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-simpintlists/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-simpintlists/lilac.yaml b/prepare/r-simpintlists/lilac.yaml new file mode 100644 index 0000000000..93bd9a0efc --- /dev/null +++ b/prepare/r-simpintlists/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: simpIntLists_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/simpIntLists diff --git a/prepare/r-simplecache/PKGBUILD b/prepare/r-simplecache/PKGBUILD new file mode 100644 index 0000000000..726ee2b743 --- /dev/null +++ b/prepare/r-simplecache/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=simpleCache +_pkgver=0.4.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Simply Caching R Objects' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +optdepends=( + r-batchtools + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-simplecache/lilac.py b/prepare/r-simplecache/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-simplecache/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-simplecache/lilac.yaml b/prepare/r-simplecache/lilac.yaml new file mode 100644 index 0000000000..7b1dfbb0c6 --- /dev/null +++ b/prepare/r-simplecache/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: simpleCache_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=simpleCache diff --git a/prepare/r-simplifyenrichment/PKGBUILD b/prepare/r-simplifyenrichment/PKGBUILD new file mode 100644 index 0000000000..b6d2a4e083 --- /dev/null +++ b/prepare/r-simplifyenrichment/PKGBUILD @@ -0,0 +1,67 @@ +# Maintainer: Guoyi Zhang + +_pkgname=simplifyEnrichment +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Simplify Functional Enrichment Results' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-biocgenerics + r-circlize + r-clue + r-complexheatmap + r-digest + r-getoptlong + r-go.db + r-gosemsim + r-org.hs.eg.db + r-proxyc + r-slam + r-tm +) +optdepends=( + r-apcluster + r-biocmanager + r-clusterprofiler + r-cola + r-cowplot + r-dbscan + r-do.db + r-dose + r-dynamictreecut + r-flexclust + r-ggplot2 + r-gridextra + r-gridgraphics + r-hu6800.db + r-igraph + r-interactivecomplexheatmap + r-knitr + r-mcl + r-mclust + r-msigdbr + r-reactome.db + r-rmarkdown + r-shiny + r-shinydashboard + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-simplifyenrichment/lilac.py b/prepare/r-simplifyenrichment/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-simplifyenrichment/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-simplifyenrichment/lilac.yaml b/prepare/r-simplifyenrichment/lilac.yaml new file mode 100644 index 0000000000..89d564c911 --- /dev/null +++ b/prepare/r-simplifyenrichment/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-circlize +- r-clue +- r-complexheatmap +- r-digest +- r-getoptlong +- r-go.db +- r-gosemsim +- r-org.hs.eg.db +- r-proxyc +- r-slam +- r-tm +update_on: +- regex: simplifyEnrichment_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/simplifyEnrichment diff --git a/prepare/r-sincell/PKGBUILD b/prepare/r-sincell/PKGBUILD new file mode 100644 index 0000000000..eae8a23b3e --- /dev/null +++ b/prepare/r-sincell/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sincell +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-entropy + r-fastica + r-fields + r-ggplot2 + r-igraph + r-proxy + r-rcpp + r-reshape2 + r-rtsne + r-scatterplot3d + r-statmod + r-tsp +) +optdepends=( + r-biocstyle + r-biomart + r-knitr + r-monocle + r-stringr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sincell/lilac.py b/prepare/r-sincell/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sincell/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sincell/lilac.yaml b/prepare/r-sincell/lilac.yaml new file mode 100644 index 0000000000..d9950d0f38 --- /dev/null +++ b/prepare/r-sincell/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-entropy +- r-fastica +- r-fields +- r-ggplot2 +- r-igraph +- r-proxy +- r-rcpp +- r-reshape2 +- r-rtsne +- r-scatterplot3d +- r-statmod +- r-tsp +update_on: +- regex: sincell_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sincell diff --git a/prepare/r-singlecellexperiment/PKGBUILD b/prepare/r-singlecellexperiment/PKGBUILD new file mode 100644 index 0000000000..78f75b7439 --- /dev/null +++ b/prepare/r-singlecellexperiment/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SingleCellExperiment +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='S4 Classes for Single Cell Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-delayedarray + r-genomicranges + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-matrix + r-rmarkdown + r-rtsne + r-scrnaseq + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-singlecellexperiment/lilac.py b/prepare/r-singlecellexperiment/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-singlecellexperiment/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-singlecellexperiment/lilac.yaml b/prepare/r-singlecellexperiment/lilac.yaml new file mode 100644 index 0000000000..28f11c5a63 --- /dev/null +++ b/prepare/r-singlecellexperiment/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-delayedarray +- r-genomicranges +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: SingleCellExperiment_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SingleCellExperiment diff --git a/prepare/r-singlecellsignalr/PKGBUILD b/prepare/r-singlecellsignalr/PKGBUILD new file mode 100644 index 0000000000..371f82a0e9 --- /dev/null +++ b/prepare/r-singlecellsignalr/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SingleCellSignalR +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cell Signalling Using Single Cell RNAseq Data Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocmanager + r-circlize + r-data.table + r-edger + r-foreach + r-gplots + r-igraph + r-limma + r-multtest + r-pheatmap + r-rtsne + r-scran + r-simlr + r-stringr +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-singlecellsignalr/lilac.py b/prepare/r-singlecellsignalr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-singlecellsignalr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-singlecellsignalr/lilac.yaml b/prepare/r-singlecellsignalr/lilac.yaml new file mode 100644 index 0000000000..13720faac2 --- /dev/null +++ b/prepare/r-singlecellsignalr/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocmanager +- r-circlize +- r-data.table +- r-edger +- r-foreach +- r-gplots +- r-igraph +- r-limma +- r-multtest +- r-pheatmap +- r-rtsne +- r-scran +- r-simlr +- r-stringr +update_on: +- regex: SingleCellSignalR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SingleCellSignalR diff --git a/prepare/r-singlecelltk/PKGBUILD b/prepare/r-singlecelltk/PKGBUILD new file mode 100644 index 0000000000..101001a80e --- /dev/null +++ b/prepare/r-singlecelltk/PKGBUILD @@ -0,0 +1,116 @@ +# Maintainer: Guoyi Zhang + +_pkgname=singleCellTK +_pkgver=2.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-annotationdbi + r-ape + r-batchelor + r-biobase + r-biocparallel + r-celda + r-celldex + r-circlize + r-colorspace + r-colourpicker + r-complexheatmap + r-cowplot + r-data.table + r-delayedarray + r-delayedmatrixstats + r-deseq2 + r-dplyr + r-dropletutils + r-dt + r-enrichr + r-experimenthub + r-fields + r-fishpond + r-ggplot2 + r-ggplotify + r-ggrepel + r-ggtree + r-gridextra + r-gseabase + r-gsva + r-gsvadata + r-igraph + r-limma + r-magrittr + r-mast + r-matrixstats + r-metap + r-msigdbr + r-multtest + r-plotly + r-r.utils + r-rcolorbrewer + r-reshape2 + r-reticulate + r-rlang + r-rmarkdown + r-rocr + r-rtsne + r-s4vectors + r-scater + r-scdblfinder + r-scds + r-scmerge + r-scran + r-scrnaseq + r-seurat + r-shiny + r-shinyalert + r-shinycssloaders + r-shinyjs + r-singlecellexperiment + r-singler + r-summarizedexperiment + r-sva + r-tenxpbmcdata + r-tibble + r-tximport + r-vam + r-withr + r-yaml + r-zinbwave +) +optdepends=( + r-biocgenerics + r-biocstyle + r-kableextra + r-knitr + r-lintr + r-org.mm.eg.db + r-rsubread + r-shinybs + r-shinyfiles + r-shinyjqui + r-shinythemes + r-shinywidgets + r-spelling + r-stringr + r-testthat + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-singlecelltk/lilac.py b/prepare/r-singlecelltk/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-singlecelltk/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-singlecelltk/lilac.yaml b/prepare/r-singlecelltk/lilac.yaml new file mode 100644 index 0000000000..f0c882d922 --- /dev/null +++ b/prepare/r-singlecelltk/lilac.yaml @@ -0,0 +1,80 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-ape +- r-batchelor +- r-biobase +- r-biocparallel +- r-celda +- r-celldex +- r-circlize +- r-colorspace +- r-colourpicker +- r-complexheatmap +- r-cowplot +- r-data.table +- r-delayedarray +- r-delayedmatrixstats +- r-deseq2 +- r-dplyr +- r-dropletutils +- r-dt +- r-enrichr +- r-experimenthub +- r-fields +- r-fishpond +- r-ggplot2 +- r-ggplotify +- r-ggrepel +- r-ggtree +- r-gridextra +- r-gseabase +- r-gsva +- r-gsvadata +- r-igraph +- r-limma +- r-magrittr +- r-mast +- r-matrixstats +- r-metap +- r-msigdbr +- r-multtest +- r-plotly +- r-r.utils +- r-rcolorbrewer +- r-reshape2 +- r-reticulate +- r-rlang +- r-rmarkdown +- r-rocr +- r-rtsne +- r-s4vectors +- r-scater +- r-scdblfinder +- r-scds +- r-scmerge +- r-scran +- r-scrnaseq +- r-seurat +- r-shiny +- r-shinyalert +- r-shinycssloaders +- r-shinyjs +- r-singlecellexperiment +- r-singler +- r-summarizedexperiment +- r-sva +- r-tenxpbmcdata +- r-tibble +- r-tximport +- r-vam +- r-withr +- r-yaml +- r-zinbwave +update_on: +- regex: singleCellTK_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/singleCellTK diff --git a/prepare/r-singlemoleculefootprinting/PKGBUILD b/prepare/r-singlemoleculefootprinting/PKGBUILD new file mode 100644 index 0000000000..d3829cba65 --- /dev/null +++ b/prepare/r-singlemoleculefootprinting/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SingleMoleculeFootprinting +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis tools for Single Molecule Footprinting (SMF) data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-bsgenome + r-data.table + r-genomeinfodb + r-genomicranges + r-iranges + r-plyr + r-quasr + r-rcolorbrewer +) +optdepends=( + r-bsgenome.mmusculus.ucsc.mm10 + r-devtools + r-experimenthub + r-knitr + r-parallel + r-readr + r-rmarkdown + r-singlemoleculefootprintingdata + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-singlemoleculefootprinting/lilac.py b/prepare/r-singlemoleculefootprinting/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-singlemoleculefootprinting/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-singlemoleculefootprinting/lilac.yaml b/prepare/r-singlemoleculefootprinting/lilac.yaml new file mode 100644 index 0000000000..b15897241f --- /dev/null +++ b/prepare/r-singlemoleculefootprinting/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-data.table +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-plyr +- r-quasr +- r-rcolorbrewer +update_on: +- regex: SingleMoleculeFootprinting_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SingleMoleculeFootprinting diff --git a/prepare/r-singler/PKGBUILD b/prepare/r-singler/PKGBUILD new file mode 100644 index 0000000000..ca82e2e664 --- /dev/null +++ b/prepare/r-singler/PKGBUILD @@ -0,0 +1,54 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=SingleR +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Reference-Based Single-Cell RNA-Seq Annotation' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-beachmat + r-biocneighbors + r-biocparallel + r-biocsingular + r-delayedarray + r-delayedmatrixstats + r-rcpp + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocgenerics + r-biocstyle + r-celldex + r-ggplot2 + r-grdevices + r-gridextra + r-knitr + r-pheatmap + r-rmarkdown + r-scater + r-scran + r-scrnaseq + r-scuttle + r-singlecellexperiment + r-testthat + r-viridis +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-singler/lilac.py b/prepare/r-singler/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-singler/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-singler/lilac.yaml b/prepare/r-singler/lilac.yaml new file mode 100644 index 0000000000..e83ac2c31d --- /dev/null +++ b/prepare/r-singler/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-beachmat +- r-biocneighbors +- r-biocparallel +- r-biocsingular +- r-delayedarray +- r-delayedmatrixstats +- r-rcpp +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: SingleR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SingleR diff --git a/prepare/r-singscore/PKGBUILD b/prepare/r-singscore/PKGBUILD new file mode 100644 index 0000000000..1b3cfb5999 --- /dev/null +++ b/prepare/r-singscore/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=singscore +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Rank-based single-sample gene set scoring method' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocparallel + r-edger + r-ggplot2 + r-ggrepel + r-gseabase + r-magrittr + r-matrixstats + r-plotly + r-plyr + r-rcolorbrewer + r-reshape + r-reshape2 + r-s4vectors + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-hexbin + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-singscore/lilac.py b/prepare/r-singscore/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-singscore/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-singscore/lilac.yaml b/prepare/r-singscore/lilac.yaml new file mode 100644 index 0000000000..eb6209133e --- /dev/null +++ b/prepare/r-singscore/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocparallel +- r-edger +- r-ggplot2 +- r-ggrepel +- r-gseabase +- r-magrittr +- r-matrixstats +- r-plotly +- r-plyr +- r-rcolorbrewer +- r-reshape +- r-reshape2 +- r-s4vectors +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: singscore_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/singscore diff --git a/prepare/r-sispa/PKGBUILD b/prepare/r-sispa/PKGBUILD new file mode 100644 index 0000000000..d5a69d0903 --- /dev/null +++ b/prepare/r-sispa/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SISPA +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SISPA: Method for Sample Integrated Set Profile Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-changepoint + r-data.table + r-genefilter + r-ggplot2 + r-gsva + r-plyr +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sispa/lilac.py b/prepare/r-sispa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sispa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sispa/lilac.yaml b/prepare/r-sispa/lilac.yaml new file mode 100644 index 0000000000..03356b07a7 --- /dev/null +++ b/prepare/r-sispa/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-changepoint +- r-data.table +- r-genefilter +- r-ggplot2 +- r-gsva +- r-plyr +update_on: +- regex: SISPA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SISPA diff --git a/prepare/r-sitadela/PKGBUILD b/prepare/r-sitadela/PKGBUILD new file mode 100644 index 0000000000..d92fcca21b --- /dev/null +++ b/prepare/r-sitadela/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sitadela +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-biomart + r-biostrings + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-rsamtools + r-rsqlite + r-rtracklayer + r-s4vectors +) +optdepends=( + r-bsgenome + r-knitr + r-rmarkdown + r-rmysql + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sitadela/lilac.py b/prepare/r-sitadela/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sitadela/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sitadela/lilac.yaml b/prepare/r-sitadela/lilac.yaml new file mode 100644 index 0000000000..7e0a46d47c --- /dev/null +++ b/prepare/r-sitadela/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biomart +- r-biostrings +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-rsamtools +- r-rsqlite +- r-rtracklayer +- r-s4vectors +update_on: +- regex: sitadela_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sitadela diff --git a/prepare/r-sitepath/PKGBUILD b/prepare/r-sitepath/PKGBUILD new file mode 100644 index 0000000000..8e4343ad30 --- /dev/null +++ b/prepare/r-sitepath/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sitePath +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Phylogenetic pathway–dependent recognition of fixed substitutions and parallel mutations' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-ape + r-aplot + r-ggplot2 + r-ggrepel + r-ggtree + r-gridextra + r-rcolorbrewer + r-rcpp + r-seqinr + r-tidytree +) +optdepends=( + r-biocstyle + r-devtools + r-knitr + r-magick + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sitepath/lilac.py b/prepare/r-sitepath/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sitepath/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sitepath/lilac.yaml b/prepare/r-sitepath/lilac.yaml new file mode 100644 index 0000000000..c80d82c0ca --- /dev/null +++ b/prepare/r-sitepath/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-aplot +- r-ggplot2 +- r-ggrepel +- r-ggtree +- r-gridextra +- r-rcolorbrewer +- r-rcpp +- r-seqinr +- r-tidytree +update_on: +- regex: sitePath_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sitePath diff --git a/prepare/r-sitmo/PKGBUILD b/prepare/r-sitmo/PKGBUILD new file mode 100644 index 0000000000..042acb301f --- /dev/null +++ b/prepare/r-sitmo/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sitmo +_pkgver=2.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Parallel Pseudo Random Number Generator (PPRNG) 'sitmo' Header Files" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-rcpp +) +optdepends=( + r-ggplot2 + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sitmo/lilac.py b/prepare/r-sitmo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sitmo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sitmo/lilac.yaml b/prepare/r-sitmo/lilac.yaml new file mode 100644 index 0000000000..01bde30fb4 --- /dev/null +++ b/prepare/r-sitmo/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: sitmo_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sitmo diff --git a/prepare/r-sizepower/PKGBUILD b/prepare/r-sizepower/PKGBUILD new file mode 100644 index 0000000000..65c9b63dfd --- /dev/null +++ b/prepare/r-sizepower/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sizepower +_pkgver=1.64.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sample Size and Power Calculation in Micorarray Studies' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sizepower/lilac.py b/prepare/r-sizepower/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sizepower/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sizepower/lilac.yaml b/prepare/r-sizepower/lilac.yaml new file mode 100644 index 0000000000..664dfd4e28 --- /dev/null +++ b/prepare/r-sizepower/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: sizepower_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sizepower diff --git a/prepare/r-sjlabelled/PKGBUILD b/prepare/r-sjlabelled/PKGBUILD new file mode 100644 index 0000000000..451379d091 --- /dev/null +++ b/prepare/r-sjlabelled/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sjlabelled +_pkgver=1.1.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Labelled Data Utility Functions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-insight +) +optdepends=( + r-dplyr + r-haven + r-knitr + r-magrittr + r-rlang + r-rmarkdown + r-sjmisc + r-sjplot + r-snakecase + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sjlabelled/lilac.py b/prepare/r-sjlabelled/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sjlabelled/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sjlabelled/lilac.yaml b/prepare/r-sjlabelled/lilac.yaml new file mode 100644 index 0000000000..7b320a14e3 --- /dev/null +++ b/prepare/r-sjlabelled/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-insight +update_on: +- regex: sjlabelled_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sjlabelled diff --git a/prepare/r-sjmisc/PKGBUILD b/prepare/r-sjmisc/PKGBUILD new file mode 100644 index 0000000000..bc02997cd9 --- /dev/null +++ b/prepare/r-sjmisc/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sjmisc +_pkgver=2.8.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data and Variable Transformation Functions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-insight + r-magrittr + r-purrr + r-rlang + r-sjlabelled + r-tidyselect +) +optdepends=( + r-ggplot2 + r-graphics + r-haven + r-knitr + r-mice + r-nnet + r-rmarkdown + r-sjplot + r-sjstats + r-stringdist + r-testthat + r-tidyr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sjmisc/lilac.py b/prepare/r-sjmisc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sjmisc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sjmisc/lilac.yaml b/prepare/r-sjmisc/lilac.yaml new file mode 100644 index 0000000000..4e6356a885 --- /dev/null +++ b/prepare/r-sjmisc/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-insight +- r-magrittr +- r-purrr +- r-rlang +- r-sjlabelled +- r-tidyselect +update_on: +- regex: sjmisc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sjmisc diff --git a/prepare/r-skewr/PKGBUILD b/prepare/r-skewr/PKGBUILD new file mode 100644 index 0000000000..dae3dea56e --- /dev/null +++ b/prepare/r-skewr/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=skewr +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip" +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-illuminahumanmethylation450kmanifest + r-methylumi + r-minfi + r-mixsmsn + r-rcolorbrewer + r-s4vectors + r-watermelon +) +optdepends=( + r-geoquery + r-knitr + r-minfidata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-skewr/lilac.py b/prepare/r-skewr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-skewr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-skewr/lilac.yaml b/prepare/r-skewr/lilac.yaml new file mode 100644 index 0000000000..f423a93dcc --- /dev/null +++ b/prepare/r-skewr/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-illuminahumanmethylation450kmanifest +- r-methylumi +- r-minfi +- r-mixsmsn +- r-rcolorbrewer +- r-s4vectors +- r-watermelon +update_on: +- regex: skewr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/skewr diff --git a/prepare/r-skmeans/PKGBUILD b/prepare/r-skmeans/PKGBUILD new file mode 100644 index 0000000000..6467770035 --- /dev/null +++ b/prepare/r-skmeans/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=skmeans +_pkgver=0.2-14 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Spherical k-Means Clustering' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-clue + r-slam +) +optdepends=( + r-kmndirs + r-matrix +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-skmeans/lilac.py b/prepare/r-skmeans/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-skmeans/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-skmeans/lilac.yaml b/prepare/r-skmeans/lilac.yaml new file mode 100644 index 0000000000..f2e0af0ab6 --- /dev/null +++ b/prepare/r-skmeans/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clue +- r-slam +update_on: +- regex: skmeans_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=skmeans diff --git a/prepare/r-slalom/PKGBUILD b/prepare/r-slalom/PKGBUILD new file mode 100644 index 0000000000..321ba49c8e --- /dev/null +++ b/prepare/r-slalom/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=slalom +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bh + r-ggplot2 + r-gseabase + r-rcpp + r-rcpparmadillo + r-rsvd + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rhdf5 + r-rmarkdown + r-scater + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-slalom/lilac.py b/prepare/r-slalom/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-slalom/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-slalom/lilac.yaml b/prepare/r-slalom/lilac.yaml new file mode 100644 index 0000000000..56cc6ec0f6 --- /dev/null +++ b/prepare/r-slalom/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-ggplot2 +- r-gseabase +- r-rcpp +- r-rcpparmadillo +- r-rsvd +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: slalom_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/slalom diff --git a/prepare/r-slam/PKGBUILD b/prepare/r-slam/PKGBUILD new file mode 100644 index 0000000000..548ca58a3b --- /dev/null +++ b/prepare/r-slam/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=slam +_pkgver=0.1-50 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sparse Lightweight Arrays and Matrices' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-matrix + r-spam + r-sparsem +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-slam/lilac.py b/prepare/r-slam/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-slam/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-slam/lilac.yaml b/prepare/r-slam/lilac.yaml new file mode 100644 index 0000000000..783a0674f8 --- /dev/null +++ b/prepare/r-slam/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: slam_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=slam diff --git a/prepare/r-slgi/PKGBUILD b/prepare/r-slgi/PKGBUILD new file mode 100644 index 0000000000..3c9a0ef74b --- /dev/null +++ b/prepare/r-slgi/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SLGI +_pkgver=1.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Synthetic Lethal Genetic Interaction' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biobase + r-biocgenerics + r-go.db + r-scisi +) +optdepends=( + r-go.db + r-org.sc.sgd.db +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-slgi/lilac.py b/prepare/r-slgi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-slgi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-slgi/lilac.yaml b/prepare/r-slgi/lilac.yaml new file mode 100644 index 0000000000..7639a3eccf --- /dev/null +++ b/prepare/r-slgi/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-go.db +- r-scisi +update_on: +- regex: SLGI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SLGI diff --git a/prepare/r-slider/PKGBUILD b/prepare/r-slider/PKGBUILD new file mode 100644 index 0000000000..b7165088be --- /dev/null +++ b/prepare/r-slider/PKGBUILD @@ -0,0 +1,41 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=slider +_pkgver=0.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sliding Window Functions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-ellipsis + r-glue + r-rlang + r-vctrs + r-warp +) +optdepends=( + r-covr + r-dplyr + r-knitr + r-lubridate + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-slider/lilac.py b/prepare/r-slider/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-slider/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-slider/lilac.yaml b/prepare/r-slider/lilac.yaml new file mode 100644 index 0000000000..baeb913994 --- /dev/null +++ b/prepare/r-slider/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ellipsis +- r-glue +- r-rlang +- r-vctrs +- r-warp +update_on: +- regex: slider_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=slider diff --git a/prepare/r-slingshot/PKGBUILD b/prepare/r-slingshot/PKGBUILD new file mode 100644 index 0000000000..d736fc3302 --- /dev/null +++ b/prepare/r-slingshot/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=slingshot +_pkgver=2.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for ordering single-cell sequencing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-igraph + r-matrixstats + r-princurve + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-trajectoryutils +) +optdepends=( + r-biocgenerics + r-biocstyle + r-clusterexperiment + r-covr + r-knitr + r-mclust + r-mgcv + r-rcolorbrewer + r-rgl + r-rmarkdown + r-testthat + r-uwot +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-slingshot/lilac.py b/prepare/r-slingshot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-slingshot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-slingshot/lilac.yaml b/prepare/r-slingshot/lilac.yaml new file mode 100644 index 0000000000..0737cdb561 --- /dev/null +++ b/prepare/r-slingshot/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +- r-matrixstats +- r-princurve +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +- r-trajectoryutils +update_on: +- regex: slingshot_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/slingshot diff --git a/prepare/r-slinky/PKGBUILD b/prepare/r-slinky/PKGBUILD new file mode 100644 index 0000000000..b1da090bdc --- /dev/null +++ b/prepare/r-slinky/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=slinky +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Putting the fun in LINCS L1000 data analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-curl + r-dplyr + r-foreach + r-httr + r-jsonlite + r-readr + r-rhdf5 + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-biobase + r-biocstyle + r-doparallel + r-geode + r-ggplot2 + r-knitr + r-rmarkdown + r-rtsne + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-slinky/lilac.py b/prepare/r-slinky/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-slinky/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-slinky/lilac.yaml b/prepare/r-slinky/lilac.yaml new file mode 100644 index 0000000000..f18e2b61c0 --- /dev/null +++ b/prepare/r-slinky/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-dplyr +- r-foreach +- r-httr +- r-jsonlite +- r-readr +- r-rhdf5 +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: slinky_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/slinky diff --git a/prepare/r-slqpcr/PKGBUILD b/prepare/r-slqpcr/PKGBUILD new file mode 100644 index 0000000000..98430463e0 --- /dev/null +++ b/prepare/r-slqpcr/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SLqPCR +_pkgver=1.60.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-rcolorbrewer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-slqpcr/lilac.py b/prepare/r-slqpcr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-slqpcr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-slqpcr/lilac.yaml b/prepare/r-slqpcr/lilac.yaml new file mode 100644 index 0000000000..ea92c1ad95 --- /dev/null +++ b/prepare/r-slqpcr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: SLqPCR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SLqPCR diff --git a/prepare/r-sm/PKGBUILD b/prepare/r-sm/PKGBUILD new file mode 100644 index 0000000000..6a3f793963 --- /dev/null +++ b/prepare/r-sm/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sm +_pkgver=2.2-5.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Smoothing Methods for Nonparametric Regression and Density Estimation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-akima + r-gam + r-misc3d + r-rgl + r-rpanel + r-tcltk + r-tkrplot +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sm/lilac.py b/prepare/r-sm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sm/lilac.yaml b/prepare/r-sm/lilac.yaml new file mode 100644 index 0000000000..952b1f4c0f --- /dev/null +++ b/prepare/r-sm/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: sm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sm diff --git a/prepare/r-smad/PKGBUILD b/prepare/r-smad/PKGBUILD new file mode 100644 index 0000000000..fbf9370d1d --- /dev/null +++ b/prepare/r-smad/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SMAD +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Modelling of AP-MS Data (SMAD)' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-magrittr + r-rcpp + r-rcppalgos + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-smad/lilac.py b/prepare/r-smad/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-smad/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-smad/lilac.yaml b/prepare/r-smad/lilac.yaml new file mode 100644 index 0000000000..bdfac13c96 --- /dev/null +++ b/prepare/r-smad/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-magrittr +- r-rcpp +- r-rcppalgos +- r-tidyr +update_on: +- regex: SMAD_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SMAD diff --git a/prepare/r-smap/PKGBUILD b/prepare/r-smap/PKGBUILD new file mode 100644 index 0000000000..c398229af6 --- /dev/null +++ b/prepare/r-smap/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SMAP +_pkgver=1.58.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-smap/lilac.py b/prepare/r-smap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-smap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-smap/lilac.yaml b/prepare/r-smap/lilac.yaml new file mode 100644 index 0000000000..73cd266b3a --- /dev/null +++ b/prepare/r-smap/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: SMAP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SMAP diff --git a/prepare/r-smartsva/PKGBUILD b/prepare/r-smartsva/PKGBUILD new file mode 100644 index 0000000000..68257eff1d --- /dev/null +++ b/prepare/r-smartsva/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SmartSVA +_pkgver=0.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast and Robust Surrogate Variable Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-isva + r-rcpp + r-rcppeigen + r-rspectra + r-sva +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-smartsva/lilac.py b/prepare/r-smartsva/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-smartsva/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-smartsva/lilac.yaml b/prepare/r-smartsva/lilac.yaml new file mode 100644 index 0000000000..493a32454a --- /dev/null +++ b/prepare/r-smartsva/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-isva +- r-rcpp +- r-rcppeigen +- r-rspectra +- r-sva +update_on: +- regex: SmartSVA_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=SmartSVA diff --git a/prepare/r-smatr/PKGBUILD b/prepare/r-smatr/PKGBUILD new file mode 100644 index 0000000000..f7f1097316 --- /dev/null +++ b/prepare/r-smatr/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=smatr +_pkgver=3.4-8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='(Standardised) Major Axis Estimation and Testing Routines' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-smatr/lilac.py b/prepare/r-smatr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-smatr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-smatr/lilac.yaml b/prepare/r-smatr/lilac.yaml new file mode 100644 index 0000000000..4add740c85 --- /dev/null +++ b/prepare/r-smatr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: smatr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=smatr diff --git a/prepare/r-smite/PKGBUILD b/prepare/r-smite/PKGBUILD new file mode 100644 index 0000000000..247097da81 --- /dev/null +++ b/prepare/r-smite/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SMITE +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Significance-based Modules Integrating the Transcriptome and Epigenome' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biobase + r-bionet + r-genelendatabase + r-genomicranges + r-ggplot2 + r-goseq + r-hmisc + r-igraph + r-iranges + r-keggrest + r-org.hs.eg.db + r-plyr + r-reactome.db + r-s4vectors + r-scales +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-smite/lilac.py b/prepare/r-smite/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-smite/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-smite/lilac.yaml b/prepare/r-smite/lilac.yaml new file mode 100644 index 0000000000..4b10381721 --- /dev/null +++ b/prepare/r-smite/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-bionet +- r-genelendatabase +- r-genomicranges +- r-ggplot2 +- r-goseq +- r-hmisc +- r-igraph +- r-iranges +- r-keggrest +- r-org.hs.eg.db +- r-plyr +- r-reactome.db +- r-s4vectors +- r-scales +update_on: +- regex: SMITE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SMITE diff --git a/prepare/r-smoother/PKGBUILD b/prepare/r-smoother/PKGBUILD new file mode 100644 index 0000000000..0f1cdd451b --- /dev/null +++ b/prepare/r-smoother/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=smoother +_pkgver=1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions Relating to the Smoothing of Numerical Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ttr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-smoother/lilac.py b/prepare/r-smoother/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-smoother/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-smoother/lilac.yaml b/prepare/r-smoother/lilac.yaml new file mode 100644 index 0000000000..fe3efc8884 --- /dev/null +++ b/prepare/r-smoother/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ttr +update_on: +- regex: smoother_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=smoother diff --git a/prepare/r-smoothie/PKGBUILD b/prepare/r-smoothie/PKGBUILD new file mode 100644 index 0000000000..3493d83ee6 --- /dev/null +++ b/prepare/r-smoothie/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=smoothie +_pkgver=1.0-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Two-Dimensional Field Smoothing' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-fields + r-spatialvx +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-smoothie/lilac.py b/prepare/r-smoothie/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-smoothie/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-smoothie/lilac.yaml b/prepare/r-smoothie/lilac.yaml new file mode 100644 index 0000000000..9c4fe74ef3 --- /dev/null +++ b/prepare/r-smoothie/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: smoothie_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=smoothie diff --git a/prepare/r-smoothwin/PKGBUILD b/prepare/r-smoothwin/PKGBUILD new file mode 100644 index 0000000000..7b96a79031 --- /dev/null +++ b/prepare/r-smoothwin/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SmoothWin +_pkgver=3.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Soft Windowing on Linear Regression' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-rfast +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-smoothwin/lilac.py b/prepare/r-smoothwin/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-smoothwin/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-smoothwin/lilac.yaml b/prepare/r-smoothwin/lilac.yaml new file mode 100644 index 0000000000..441201de03 --- /dev/null +++ b/prepare/r-smoothwin/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rfast +update_on: +- regex: SmoothWin_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=SmoothWin diff --git a/prepare/r-smurf/PKGBUILD b/prepare/r-smurf/PKGBUILD new file mode 100644 index 0000000000..4e9c618b97 --- /dev/null +++ b/prepare/r-smurf/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=smurf +_pkgver=1.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sparse Multi-Type Regularized Feature Modeling' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-catdata + r-glmnet + r-rcolorbrewer + r-rcpp + r-rcpparmadillo + r-speedglm +) +optdepends=( + r-bookdown + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-smurf/lilac.py b/prepare/r-smurf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-smurf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-smurf/lilac.yaml b/prepare/r-smurf/lilac.yaml new file mode 100644 index 0000000000..af71d2fed1 --- /dev/null +++ b/prepare/r-smurf/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-catdata +- r-glmnet +- r-rcolorbrewer +- r-rcpp +- r-rcpparmadillo +- r-speedglm +update_on: +- regex: smurf_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=smurf diff --git a/prepare/r-smvar/PKGBUILD b/prepare/r-smvar/PKGBUILD new file mode 100644 index 0000000000..dc22e6ad51 --- /dev/null +++ b/prepare/r-smvar/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SMVar +_pkgver=1.3.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Structural Model for variances' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-smvar/lilac.py b/prepare/r-smvar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-smvar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-smvar/lilac.yaml b/prepare/r-smvar/lilac.yaml new file mode 100644 index 0000000000..430183d995 --- /dev/null +++ b/prepare/r-smvar/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: SMVar_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=SMVar diff --git a/prepare/r-sn/PKGBUILD b/prepare/r-sn/PKGBUILD new file mode 100644 index 0000000000..9d4bf0d4d7 --- /dev/null +++ b/prepare/r-sn/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sn +_pkgver=2.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The Skew-Normal and Related Distributions Such as the Skew-t and the SUN' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mnormt + r-numderiv + r-quantreg +) +optdepends=( + r-r.rsp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sn/lilac.py b/prepare/r-sn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sn/lilac.yaml b/prepare/r-sn/lilac.yaml new file mode 100644 index 0000000000..63d499e8b0 --- /dev/null +++ b/prepare/r-sn/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mnormt +- r-numderiv +- r-quantreg +update_on: +- regex: sn_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sn diff --git a/prepare/r-sna/PKGBUILD b/prepare/r-sna/PKGBUILD new file mode 100644 index 0000000000..9a899a7d44 --- /dev/null +++ b/prepare/r-sna/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sna +_pkgver=2.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Social Network Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-network + r-statnet.common +) +optdepends=( + r-numderiv + r-rgl + r-sparsem +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sna/lilac.py b/prepare/r-sna/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sna/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sna/lilac.yaml b/prepare/r-sna/lilac.yaml new file mode 100644 index 0000000000..b10584b16c --- /dev/null +++ b/prepare/r-sna/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-network +- r-statnet.common +update_on: +- regex: sna_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sna diff --git a/prepare/r-snagee/PKGBUILD b/prepare/r-snagee/PKGBUILD new file mode 100644 index 0000000000..a0fe3e8274 --- /dev/null +++ b/prepare/r-snagee/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SNAGEE +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Signal-to-Noise applied to Gene Expression Experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-snageedata +) +optdepends=( + r-all + r-hgu95av2.db + r-parallel +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-snagee/lilac.py b/prepare/r-snagee/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-snagee/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-snagee/lilac.yaml b/prepare/r-snagee/lilac.yaml new file mode 100644 index 0000000000..03c2aa29e3 --- /dev/null +++ b/prepare/r-snagee/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-snageedata +update_on: +- regex: SNAGEE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SNAGEE diff --git a/prepare/r-snageedata/PKGBUILD b/prepare/r-snageedata/PKGBUILD new file mode 100644 index 0000000000..dad260ee19 --- /dev/null +++ b/prepare/r-snageedata/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SNAGEEdata +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SNAGEE data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-all + r-hgu95av2.db + r-snagee +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-snageedata/lilac.py b/prepare/r-snageedata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-snageedata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-snageedata/lilac.yaml b/prepare/r-snageedata/lilac.yaml new file mode 100644 index 0000000000..eca66132e3 --- /dev/null +++ b/prepare/r-snageedata/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: SNAGEEdata_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SNAGEEdata diff --git a/prepare/r-snapcgh/PKGBUILD b/prepare/r-snapcgh/PKGBUILD new file mode 100644 index 0000000000..e0e626439d --- /dev/null +++ b/prepare/r-snapcgh/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=snapCGH +_pkgver=1.64.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Segmentation, normalisation and processing of aCGH data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-acgh + r-dnacopy + r-glad + r-limma + r-tilingarray +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-snapcgh/lilac.py b/prepare/r-snapcgh/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-snapcgh/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-snapcgh/lilac.yaml b/prepare/r-snapcgh/lilac.yaml new file mode 100644 index 0000000000..28b07dee57 --- /dev/null +++ b/prepare/r-snapcgh/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-acgh +- r-dnacopy +- r-glad +- r-limma +- r-tilingarray +update_on: +- regex: snapCGH_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/snapCGH diff --git a/prepare/r-snapcount/PKGBUILD b/prepare/r-snapcount/PKGBUILD new file mode 100644 index 0000000000..02407a993e --- /dev/null +++ b/prepare/r-snapcount/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=snapcount +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-assertthat + r-data.table + r-genomicranges + r-httr + r-iranges + r-jsonlite + r-magrittr + r-purrr + r-r6 + r-rlang + r-stringr + r-summarizedexperiment +) +optdepends=( + r-biocmanager + r-biocstyle + r-bit64 + r-covr + r-devtools + r-knitcitations + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-snapcount/lilac.py b/prepare/r-snapcount/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-snapcount/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-snapcount/lilac.yaml b/prepare/r-snapcount/lilac.yaml new file mode 100644 index 0000000000..dd22b510fe --- /dev/null +++ b/prepare/r-snapcount/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-data.table +- r-genomicranges +- r-httr +- r-iranges +- r-jsonlite +- r-magrittr +- r-purrr +- r-r6 +- r-rlang +- r-stringr +- r-summarizedexperiment +update_on: +- regex: snapcount_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/snapcount diff --git a/prepare/r-snifter/PKGBUILD b/prepare/r-snifter/PKGBUILD new file mode 100644 index 0000000000..591a150602 --- /dev/null +++ b/prepare/r-snifter/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=snifter +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R wrapper for the python openTSNE library' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-basilisk + r-irlba + r-reticulate +) +optdepends=( + r-biocstyle + r-ggplot2 + r-knitr + r-rmarkdown + r-scater + r-scran + r-scrnaseq + r-scuttle + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-snifter/lilac.py b/prepare/r-snifter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-snifter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-snifter/lilac.yaml b/prepare/r-snifter/lilac.yaml new file mode 100644 index 0000000000..0fac4d2e81 --- /dev/null +++ b/prepare/r-snifter/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-basilisk +- r-irlba +- r-reticulate +update_on: +- regex: snifter_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/snifter diff --git a/prepare/r-snm/PKGBUILD b/prepare/r-snm/PKGBUILD new file mode 100644 index 0000000000..b1a1d1a1a9 --- /dev/null +++ b/prepare/r-snm/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=snm +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Supervised Normalization of Microarrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-corpcor + r-lme4 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-snm/lilac.py b/prepare/r-snm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-snm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-snm/lilac.yaml b/prepare/r-snm/lilac.yaml new file mode 100644 index 0000000000..4a449355f4 --- /dev/null +++ b/prepare/r-snm/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-corpcor +- r-lme4 +update_on: +- regex: snm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/snm diff --git a/prepare/r-snowballc/PKGBUILD b/prepare/r-snowballc/PKGBUILD new file mode 100644 index 0000000000..6f26913231 --- /dev/null +++ b/prepare/r-snowballc/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SnowballC +_pkgver=0.7.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Snowball Stemmers Based on the C 'libstemmer' UTF-8 Library" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-snowballc/lilac.py b/prepare/r-snowballc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-snowballc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-snowballc/lilac.yaml b/prepare/r-snowballc/lilac.yaml new file mode 100644 index 0000000000..96c85fe1f6 --- /dev/null +++ b/prepare/r-snowballc/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: SnowballC_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=SnowballC diff --git a/prepare/r-snowfall/PKGBUILD b/prepare/r-snowfall/PKGBUILD new file mode 100644 index 0000000000..8417bb0879 --- /dev/null +++ b/prepare/r-snowfall/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=snowfall +_pkgver=1.84-6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Easier cluster computing (based on snow).' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-snow +) +optdepends=( + r-rmpi +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-snowfall/lilac.py b/prepare/r-snowfall/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-snowfall/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-snowfall/lilac.yaml b/prepare/r-snowfall/lilac.yaml new file mode 100644 index 0000000000..9e0bb83fa5 --- /dev/null +++ b/prepare/r-snowfall/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-snow +update_on: +- regex: snowfall_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=snowfall diff --git a/prepare/r-snpediar/PKGBUILD b/prepare/r-snpediar/PKGBUILD new file mode 100644 index 0000000000..1abcb1c289 --- /dev/null +++ b/prepare/r-snpediar/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SNPediaR +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Query data from SNPedia' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-jsonlite + r-rcurl +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-snpediar/lilac.py b/prepare/r-snpediar/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-snpediar/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-snpediar/lilac.yaml b/prepare/r-snpediar/lilac.yaml new file mode 100644 index 0000000000..7309e43f65 --- /dev/null +++ b/prepare/r-snpediar/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-jsonlite +- r-rcurl +update_on: +- regex: SNPediaR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SNPediaR diff --git a/prepare/r-snphood/PKGBUILD b/prepare/r-snphood/PKGBUILD new file mode 100644 index 0000000000..64b75adcbe --- /dev/null +++ b/prepare/r-snphood/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SNPhood +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-checkmate + r-data.table + r-deseq2 + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gridextra + r-iranges + r-rcolorbrewer + r-reshape2 + r-rsamtools + r-s4vectors + r-scales + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-biocstyle + r-corrplot + r-knitr + r-pryr + r-rmarkdown + r-snphooddata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-snphood/lilac.py b/prepare/r-snphood/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-snphood/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-snphood/lilac.yaml b/prepare/r-snphood/lilac.yaml new file mode 100644 index 0000000000..46000e04c4 --- /dev/null +++ b/prepare/r-snphood/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-checkmate +- r-data.table +- r-deseq2 +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-gridextra +- r-iranges +- r-rcolorbrewer +- r-reshape2 +- r-rsamtools +- r-s4vectors +- r-scales +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: SNPhood_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SNPhood diff --git a/prepare/r-snplocs.hsapiens.dbsnp144.grch37/PKGBUILD b/prepare/r-snplocs.hsapiens.dbsnp144.grch37/PKGBUILD new file mode 100644 index 0000000000..e3cfe1dcc9 --- /dev/null +++ b/prepare/r-snplocs.hsapiens.dbsnp144.grch37/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SNPlocs.Hsapiens.dbSNP144.GRCh37 +_pkgver=0.99.20 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SNP locations for Homo sapiens (dbSNP Build 144)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-bsgenome + r-genomeinfodb + r-genomicranges + r-iranges + r-s4vectors +) +optdepends=( + r-biostrings + r-bsgenome.hsapiens.ucsc.hg19 +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-snplocs.hsapiens.dbsnp144.grch37/lilac.py b/prepare/r-snplocs.hsapiens.dbsnp144.grch37/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-snplocs.hsapiens.dbsnp144.grch37/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-snplocs.hsapiens.dbsnp144.grch37/lilac.yaml b/prepare/r-snplocs.hsapiens.dbsnp144.grch37/lilac.yaml new file mode 100644 index 0000000000..157a5cf919 --- /dev/null +++ b/prepare/r-snplocs.hsapiens.dbsnp144.grch37/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-bsgenome +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-s4vectors +update_on: +- regex: SNPlocs.Hsapiens.dbSNP144.GRCh37_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37 diff --git a/prepare/r-snplocs.hsapiens.dbsnp150.grch38/PKGBUILD b/prepare/r-snplocs.hsapiens.dbsnp150.grch38/PKGBUILD new file mode 100644 index 0000000000..7238775fff --- /dev/null +++ b/prepare/r-snplocs.hsapiens.dbsnp150.grch38/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SNPlocs.Hsapiens.dbSNP150.GRCh38 +_pkgver=0.99.20 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SNP locations for Homo sapiens (dbSNP Build 150)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-bsgenome + r-genomeinfodb + r-genomicranges + r-iranges + r-s4vectors +) +optdepends=( + r-biostrings + r-bsgenome.hsapiens.ucsc.hg38 +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-snplocs.hsapiens.dbsnp150.grch38/lilac.py b/prepare/r-snplocs.hsapiens.dbsnp150.grch38/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-snplocs.hsapiens.dbsnp150.grch38/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-snplocs.hsapiens.dbsnp150.grch38/lilac.yaml b/prepare/r-snplocs.hsapiens.dbsnp150.grch38/lilac.yaml new file mode 100644 index 0000000000..7066c21fd9 --- /dev/null +++ b/prepare/r-snplocs.hsapiens.dbsnp150.grch38/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-bsgenome +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-s4vectors +update_on: +- regex: SNPlocs.Hsapiens.dbSNP150.GRCh38_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP150.GRCh38 diff --git a/prepare/r-snprelate/PKGBUILD b/prepare/r-snprelate/PKGBUILD new file mode 100644 index 0000000000..72ec0f538d --- /dev/null +++ b/prepare/r-snprelate/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SNPRelate +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-gdsfmt +) +optdepends=( + r-biocgenerics + r-knitr + r-markdown + r-mass + r-matrix + r-parallel + r-rmarkdown + r-runit + r-seqarray +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-snprelate/lilac.py b/prepare/r-snprelate/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-snprelate/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-snprelate/lilac.yaml b/prepare/r-snprelate/lilac.yaml new file mode 100644 index 0000000000..31b6aa0a46 --- /dev/null +++ b/prepare/r-snprelate/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gdsfmt +update_on: +- regex: SNPRelate_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SNPRelate diff --git a/prepare/r-snpstats/PKGBUILD b/prepare/r-snpstats/PKGBUILD new file mode 100644 index 0000000000..431aefda56 --- /dev/null +++ b/prepare/r-snpstats/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=snpStats +_pkgver=1.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SnpMatrix and XSnpMatrix classes and methods' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-zlibbioc +) +optdepends=( + r-hexbin +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-snpstats/lilac.py b/prepare/r-snpstats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-snpstats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-snpstats/lilac.yaml b/prepare/r-snpstats/lilac.yaml new file mode 100644 index 0000000000..c7680e341a --- /dev/null +++ b/prepare/r-snpstats/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-zlibbioc +update_on: +- regex: snpStats_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/snpStats diff --git a/prepare/r-softimpute/PKGBUILD b/prepare/r-softimpute/PKGBUILD new file mode 100644 index 0000000000..20a01436f9 --- /dev/null +++ b/prepare/r-softimpute/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=softImpute +_pkgver=1.4-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Matrix Completion via Iterative Soft-Thresholded SVD' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-softimpute/lilac.py b/prepare/r-softimpute/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-softimpute/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-softimpute/lilac.yaml b/prepare/r-softimpute/lilac.yaml new file mode 100644 index 0000000000..564c04d0d2 --- /dev/null +++ b/prepare/r-softimpute/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: softImpute_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=softImpute diff --git a/prepare/r-soggi/PKGBUILD b/prepare/r-soggi/PKGBUILD new file mode 100644 index 0000000000..2ee5f15487 --- /dev/null +++ b/prepare/r-soggi/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=soGGi +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-chipseq + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-preprocesscore + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-soggi/lilac.py b/prepare/r-soggi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-soggi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-soggi/lilac.yaml b/prepare/r-soggi/lilac.yaml new file mode 100644 index 0000000000..f6eddbfe45 --- /dev/null +++ b/prepare/r-soggi/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-chipseq +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-preprocesscore +- r-reshape2 +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: soGGi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/soGGi diff --git a/prepare/r-sojourner/PKGBUILD b/prepare/r-sojourner/PKGBUILD new file mode 100644 index 0000000000..5e5c0881a1 --- /dev/null +++ b/prepare/r-sojourner/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sojourner +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical analysis of single molecule trajectories' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-dplyr + r-ebimage + r-fitdistrplus + r-ggplot2 + r-gridextra + r-mclust + r-minpack.lm + r-mixtools + r-mltools + r-nls2 + r-pixmap + r-plyr + r-r.matlab + r-rcpp + r-reshape2 + r-rlang + r-sampsurf + r-scales + r-shiny + r-shinyjs + r-sp + r-truncnorm +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sojourner/lilac.py b/prepare/r-sojourner/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sojourner/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sojourner/lilac.yaml b/prepare/r-sojourner/lilac.yaml new file mode 100644 index 0000000000..6f92e6864d --- /dev/null +++ b/prepare/r-sojourner/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ebimage +- r-fitdistrplus +- r-ggplot2 +- r-gridextra +- r-mclust +- r-minpack.lm +- r-mixtools +- r-mltools +- r-nls2 +- r-pixmap +- r-plyr +- r-r.matlab +- r-rcpp +- r-reshape2 +- r-rlang +- r-sampsurf +- r-scales +- r-shiny +- r-shinyjs +- r-sp +- r-truncnorm +update_on: +- regex: sojourner_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sojourner diff --git a/prepare/r-som/PKGBUILD b/prepare/r-som/PKGBUILD new file mode 100644 index 0000000000..6c0dc648db --- /dev/null +++ b/prepare/r-som/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=som +_pkgver=0.3-5.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Self-Organizing Map' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-som/lilac.py b/prepare/r-som/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-som/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-som/lilac.yaml b/prepare/r-som/lilac.yaml new file mode 100644 index 0000000000..140e303498 --- /dev/null +++ b/prepare/r-som/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: som_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=som diff --git a/prepare/r-somaticsignatures/PKGBUILD b/prepare/r-somaticsignatures/PKGBUILD new file mode 100644 index 0000000000..822c06ee68 --- /dev/null +++ b/prepare/r-somaticsignatures/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SomaticSignatures +_pkgver=2.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Somatic Signatures' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-biostrings + r-genomeinfodb + r-genomicranges + r-ggbio + r-ggplot2 + r-iranges + r-nmf + r-pcamethods + r-proxy + r-reshape2 + r-s4vectors + r-variantannotation +) +optdepends=( + r-bsgenome.hsapiens.1000genomes.hs37d5 + r-fastica + r-ggdendro + r-knitr + r-parallel + r-somaticcanceralterations + r-sva + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-somaticsignatures/lilac.py b/prepare/r-somaticsignatures/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-somaticsignatures/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-somaticsignatures/lilac.yaml b/prepare/r-somaticsignatures/lilac.yaml new file mode 100644 index 0000000000..0a7c602995 --- /dev/null +++ b/prepare/r-somaticsignatures/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biostrings +- r-genomeinfodb +- r-genomicranges +- r-ggbio +- r-ggplot2 +- r-iranges +- r-nmf +- r-pcamethods +- r-proxy +- r-reshape2 +- r-s4vectors +- r-variantannotation +update_on: +- regex: SomaticSignatures_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SomaticSignatures diff --git a/prepare/r-sombrero/PKGBUILD b/prepare/r-sombrero/PKGBUILD new file mode 100644 index 0000000000..1305e9d171 --- /dev/null +++ b/prepare/r-sombrero/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SOMbrero +_pkgver=1.4-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SOM Bound to Realize Euclidean and Relational Outputs' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-ggwordcloud + r-igraph + r-interp + r-markdown + r-metr + r-scatterplot3d + r-shiny +) +optdepends=( + r-hexbin + r-knitr + r-rmarkdown + r-shinybs + r-shinycssloaders + r-shinyjqui + r-shinyjs + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sombrero/lilac.py b/prepare/r-sombrero/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sombrero/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sombrero/lilac.yaml b/prepare/r-sombrero/lilac.yaml new file mode 100644 index 0000000000..215eb062c9 --- /dev/null +++ b/prepare/r-sombrero/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-ggwordcloud +- r-igraph +- r-interp +- r-markdown +- r-metr +- r-scatterplot3d +- r-shiny +update_on: +- regex: SOMbrero_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=SOMbrero diff --git a/prepare/r-somnibus/PKGBUILD b/prepare/r-somnibus/PKGBUILD new file mode 100644 index 0000000000..5403f20fc8 --- /dev/null +++ b/prepare/r-somnibus/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SOMNiBUS +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Smooth modeling of bisulfite sequencing' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-vgam +) +optdepends=( + r-biocstyle + r-covr + r-devtools + r-dplyr + r-knitr + r-magick + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-somnibus/lilac.py b/prepare/r-somnibus/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-somnibus/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-somnibus/lilac.yaml b/prepare/r-somnibus/lilac.yaml new file mode 100644 index 0000000000..8bbf65f06b --- /dev/null +++ b/prepare/r-somnibus/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-vgam +update_on: +- regex: SOMNiBUS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SOMNiBUS diff --git a/prepare/r-soniclength/PKGBUILD b/prepare/r-soniclength/PKGBUILD new file mode 100644 index 0000000000..5762cf81c0 --- /dev/null +++ b/prepare/r-soniclength/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sonicLength +_pkgver=1.4.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimating Abundance of Clones from DNA Fragmentation Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-soniclength/lilac.py b/prepare/r-soniclength/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-soniclength/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-soniclength/lilac.yaml b/prepare/r-soniclength/lilac.yaml new file mode 100644 index 0000000000..fc056f7a1d --- /dev/null +++ b/prepare/r-soniclength/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: sonicLength_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sonicLength diff --git a/prepare/r-sortable/PKGBUILD b/prepare/r-sortable/PKGBUILD new file mode 100644 index 0000000000..9a3eba054b --- /dev/null +++ b/prepare/r-sortable/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sortable +_pkgver=0.4.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Drag-and-Drop in 'shiny' Apps with 'SortableJS'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-assertthat + r-ellipsis + r-htmltools + r-htmlwidgets + r-jsonlite + r-learnr + r-rlang + r-shiny +) +optdepends=( + r-base64 + r-covr + r-knitr + r-magrittr + r-rmarkdown + r-spelling + r-testthat + r-webshot + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sortable/lilac.py b/prepare/r-sortable/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sortable/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sortable/lilac.yaml b/prepare/r-sortable/lilac.yaml new file mode 100644 index 0000000000..b78fa00831 --- /dev/null +++ b/prepare/r-sortable/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-ellipsis +- r-htmltools +- r-htmlwidgets +- r-jsonlite +- r-learnr +- r-rlang +- r-shiny +update_on: +- regex: sortable_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sortable diff --git a/prepare/r-sourcetools/PKGBUILD b/prepare/r-sourcetools/PKGBUILD new file mode 100644 index 0000000000..051c0eaae5 --- /dev/null +++ b/prepare/r-sourcetools/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sourcetools +_pkgver=0.1.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Reading, Tokenizing and Parsing R Code' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sourcetools/lilac.py b/prepare/r-sourcetools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sourcetools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sourcetools/lilac.yaml b/prepare/r-sourcetools/lilac.yaml new file mode 100644 index 0000000000..fde8d41824 --- /dev/null +++ b/prepare/r-sourcetools/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: sourcetools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sourcetools diff --git a/prepare/r-sp/PKGBUILD b/prepare/r-sp/PKGBUILD new file mode 100644 index 0000000000..a359b4371a --- /dev/null +++ b/prepare/r-sp/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sp +_pkgver=1.4-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Classes and Methods for Spatial Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-deldir + r-gstat + r-knitr + r-maptools + r-rcolorbrewer + r-rgdal + r-rgeos + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sp/lilac.py b/prepare/r-sp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sp/lilac.yaml b/prepare/r-sp/lilac.yaml new file mode 100644 index 0000000000..94e3f8a10a --- /dev/null +++ b/prepare/r-sp/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: sp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sp diff --git a/prepare/r-spacepac/PKGBUILD b/prepare/r-spacepac/PKGBUILD new file mode 100644 index 0000000000..bf9502020a --- /dev/null +++ b/prepare/r-spacepac/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SpacePAC +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identification of Mutational Clusters in 3D Protein Space via Simulation.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ipac +) +optdepends=( + r-biocgenerics + r-rgl + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spacepac/lilac.py b/prepare/r-spacepac/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spacepac/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spacepac/lilac.yaml b/prepare/r-spacepac/lilac.yaml new file mode 100644 index 0000000000..d19ec9a9a2 --- /dev/null +++ b/prepare/r-spacepac/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ipac +update_on: +- regex: SpacePAC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SpacePAC diff --git a/prepare/r-spacetime/PKGBUILD b/prepare/r-spacetime/PKGBUILD new file mode 100644 index 0000000000..be75e57048 --- /dev/null +++ b/prepare/r-spacetime/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spacetime +_pkgver=1.2-5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Classes and Methods for Spatio-Temporal Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-intervals + r-sp + r-xts + r-zoo +) +optdepends=( + r-adehabitatlt + r-cshapes + r-foreign + r-googlevis + r-gstat + r-isocodes + r-knitr + r-mapdata + r-maps + r-maptools + r-markdown + r-plm + r-raster + r-rcolorbrewer + r-rgdal + r-rgeos + r-rpostgresql + r-sf +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spacetime/lilac.py b/prepare/r-spacetime/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spacetime/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spacetime/lilac.yaml b/prepare/r-spacetime/lilac.yaml new file mode 100644 index 0000000000..bf9a149c59 --- /dev/null +++ b/prepare/r-spacetime/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-intervals +- r-sp +- r-xts +- r-zoo +update_on: +- regex: spacetime_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=spacetime diff --git a/prepare/r-spam/PKGBUILD b/prepare/r-spam/PKGBUILD new file mode 100644 index 0000000000..1af45c07e1 --- /dev/null +++ b/prepare/r-spam/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spam +_pkgver=2.8-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SPArse Matrix' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-dotcall64 +) +optdepends=( + r-fields + r-knitr + r-matrix + r-r.rsp + r-rmarkdown + r-spam64 + r-testthat + r-truncdist +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spam/lilac.py b/prepare/r-spam/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spam/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spam/lilac.yaml b/prepare/r-spam/lilac.yaml new file mode 100644 index 0000000000..beda1824e8 --- /dev/null +++ b/prepare/r-spam/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dotcall64 +update_on: +- regex: spam_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=spam diff --git a/prepare/r-spaniel/PKGBUILD b/prepare/r-spaniel/PKGBUILD new file mode 100644 index 0000000000..965fef4b01 --- /dev/null +++ b/prepare/r-spaniel/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Spaniel +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Spatial Transcriptomics Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-dropletutils + r-ggplot2 + r-igraph + r-jpeg + r-jsonlite + r-magrittr + r-png + r-s4vectors + r-scater + r-scran + r-seurat + r-shiny + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-devtools + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spaniel/lilac.py b/prepare/r-spaniel/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spaniel/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spaniel/lilac.yaml b/prepare/r-spaniel/lilac.yaml new file mode 100644 index 0000000000..8371887b10 --- /dev/null +++ b/prepare/r-spaniel/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-dropletutils +- r-ggplot2 +- r-igraph +- r-jpeg +- r-jsonlite +- r-magrittr +- r-png +- r-s4vectors +- r-scater +- r-scran +- r-seurat +- r-shiny +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: Spaniel_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Spaniel diff --git a/prepare/r-sparql/PKGBUILD b/prepare/r-sparql/PKGBUILD new file mode 100644 index 0000000000..9ce67ecaba --- /dev/null +++ b/prepare/r-sparql/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SPARQL +_pkgver=1.16 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SPARQL client' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcurl + r-xml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sparql/lilac.py b/prepare/r-sparql/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sparql/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sparql/lilac.yaml b/prepare/r-sparql/lilac.yaml new file mode 100644 index 0000000000..17ea351a86 --- /dev/null +++ b/prepare/r-sparql/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcurl +- r-xml +update_on: +- regex: SPARQL_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=SPARQL diff --git a/prepare/r-sparrow/PKGBUILD b/prepare/r-sparrow/PKGBUILD new file mode 100644 index 0000000000..2225da2fd4 --- /dev/null +++ b/prepare/r-sparrow/PKGBUILD @@ -0,0 +1,71 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sparrow +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Take command of set enrichment analyses through a unified interface' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-babelgene + r-biocgenerics + r-biocparallel + r-biocset + r-checkmate + r-circlize + r-complexheatmap + r-data.table + r-delayedmatrixstats + r-edger + r-ggplot2 + r-gseabase + r-irlba + r-limma + r-plotly + r-viridis +) +optdepends=( + r-annotationdbi + r-biasedurn + r-biobase + r-biocstyle + r-deseq2 + r-dplyr + r-dtplyr + r-fgsea + r-go.db + r-goseq + r-gsva + r-hexbin + r-kernsmooth + r-knitr + r-magrittr + r-matrixstats + r-msigdbr + r-panther.db + r-r.utils + r-reactome.db + r-rmarkdown + r-statmod + r-stringr + r-summarizedexperiment + r-testthat + r-webshot +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sparrow/lilac.py b/prepare/r-sparrow/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sparrow/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sparrow/lilac.yaml b/prepare/r-sparrow/lilac.yaml new file mode 100644 index 0000000000..e8e7ab65f9 --- /dev/null +++ b/prepare/r-sparrow/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-babelgene +- r-biocgenerics +- r-biocparallel +- r-biocset +- r-checkmate +- r-circlize +- r-complexheatmap +- r-data.table +- r-delayedmatrixstats +- r-edger +- r-ggplot2 +- r-gseabase +- r-irlba +- r-limma +- r-plotly +- r-viridis +update_on: +- regex: sparrow_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sparrow diff --git a/prepare/r-sparsebn/PKGBUILD b/prepare/r-sparsebn/PKGBUILD new file mode 100644 index 0000000000..504338b6bb --- /dev/null +++ b/prepare/r-sparsebn/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sparsebn +_pkgver=0.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Learning Sparse Bayesian Networks from High-Dimensional Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ccdralgorithm + r-discretecdalgorithm + r-sparsebnutils +) +optdepends=( + r-graph + r-igraph + r-knitr + r-mvtnorm + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sparsebn/lilac.py b/prepare/r-sparsebn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sparsebn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sparsebn/lilac.yaml b/prepare/r-sparsebn/lilac.yaml new file mode 100644 index 0000000000..8eea926d86 --- /dev/null +++ b/prepare/r-sparsebn/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ccdralgorithm +- r-discretecdalgorithm +- r-sparsebnutils +update_on: +- regex: sparsebn_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sparsebn diff --git a/prepare/r-sparsebnutils/PKGBUILD b/prepare/r-sparsebnutils/PKGBUILD new file mode 100644 index 0000000000..aa1cc5c007 --- /dev/null +++ b/prepare/r-sparsebnutils/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sparsebnUtils +_pkgver=0.0.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities for Learning Sparse Bayesian Networks' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-bnlearn + r-graph + r-igraph + r-network + r-rcy3 + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sparsebnutils/lilac.py b/prepare/r-sparsebnutils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sparsebnutils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sparsebnutils/lilac.yaml b/prepare/r-sparsebnutils/lilac.yaml new file mode 100644 index 0000000000..b1b33ab6ec --- /dev/null +++ b/prepare/r-sparsebnutils/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: sparsebnUtils_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sparsebnUtils diff --git a/prepare/r-sparsedossa/PKGBUILD b/prepare/r-sparsedossa/PKGBUILD new file mode 100644 index 0000000000..1ec9496bb4 --- /dev/null +++ b/prepare/r-sparsedossa/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sparseDOSSA +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sparse Data Observations for Simulating Synthetic Abundance' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-mcmcpack + r-optparse + r-tmvtnorm +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sparsedossa/lilac.py b/prepare/r-sparsedossa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sparsedossa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sparsedossa/lilac.yaml b/prepare/r-sparsedossa/lilac.yaml new file mode 100644 index 0000000000..b417d9d478 --- /dev/null +++ b/prepare/r-sparsedossa/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mcmcpack +- r-optparse +- r-tmvtnorm +update_on: +- regex: sparseDOSSA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sparseDOSSA diff --git a/prepare/r-sparseinv/PKGBUILD b/prepare/r-sparseinv/PKGBUILD new file mode 100644 index 0000000000..65aa82120a --- /dev/null +++ b/prepare/r-sparseinv/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sparseinv +_pkgver=0.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Computation of the Sparse Inverse Subset' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-spam +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sparseinv/lilac.py b/prepare/r-sparseinv/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sparseinv/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sparseinv/lilac.yaml b/prepare/r-sparseinv/lilac.yaml new file mode 100644 index 0000000000..2f159393b2 --- /dev/null +++ b/prepare/r-sparseinv/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-spam +update_on: +- regex: sparseinv_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sparseinv diff --git a/prepare/r-sparsem/PKGBUILD b/prepare/r-sparsem/PKGBUILD new file mode 100644 index 0000000000..a005e0b3c5 --- /dev/null +++ b/prepare/r-sparsem/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SparseM +_pkgver=1.81 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sparse Linear Algebra' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sparsem/lilac.py b/prepare/r-sparsem/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sparsem/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sparsem/lilac.yaml b/prepare/r-sparsem/lilac.yaml new file mode 100644 index 0000000000..88dfcdac17 --- /dev/null +++ b/prepare/r-sparsem/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: SparseM_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=SparseM diff --git a/prepare/r-sparsematrixstats/PKGBUILD b/prepare/r-sparsematrixstats/PKGBUILD new file mode 100644 index 0000000000..f104a8f2c6 --- /dev/null +++ b/prepare/r-sparsematrixstats/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sparseMatrixStats +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Summary Statistics for Rows and Columns of Sparse Matrices' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-matrixgenerics + r-matrixstats + r-rcpp +) +optdepends=( + r-bench + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sparsematrixstats/lilac.py b/prepare/r-sparsematrixstats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sparsematrixstats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sparsematrixstats/lilac.yaml b/prepare/r-sparsematrixstats/lilac.yaml new file mode 100644 index 0000000000..b3a7d6ab17 --- /dev/null +++ b/prepare/r-sparsematrixstats/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-matrixgenerics +- r-matrixstats +- r-rcpp +update_on: +- regex: sparseMatrixStats_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sparseMatrixStats diff --git a/prepare/r-sparsemvn/PKGBUILD b/prepare/r-sparsemvn/PKGBUILD new file mode 100644 index 0000000000..2cc23ef2ec --- /dev/null +++ b/prepare/r-sparsemvn/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sparseMVN +_pkgver=0.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multivariate Normal Functions for Sparse Covariance and Precision Matrices' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MPL2') +depends=( + r +) +optdepends=( + r-bookdown + r-dplyr + r-forcats + r-ggplot2 + r-kableextra + r-knitr + r-mvtnorm + r-scales + r-testthat + r-tidyr + r-trustoptim +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sparsemvn/lilac.py b/prepare/r-sparsemvn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sparsemvn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sparsemvn/lilac.yaml b/prepare/r-sparsemvn/lilac.yaml new file mode 100644 index 0000000000..a9a695eaab --- /dev/null +++ b/prepare/r-sparsemvn/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: sparseMVN_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sparseMVN diff --git a/prepare/r-sparsenetgls/PKGBUILD b/prepare/r-sparsenetgls/PKGBUILD new file mode 100644 index 0000000000..84f82c6549 --- /dev/null +++ b/prepare/r-sparsenetgls/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=sparsenetgls +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-glmnet + r-huge +) +optdepends=( + r-biocstyle + r-knitr + r-lme4 + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sparsenetgls/lilac.py b/prepare/r-sparsenetgls/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sparsenetgls/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sparsenetgls/lilac.yaml b/prepare/r-sparsenetgls/lilac.yaml new file mode 100644 index 0000000000..bf7d1f2809 --- /dev/null +++ b/prepare/r-sparsenetgls/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-glmnet +- r-huge +update_on: +- regex: sparsenetgls_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sparsenetgls diff --git a/prepare/r-sparsepca/PKGBUILD b/prepare/r-sparsepca/PKGBUILD new file mode 100644 index 0000000000..7e94399258 --- /dev/null +++ b/prepare/r-sparsepca/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sparsepca +_pkgver=0.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sparse Principal Component Analysis (SPCA)' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rsvd +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sparsepca/lilac.py b/prepare/r-sparsepca/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sparsepca/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sparsepca/lilac.yaml b/prepare/r-sparsepca/lilac.yaml new file mode 100644 index 0000000000..38512634f1 --- /dev/null +++ b/prepare/r-sparsepca/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rsvd +update_on: +- regex: sparsepca_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sparsepca diff --git a/prepare/r-sparsesignatures/PKGBUILD b/prepare/r-sparsesignatures/PKGBUILD new file mode 100644 index 0000000000..c05c1941dd --- /dev/null +++ b/prepare/r-sparsesignatures/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SparseSignatures +_pkgver=2.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SparseSignatures' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-biostrings + r-bsgenome + r-data.table + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gridextra + r-iranges + r-nmf + r-nnlasso + r-nnls + r-reshape2 +) +optdepends=( + r-biocgenerics + r-biocstyle + r-bsgenome.hsapiens.1000genomes.hs37d5 + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sparsesignatures/lilac.py b/prepare/r-sparsesignatures/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sparsesignatures/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sparsesignatures/lilac.yaml b/prepare/r-sparsesignatures/lilac.yaml new file mode 100644 index 0000000000..622f4925a2 --- /dev/null +++ b/prepare/r-sparsesignatures/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome +- r-data.table +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-gridextra +- r-iranges +- r-nmf +- r-nnlasso +- r-nnls +- r-reshape2 +update_on: +- regex: SparseSignatures_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SparseSignatures diff --git a/prepare/r-sparsesvd/PKGBUILD b/prepare/r-sparsesvd/PKGBUILD new file mode 100644 index 0000000000..7184607504 --- /dev/null +++ b/prepare/r-sparsesvd/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sparsesvd +_pkgver=0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Sparse Truncated Singular Value Decomposition (from 'SVDLIBC')" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sparsesvd/lilac.py b/prepare/r-sparsesvd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sparsesvd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sparsesvd/lilac.yaml b/prepare/r-sparsesvd/lilac.yaml new file mode 100644 index 0000000000..60220565da --- /dev/null +++ b/prepare/r-sparsesvd/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: sparsesvd_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sparsesvd diff --git a/prepare/r-spatest/PKGBUILD b/prepare/r-spatest/PKGBUILD new file mode 100644 index 0000000000..72a1c7dca6 --- /dev/null +++ b/prepare/r-spatest/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SPAtest +_pkgver=3.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Score Test and Meta-Analysis Based on Saddlepoint Approximation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spatest/lilac.py b/prepare/r-spatest/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spatest/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spatest/lilac.yaml b/prepare/r-spatest/lilac.yaml new file mode 100644 index 0000000000..304fec711e --- /dev/null +++ b/prepare/r-spatest/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: SPAtest_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=SPAtest diff --git a/prepare/r-spatialcpie/PKGBUILD b/prepare/r-spatialcpie/PKGBUILD new file mode 100644 index 0000000000..a3da1f5ee8 --- /dev/null +++ b/prepare/r-spatialcpie/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SpatialCPie +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cluster analysis of Spatial Transcriptomics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-colorspace + r-data.table + r-digest + r-dplyr + r-ggforce + r-ggiraph + r-ggplot2 + r-ggrepel + r-igraph + r-lpsolve + r-purrr + r-readr + r-rlang + r-shiny + r-shinycssloaders + r-shinyjs + r-shinywidgets + r-summarizedexperiment + r-tibble + r-tidyr + r-tidyselect + r-zeallot +) +optdepends=( + r-biocstyle + r-jpeg + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spatialcpie/lilac.py b/prepare/r-spatialcpie/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spatialcpie/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spatialcpie/lilac.yaml b/prepare/r-spatialcpie/lilac.yaml new file mode 100644 index 0000000000..74f348e6df --- /dev/null +++ b/prepare/r-spatialcpie/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colorspace +- r-data.table +- r-digest +- r-dplyr +- r-ggforce +- r-ggiraph +- r-ggplot2 +- r-ggrepel +- r-igraph +- r-lpsolve +- r-purrr +- r-readr +- r-rlang +- r-shiny +- r-shinycssloaders +- r-shinyjs +- r-shinywidgets +- r-summarizedexperiment +- r-tibble +- r-tidyr +- r-tidyselect +- r-zeallot +update_on: +- regex: SpatialCPie_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SpatialCPie diff --git a/prepare/r-spatialde/PKGBUILD b/prepare/r-spatialde/PKGBUILD new file mode 100644 index 0000000000..80dce4994d --- /dev/null +++ b/prepare/r-spatialde/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spatialDE +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R wrapper for SpatialDE' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-basilisk + r-checkmate + r-ggplot2 + r-ggrepel + r-gridextra + r-reticulate + r-s4vectors + r-scales + r-spatialexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spatialde/lilac.py b/prepare/r-spatialde/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spatialde/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spatialde/lilac.yaml b/prepare/r-spatialde/lilac.yaml new file mode 100644 index 0000000000..2a71613fc0 --- /dev/null +++ b/prepare/r-spatialde/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-basilisk +- r-checkmate +- r-ggplot2 +- r-ggrepel +- r-gridextra +- r-reticulate +- r-s4vectors +- r-scales +- r-spatialexperiment +- r-summarizedexperiment +update_on: +- regex: spatialDE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/spatialDE diff --git a/prepare/r-spatialdecon/PKGBUILD b/prepare/r-spatialdecon/PKGBUILD new file mode 100644 index 0000000000..bdc60c5e7f --- /dev/null +++ b/prepare/r-spatialdecon/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SpatialDecon +_pkgver=1.4.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Deconvolution of mixed cells from spatial and/or bulk gene expression data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-geomxtools + r-repmis + r-seuratobject +) +optdepends=( + r-knitr + r-qpdf + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spatialdecon/lilac.py b/prepare/r-spatialdecon/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spatialdecon/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spatialdecon/lilac.yaml b/prepare/r-spatialdecon/lilac.yaml new file mode 100644 index 0000000000..bef68b8405 --- /dev/null +++ b/prepare/r-spatialdecon/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-geomxtools +- r-repmis +- r-seuratobject +update_on: +- regex: SpatialDecon_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SpatialDecon diff --git a/prepare/r-spatialexperiment/PKGBUILD b/prepare/r-spatialexperiment/PKGBUILD new file mode 100644 index 0000000000..a3f9feff96 --- /dev/null +++ b/prepare/r-spatialexperiment/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SpatialExperiment +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='S4 Class for Spatial Experiments handling' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocfilecache + r-biocgenerics + r-dropletutils + r-magick + r-rjson + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-bumpymatrix + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spatialexperiment/lilac.py b/prepare/r-spatialexperiment/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spatialexperiment/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spatialexperiment/lilac.yaml b/prepare/r-spatialexperiment/lilac.yaml new file mode 100644 index 0000000000..a513557027 --- /dev/null +++ b/prepare/r-spatialexperiment/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-biocgenerics +- r-dropletutils +- r-magick +- r-rjson +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: SpatialExperiment_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SpatialExperiment diff --git a/prepare/r-spatialextremes/PKGBUILD b/prepare/r-spatialextremes/PKGBUILD new file mode 100644 index 0000000000..ea80dbd83f --- /dev/null +++ b/prepare/r-spatialextremes/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SpatialExtremes +_pkgver=2.0-9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Modelling Spatial Extremes' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-fields + r-maps +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spatialextremes/lilac.py b/prepare/r-spatialextremes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spatialextremes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spatialextremes/lilac.yaml b/prepare/r-spatialextremes/lilac.yaml new file mode 100644 index 0000000000..5407cdce82 --- /dev/null +++ b/prepare/r-spatialextremes/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-fields +- r-maps +update_on: +- regex: SpatialExtremes_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=SpatialExtremes diff --git a/prepare/r-spatialheatmap/PKGBUILD b/prepare/r-spatialheatmap/PKGBUILD new file mode 100644 index 0000000000..e0f07c6c99 --- /dev/null +++ b/prepare/r-spatialheatmap/PKGBUILD @@ -0,0 +1,79 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spatialHeatmap +_pkgver=2.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='spatialHeatmap' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-av + r-biocfilecache + r-data.table + r-deseq2 + r-distinct + r-dynamictreecut + r-edger + r-flashclust + r-genefilter + r-ggdendro + r-ggplot2 + r-ggplotify + r-gplots + r-gridextra + r-grimport + r-hdf5array + r-htmlwidgets + r-igraph + r-limma + r-magick + r-plotly + r-rappdirs + r-reshape2 + r-rols + r-rsvg + r-s4vectors + r-shiny + r-shinydashboard + r-summarizedexperiment + r-upsetr + r-visnetwork + r-wgcna + r-xml2 + r-yaml +) +optdepends=( + r-biobase + r-biocgenerics + r-biocsingular + r-biocstyle + r-dt + r-expressionatlas + r-geoquery + r-htmltools + r-knitr + r-rmarkdown + r-runit + r-scater + r-scran + r-shinybs + r-shinyjs + r-shinywidgets + r-sortable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spatialheatmap/lilac.py b/prepare/r-spatialheatmap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spatialheatmap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spatialheatmap/lilac.yaml b/prepare/r-spatialheatmap/lilac.yaml new file mode 100644 index 0000000000..1543a10056 --- /dev/null +++ b/prepare/r-spatialheatmap/lilac.yaml @@ -0,0 +1,43 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-av +- r-biocfilecache +- r-data.table +- r-deseq2 +- r-distinct +- r-dynamictreecut +- r-edger +- r-flashclust +- r-genefilter +- r-ggdendro +- r-ggplot2 +- r-ggplotify +- r-gplots +- r-gridextra +- r-grimport +- r-hdf5array +- r-htmlwidgets +- r-igraph +- r-limma +- r-magick +- r-plotly +- r-rappdirs +- r-reshape2 +- r-rols +- r-rsvg +- r-s4vectors +- r-shiny +- r-shinydashboard +- r-summarizedexperiment +- r-upsetr +- r-visnetwork +- r-wgcna +- r-xml2 +- r-yaml +update_on: +- regex: spatialHeatmap_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/spatialHeatmap diff --git a/prepare/r-spatialtools/PKGBUILD b/prepare/r-spatialtools/PKGBUILD new file mode 100644 index 0000000000..625b42787a --- /dev/null +++ b/prepare/r-spatialtools/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SpatialTools +_pkgver=1.0.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Spatial Data Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcpparmadillo + r-spbayes +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spatialtools/lilac.py b/prepare/r-spatialtools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spatialtools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spatialtools/lilac.yaml b/prepare/r-spatialtools/lilac.yaml new file mode 100644 index 0000000000..3dad4de766 --- /dev/null +++ b/prepare/r-spatialtools/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcpparmadillo +- r-spbayes +update_on: +- regex: SpatialTools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=SpatialTools diff --git a/prepare/r-spatstat.core/PKGBUILD b/prepare/r-spatstat.core/PKGBUILD new file mode 100644 index 0000000000..0ef322aa5f --- /dev/null +++ b/prepare/r-spatstat.core/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spatstat.core +_pkgver=2.3-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Core Functionality of the 'spatstat' Family" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-goftest + r-spatstat.data + r-spatstat.geom + r-spatstat.sparse + r-spatstat.utils + r-tensor +) +optdepends=( + r-fftwtools + r-gsl + r-locfit + r-maptools + r-nleqslv + r-randomfields + r-randomfieldsutils + r-sm + r-spatial + r-spatstat + r-spatstat.linnet +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spatstat.core/lilac.py b/prepare/r-spatstat.core/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spatstat.core/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spatstat.core/lilac.yaml b/prepare/r-spatstat.core/lilac.yaml new file mode 100644 index 0000000000..4cfd3a29c8 --- /dev/null +++ b/prepare/r-spatstat.core/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-goftest +- r-spatstat.data +- r-spatstat.geom +- r-spatstat.sparse +- r-spatstat.utils +- r-tensor +update_on: +- regex: spatstat.core_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=spatstat.core diff --git a/prepare/r-spatstat.data/PKGBUILD b/prepare/r-spatstat.data/PKGBUILD new file mode 100644 index 0000000000..a34168725a --- /dev/null +++ b/prepare/r-spatstat.data/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spatstat.data +_pkgver=2.1-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Datasets for 'spatstat' Family" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-spatstat.utils +) +optdepends=( + r-spatstat.core + r-spatstat.geom + r-spatstat.linnet +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spatstat.data/lilac.py b/prepare/r-spatstat.data/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spatstat.data/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spatstat.data/lilac.yaml b/prepare/r-spatstat.data/lilac.yaml new file mode 100644 index 0000000000..aee346cf02 --- /dev/null +++ b/prepare/r-spatstat.data/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-spatstat.utils +update_on: +- regex: spatstat.data_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=spatstat.data diff --git a/prepare/r-spatstat.geom/PKGBUILD b/prepare/r-spatstat.geom/PKGBUILD new file mode 100644 index 0000000000..04c50cebed --- /dev/null +++ b/prepare/r-spatstat.geom/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spatstat.geom +_pkgver=2.3-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Geometrical Functionality of the 'spatstat' Family" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-deldir + r-polyclip + r-spatstat.data + r-spatstat.utils +) +optdepends=( + r-fftwtools + r-maptools + r-spatial + r-spatstat + r-spatstat.core + r-spatstat.linnet +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spatstat.geom/lilac.py b/prepare/r-spatstat.geom/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spatstat.geom/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spatstat.geom/lilac.yaml b/prepare/r-spatstat.geom/lilac.yaml new file mode 100644 index 0000000000..fe11f59a62 --- /dev/null +++ b/prepare/r-spatstat.geom/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-deldir +- r-polyclip +- r-spatstat.data +- r-spatstat.utils +update_on: +- regex: spatstat.geom_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=spatstat.geom diff --git a/prepare/r-spatstat.linnet/PKGBUILD b/prepare/r-spatstat.linnet/PKGBUILD new file mode 100644 index 0000000000..147de1b0c5 --- /dev/null +++ b/prepare/r-spatstat.linnet/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spatstat.linnet +_pkgver=2.3-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Linear Networks Functionality of the 'spatstat' Family" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-spatstat.core + r-spatstat.data + r-spatstat.geom + r-spatstat.sparse + r-spatstat.utils +) +optdepends=( + r-goftest + r-locfit + r-spatstat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spatstat.linnet/lilac.py b/prepare/r-spatstat.linnet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spatstat.linnet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spatstat.linnet/lilac.yaml b/prepare/r-spatstat.linnet/lilac.yaml new file mode 100644 index 0000000000..6facaf426c --- /dev/null +++ b/prepare/r-spatstat.linnet/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-spatstat.core +- r-spatstat.data +- r-spatstat.geom +- r-spatstat.sparse +- r-spatstat.utils +update_on: +- regex: spatstat.linnet_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=spatstat.linnet diff --git a/prepare/r-spatstat.sparse/PKGBUILD b/prepare/r-spatstat.sparse/PKGBUILD new file mode 100644 index 0000000000..ceff6a60eb --- /dev/null +++ b/prepare/r-spatstat.sparse/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spatstat.sparse +_pkgver=2.1-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sparse Three-Dimensional Arrays and Linear Algebra Utilities' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-abind + r-spatstat.utils + r-tensor +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spatstat.sparse/lilac.py b/prepare/r-spatstat.sparse/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spatstat.sparse/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spatstat.sparse/lilac.yaml b/prepare/r-spatstat.sparse/lilac.yaml new file mode 100644 index 0000000000..653968a287 --- /dev/null +++ b/prepare/r-spatstat.sparse/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-abind +- r-spatstat.utils +- r-tensor +update_on: +- regex: spatstat.sparse_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=spatstat.sparse diff --git a/prepare/r-spatstat.utils/PKGBUILD b/prepare/r-spatstat.utils/PKGBUILD new file mode 100644 index 0000000000..6378d189a2 --- /dev/null +++ b/prepare/r-spatstat.utils/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spatstat.utils +_pkgver=2.3-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Utility Functions for 'spatstat'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-spatstat.core +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spatstat.utils/lilac.py b/prepare/r-spatstat.utils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spatstat.utils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spatstat.utils/lilac.yaml b/prepare/r-spatstat.utils/lilac.yaml new file mode 100644 index 0000000000..7ec1edb7b6 --- /dev/null +++ b/prepare/r-spatstat.utils/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: spatstat.utils_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=spatstat.utils diff --git a/prepare/r-spatstat/PKGBUILD b/prepare/r-spatstat/PKGBUILD new file mode 100644 index 0000000000..4d301be9a6 --- /dev/null +++ b/prepare/r-spatstat/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spatstat +_pkgver=2.3-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-spatstat.core + r-spatstat.data + r-spatstat.geom + r-spatstat.linnet + r-spatstat.utils +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spatstat/lilac.py b/prepare/r-spatstat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spatstat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spatstat/lilac.yaml b/prepare/r-spatstat/lilac.yaml new file mode 100644 index 0000000000..ef127cc670 --- /dev/null +++ b/prepare/r-spatstat/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-spatstat.core +- r-spatstat.data +- r-spatstat.geom +- r-spatstat.linnet +- r-spatstat.utils +update_on: +- regex: spatstat_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=spatstat diff --git a/prepare/r-spatzie/PKGBUILD b/prepare/r-spatzie/PKGBUILD new file mode 100644 index 0000000000..4961b86282 --- /dev/null +++ b/prepare/r-spatzie/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spatzie +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identification of enriched motif pairs from chromatin interaction data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-bsgenome + r-genomeinfodb + r-genomicfeatures + r-genomicinteractions + r-genomicranges + r-ggplot2 + r-iranges + r-matrixstats + r-motifmatchr + r-s4vectors + r-summarizedexperiment + r-tfbstools +) +optdepends=( + r-biocmanager + r-biostrings + r-knitr + r-pheatmap + r-rmarkdown + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.hsapiens.ucsc.hg38.knowngene + r-txdb.mmusculus.ucsc.mm10.knowngene + r-txdb.mmusculus.ucsc.mm9.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spatzie/lilac.py b/prepare/r-spatzie/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spatzie/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spatzie/lilac.yaml b/prepare/r-spatzie/lilac.yaml new file mode 100644 index 0000000000..6ef4f70b52 --- /dev/null +++ b/prepare/r-spatzie/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-bsgenome +- r-genomeinfodb +- r-genomicfeatures +- r-genomicinteractions +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-matrixstats +- r-motifmatchr +- r-s4vectors +- r-summarizedexperiment +- r-tfbstools +update_on: +- regex: spatzie_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/spatzie diff --git a/prepare/r-spbayes/PKGBUILD b/prepare/r-spbayes/PKGBUILD new file mode 100644 index 0000000000..deb942a3b3 --- /dev/null +++ b/prepare/r-spbayes/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spBayes +_pkgver=0.4-5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Univariate and Multivariate Spatial-Temporal Modeling' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-coda + r-formula + r-magic + r-sp +) +optdepends=( + r-geor + r-mba +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spbayes/lilac.py b/prepare/r-spbayes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spbayes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spbayes/lilac.yaml b/prepare/r-spbayes/lilac.yaml new file mode 100644 index 0000000000..67bf78da5a --- /dev/null +++ b/prepare/r-spbayes/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-coda +- r-formula +- r-magic +- r-sp +update_on: +- regex: spBayes_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=spBayes diff --git a/prepare/r-speaq/PKGBUILD b/prepare/r-speaq/PKGBUILD new file mode 100644 index 0000000000..5fef5646a4 --- /dev/null +++ b/prepare/r-speaq/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=speaq +_pkgver=2.6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment, Peak Based Processing, Quantitative Analysis and Visualizations' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-data.table + r-dosnow + r-foreach + r-ggplot2 + r-gridextra + r-impute + r-massspecwavelet + r-missforest + r-mqtl + r-reshape2 + r-rfast + r-rvest + r-xml2 +) +optdepends=( + r-datasets + r-grid + r-gridbase + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-speaq/lilac.py b/prepare/r-speaq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-speaq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-speaq/lilac.yaml b/prepare/r-speaq/lilac.yaml new file mode 100644 index 0000000000..f9ded594e5 --- /dev/null +++ b/prepare/r-speaq/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-dosnow +- r-foreach +- r-ggplot2 +- r-gridextra +- r-impute +- r-massspecwavelet +- r-missforest +- r-mqtl +- r-reshape2 +- r-rfast +- r-rvest +- r-xml2 +update_on: +- regex: speaq_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=speaq diff --git a/prepare/r-specl/PKGBUILD b/prepare/r-specl/PKGBUILD new file mode 100644 index 0000000000..fc2fceeda6 --- /dev/null +++ b/prepare/r-specl/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=specL +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dbi + r-protviz + r-rsqlite + r-seqinr +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-specl/lilac.py b/prepare/r-specl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-specl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-specl/lilac.yaml b/prepare/r-specl/lilac.yaml new file mode 100644 index 0000000000..dc33d6657c --- /dev/null +++ b/prepare/r-specl/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dbi +- r-protviz +- r-rsqlite +- r-seqinr +update_on: +- regex: specL_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/specL diff --git a/prepare/r-specond/PKGBUILD b/prepare/r-specond/PKGBUILD new file mode 100644 index 0000000000..7f94bd80db --- /dev/null +++ b/prepare/r-specond/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SpeCond +_pkgver=1.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Condition specific detection from expression data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-fields + r-hwriter + r-mclust + r-rcolorbrewer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-specond/lilac.py b/prepare/r-specond/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-specond/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-specond/lilac.yaml b/prepare/r-specond/lilac.yaml new file mode 100644 index 0000000000..bc8d4041a2 --- /dev/null +++ b/prepare/r-specond/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-fields +- r-hwriter +- r-mclust +- r-rcolorbrewer +update_on: +- regex: SpeCond_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SpeCond diff --git a/prepare/r-spectra/PKGBUILD b/prepare/r-spectra/PKGBUILD new file mode 100644 index 0000000000..72a30f08f1 --- /dev/null +++ b/prepare/r-spectra/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Spectra +_pkgver=1.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Spectra Infrastructure for Mass Spectrometry Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biocparallel + r-fs + r-iranges + r-mscoreutils + r-protgenerics + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-magrittr + r-msdata + r-mzr + r-rhdf5 + r-rmarkdown + r-roxygen2 + r-testthat + r-vdiffr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spectra/lilac.py b/prepare/r-spectra/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spectra/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spectra/lilac.yaml b/prepare/r-spectra/lilac.yaml new file mode 100644 index 0000000000..54becb5ab5 --- /dev/null +++ b/prepare/r-spectra/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-fs +- r-iranges +- r-mscoreutils +- r-protgenerics +- r-s4vectors +update_on: +- regex: Spectra_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Spectra diff --git a/prepare/r-spectraltad/PKGBUILD b/prepare/r-spectraltad/PKGBUILD new file mode 100644 index 0000000000..714ff33e67 --- /dev/null +++ b/prepare/r-spectraltad/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SpectralTAD +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SpectralTAD: Hierarchical TAD detection using spectral clustering' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocparallel + r-dplyr + r-genomicranges + r-hiccompare + r-magrittr + r-primme +) +optdepends=( + r-bioccheck + r-biocmanager + r-biocstyle + r-covr + r-knitr + r-microbenchmark + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spectraltad/lilac.py b/prepare/r-spectraltad/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spectraltad/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spectraltad/lilac.yaml b/prepare/r-spectraltad/lilac.yaml new file mode 100644 index 0000000000..2e84a3da8f --- /dev/null +++ b/prepare/r-spectraltad/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-dplyr +- r-genomicranges +- r-hiccompare +- r-magrittr +- r-primme +update_on: +- regex: SpectralTAD_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SpectralTAD diff --git a/prepare/r-speedglm/PKGBUILD b/prepare/r-speedglm/PKGBUILD new file mode 100644 index 0000000000..b97154cee8 --- /dev/null +++ b/prepare/r-speedglm/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=speedglm +_pkgver=0.3-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fitting Linear and Generalized Linear Models to Large Data Sets' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-speedglm/lilac.py b/prepare/r-speedglm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-speedglm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-speedglm/lilac.yaml b/prepare/r-speedglm/lilac.yaml new file mode 100644 index 0000000000..2f0e197145 --- /dev/null +++ b/prepare/r-speedglm/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: speedglm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=speedglm diff --git a/prepare/r-spem/PKGBUILD b/prepare/r-spem/PKGBUILD new file mode 100644 index 0000000000..971cdb548c --- /dev/null +++ b/prepare/r-spem/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SPEM +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='S-system parameter estimation method' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-rsolnp +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spem/lilac.py b/prepare/r-spem/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spem/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spem/lilac.yaml b/prepare/r-spem/lilac.yaml new file mode 100644 index 0000000000..7487620e1f --- /dev/null +++ b/prepare/r-spem/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-rsolnp +update_on: +- regex: SPEM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SPEM diff --git a/prepare/r-spia/PKGBUILD b/prepare/r-spia/PKGBUILD new file mode 100644 index 0000000000..c0c25fa9ab --- /dev/null +++ b/prepare/r-spia/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SPIA +_pkgver=2.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-kegggraph +) +optdepends=( + r-graph + r-hgu133plus2.db + r-rgraphviz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spia/lilac.py b/prepare/r-spia/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spia/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spia/lilac.yaml b/prepare/r-spia/lilac.yaml new file mode 100644 index 0000000000..01de0caa94 --- /dev/null +++ b/prepare/r-spia/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-kegggraph +update_on: +- regex: SPIA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SPIA diff --git a/prepare/r-spicyr/PKGBUILD b/prepare/r-spicyr/PKGBUILD new file mode 100644 index 0000000000..21b8ece2ff --- /dev/null +++ b/prepare/r-spicyr/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spicyR +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Spatial analysis of in situ cytometry data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-concaveman + r-data.table + r-dplyr + r-ggplot2 + r-iranges + r-lme4 + r-lmertest + r-pheatmap + r-rlang + r-s4vectors + r-scam + r-spatstat.core + r-spatstat.geom + r-tidyr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spicyr/lilac.py b/prepare/r-spicyr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spicyr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spicyr/lilac.yaml b/prepare/r-spicyr/lilac.yaml new file mode 100644 index 0000000000..04b52bfe7e --- /dev/null +++ b/prepare/r-spicyr/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-concaveman +- r-data.table +- r-dplyr +- r-ggplot2 +- r-iranges +- r-lme4 +- r-lmertest +- r-pheatmap +- r-rlang +- r-s4vectors +- r-scam +- r-spatstat.core +- r-spatstat.geom +- r-tidyr +update_on: +- regex: spicyR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/spicyR diff --git a/prepare/r-spidermir/PKGBUILD b/prepare/r-spidermir/PKGBUILD new file mode 100644 index 0000000000..3c73d12461 --- /dev/null +++ b/prepare/r-spidermir/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SpidermiR +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-gdata + r-ggplot2 + r-gplots + r-gridextra + r-httr + r-igraph + r-latticeextra + r-mageckflute + r-mirnatap + r-mirnatap.db + r-org.hs.eg.db + r-tcgabiolinks +) +optdepends=( + r-biocstyle + r-devtools + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spidermir/lilac.py b/prepare/r-spidermir/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spidermir/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spidermir/lilac.yaml b/prepare/r-spidermir/lilac.yaml new file mode 100644 index 0000000000..fafdf69db7 --- /dev/null +++ b/prepare/r-spidermir/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-gdata +- r-ggplot2 +- r-gplots +- r-gridextra +- r-httr +- r-igraph +- r-latticeextra +- r-mageckflute +- r-mirnatap +- r-mirnatap.db +- r-org.hs.eg.db +- r-tcgabiolinks +update_on: +- regex: SpidermiR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SpidermiR diff --git a/prepare/r-spikeli/PKGBUILD b/prepare/r-spikeli/PKGBUILD new file mode 100644 index 0000000000..140dddf46b --- /dev/null +++ b/prepare/r-spikeli/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spikeLI +_pkgver=2.54.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spikeli/lilac.py b/prepare/r-spikeli/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spikeli/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spikeli/lilac.yaml b/prepare/r-spikeli/lilac.yaml new file mode 100644 index 0000000000..7eae143f9e --- /dev/null +++ b/prepare/r-spikeli/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: spikeLI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/spikeLI diff --git a/prepare/r-spiky/PKGBUILD b/prepare/r-spiky/PKGBUILD new file mode 100644 index 0000000000..571fd89e85 --- /dev/null +++ b/prepare/r-spiky/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spiky +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Spike-in calibration for cell-free MeDIP' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bamlss + r-biostrings + r-blandaltmanleh + r-bsgenome + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-rsamtools + r-s4vectors + r-scales +) +optdepends=( + r-biocmanager + r-bsgenome.hsapiens.ucsc.hg38.masked + r-bsgenome.mmusculus.ucsc.mm10.masked + r-complexheatmap + r-covr + r-devtools + r-equatiomatic + r-kebabs + r-knitr + r-markdown + r-rmarkdown + r-testthat + r-universalmotif +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spiky/lilac.py b/prepare/r-spiky/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spiky/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spiky/lilac.yaml b/prepare/r-spiky/lilac.yaml new file mode 100644 index 0000000000..eef697905d --- /dev/null +++ b/prepare/r-spiky/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bamlss +- r-biostrings +- r-blandaltmanleh +- r-bsgenome +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-rsamtools +- r-s4vectors +- r-scales +update_on: +- regex: spiky_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/spiky diff --git a/prepare/r-spktools/PKGBUILD b/prepare/r-spktools/PKGBUILD new file mode 100644 index 0000000000..f5d8cac66e --- /dev/null +++ b/prepare/r-spktools/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spkTools +_pkgver=1.50.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Methods for Spike-in Arrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-gtools + r-rcolorbrewer +) +optdepends=( + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spktools/lilac.py b/prepare/r-spktools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spktools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spktools/lilac.yaml b/prepare/r-spktools/lilac.yaml new file mode 100644 index 0000000000..a156745ff9 --- /dev/null +++ b/prepare/r-spktools/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-gtools +- r-rcolorbrewer +update_on: +- regex: spkTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/spkTools diff --git a/prepare/r-splancs/PKGBUILD b/prepare/r-splancs/PKGBUILD new file mode 100644 index 0000000000..24274bb666 --- /dev/null +++ b/prepare/r-splancs/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=splancs +_pkgver=2.01-42 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Spatial and Space-Time Point Pattern Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-sp +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-splancs/lilac.py b/prepare/r-splancs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-splancs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-splancs/lilac.yaml b/prepare/r-splancs/lilac.yaml new file mode 100644 index 0000000000..12e92c3682 --- /dev/null +++ b/prepare/r-splancs/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-sp +update_on: +- regex: splancs_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=splancs diff --git a/prepare/r-splatter/PKGBUILD b/prepare/r-splatter/PKGBUILD new file mode 100644 index 0000000000..e812b92151 --- /dev/null +++ b/prepare/r-splatter/PKGBUILD @@ -0,0 +1,71 @@ +# Maintainer: Guoyi Zhang + +_pkgname=splatter +_pkgver=1.18.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Simple Simulation of Single-cell RNA Sequencing Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-checkmate + r-crayon + r-edger + r-fitdistrplus + r-ggplot2 + r-locfit + r-matrixstats + r-s4vectors + r-scales + r-scater + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-basics + r-biocmanager + r-biocsingular + r-biocstyle + r-biostrings + r-covr + r-cowplot + r-genomeinfodb + r-genomicranges + r-igraph + r-iranges + r-knitr + r-limsolve + r-lme4 + r-magick + r-mfa + r-phenopath + r-preprocesscore + r-progress + r-pscl + r-rmarkdown + r-scdd + r-scran + r-scuttle + r-sparsedc + r-spelling + r-testthat + r-variantannotation + r-zinbwave +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-splatter/lilac.py b/prepare/r-splatter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-splatter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-splatter/lilac.yaml b/prepare/r-splatter/lilac.yaml new file mode 100644 index 0000000000..4209ee2336 --- /dev/null +++ b/prepare/r-splatter/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-checkmate +- r-crayon +- r-edger +- r-fitdistrplus +- r-ggplot2 +- r-locfit +- r-matrixstats +- r-s4vectors +- r-scales +- r-scater +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: splatter_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/splatter diff --git a/prepare/r-splicingfactory/PKGBUILD b/prepare/r-splicingfactory/PKGBUILD new file mode 100644 index 0000000000..8c1ddfefa1 --- /dev/null +++ b/prepare/r-splicingfactory/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SplicingFactory +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Splicing Diversity Analysis for Transcriptome Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-summarizedexperiment +) +optdepends=( + r-ggplot2 + r-knitr + r-rmarkdown + r-testthat + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-splicingfactory/lilac.py b/prepare/r-splicingfactory/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-splicingfactory/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-splicingfactory/lilac.yaml b/prepare/r-splicingfactory/lilac.yaml new file mode 100644 index 0000000000..ad01d77270 --- /dev/null +++ b/prepare/r-splicingfactory/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-summarizedexperiment +update_on: +- regex: SplicingFactory_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SplicingFactory diff --git a/prepare/r-splicinggraphs/PKGBUILD b/prepare/r-splicinggraphs/PKGBUILD new file mode 100644 index 0000000000..14afd69e65 --- /dev/null +++ b/prepare/r-splicinggraphs/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SplicingGraphs +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-graph + r-igraph + r-iranges + r-rgraphviz + r-rsamtools + r-s4vectors +) +optdepends=( + r-gviz + r-igraph + r-rnaseqdata.hnrnpc.bam.chr14 + r-runit + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-splicinggraphs/lilac.py b/prepare/r-splicinggraphs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-splicinggraphs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-splicinggraphs/lilac.yaml b/prepare/r-splicinggraphs/lilac.yaml new file mode 100644 index 0000000000..74cda19892 --- /dev/null +++ b/prepare/r-splicinggraphs/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-graph +- r-igraph +- r-iranges +- r-rgraphviz +- r-rsamtools +- r-s4vectors +update_on: +- regex: SplicingGraphs_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SplicingGraphs diff --git a/prepare/r-splines2/PKGBUILD b/prepare/r-splines2/PKGBUILD new file mode 100644 index 0000000000..50db0b07a4 --- /dev/null +++ b/prepare/r-splines2/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=splines2 +_pkgver=0.4.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Regression Spline Functions and Classes' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcpparmadillo +) +optdepends=( + r-knitr + r-rmarkdown + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-splines2/lilac.py b/prepare/r-splines2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-splines2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-splines2/lilac.yaml b/prepare/r-splines2/lilac.yaml new file mode 100644 index 0000000000..045a9d72c0 --- /dev/null +++ b/prepare/r-splines2/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcpparmadillo +update_on: +- regex: splines2_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=splines2 diff --git a/prepare/r-splinetimer/PKGBUILD b/prepare/r-splinetimer/PKGBUILD new file mode 100644 index 0000000000..ec076961d9 --- /dev/null +++ b/prepare/r-splinetimer/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=splineTimeR +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-fis + r-genenet + r-gseabase + r-gtools + r-igraph + r-limma + r-longitudinal +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-splinetimer/lilac.py b/prepare/r-splinetimer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-splinetimer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-splinetimer/lilac.yaml b/prepare/r-splinetimer/lilac.yaml new file mode 100644 index 0000000000..ec1547a434 --- /dev/null +++ b/prepare/r-splinetimer/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-fis +- r-genenet +- r-gseabase +- r-gtools +- r-igraph +- r-limma +- r-longitudinal +update_on: +- regex: splineTimeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/splineTimeR diff --git a/prepare/r-splinter/PKGBUILD b/prepare/r-splinter/PKGBUILD new file mode 100644 index 0000000000..441761bec7 --- /dev/null +++ b/prepare/r-splinter/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SPLINTER +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Splice Interpreter of Transcripts' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-biostrings + r-bsgenome.mmusculus.ucsc.mm9 + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-googlevis + r-gviz + r-iranges + r-plyr + r-s4vectors + r-seqlogo + r-stringr +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-splinter/lilac.py b/prepare/r-splinter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-splinter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-splinter/lilac.yaml b/prepare/r-splinter/lilac.yaml new file mode 100644 index 0000000000..5504c23ecf --- /dev/null +++ b/prepare/r-splinter/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-biostrings +- r-bsgenome.mmusculus.ucsc.mm9 +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-googlevis +- r-gviz +- r-iranges +- r-plyr +- r-s4vectors +- r-seqlogo +- r-stringr +update_on: +- regex: SPLINTER_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SPLINTER diff --git a/prepare/r-splitstackshape/PKGBUILD b/prepare/r-splitstackshape/PKGBUILD new file mode 100644 index 0000000000..f385fd5ae7 --- /dev/null +++ b/prepare/r-splitstackshape/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=splitstackshape +_pkgver=1.4.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Stack and Reshape Datasets After Splitting Concatenated Values' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-data.table +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-splitstackshape/lilac.py b/prepare/r-splitstackshape/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-splitstackshape/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-splitstackshape/lilac.yaml b/prepare/r-splitstackshape/lilac.yaml new file mode 100644 index 0000000000..e03b5ab673 --- /dev/null +++ b/prepare/r-splitstackshape/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +update_on: +- regex: splitstackshape_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=splitstackshape diff --git a/prepare/r-splots/PKGBUILD b/prepare/r-splots/PKGBUILD new file mode 100644 index 0000000000..6ff1cd81be --- /dev/null +++ b/prepare/r-splots/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=splots +_pkgver=1.60.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization of high-throughput assays in microtitre plate or slide format' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-rcolorbrewer +) +optdepends=( + r-assertthat + r-biocstyle + r-hd2013sgi + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-splots/lilac.py b/prepare/r-splots/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-splots/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-splots/lilac.yaml b/prepare/r-splots/lilac.yaml new file mode 100644 index 0000000000..7a296e7d4d --- /dev/null +++ b/prepare/r-splots/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcolorbrewer +update_on: +- regex: splots_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/splots diff --git a/prepare/r-splus2r/PKGBUILD b/prepare/r-splus2r/PKGBUILD new file mode 100644 index 0000000000..26535d83cf --- /dev/null +++ b/prepare/r-splus2r/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=splus2R +_pkgver=1.3-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Supplemental S-PLUS Functionality in R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-splus2r/lilac.py b/prepare/r-splus2r/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-splus2r/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-splus2r/lilac.yaml b/prepare/r-splus2r/lilac.yaml new file mode 100644 index 0000000000..9910a123ce --- /dev/null +++ b/prepare/r-splus2r/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: splus2R_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=splus2R diff --git a/prepare/r-sponge/PKGBUILD b/prepare/r-sponge/PKGBUILD new file mode 100644 index 0000000000..b68d329081 --- /dev/null +++ b/prepare/r-sponge/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SPONGE +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sparse Partial Correlations On Gene Expression' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-data.table + r-dorng + r-expm + r-foreach + r-glmnet + r-grbase + r-igraph + r-iterators + r-logging + r-ppcor +) +optdepends=( + r-bigmemory + r-digest + r-doparallel + r-ggplot2 + r-ggrepel + r-gridextra + r-knitr + r-rmarkdown + r-testthat + r-visnetwork +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sponge/lilac.py b/prepare/r-sponge/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sponge/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sponge/lilac.yaml b/prepare/r-sponge/lilac.yaml new file mode 100644 index 0000000000..1d6e4856a2 --- /dev/null +++ b/prepare/r-sponge/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-data.table +- r-dorng +- r-expm +- r-foreach +- r-glmnet +- r-grbase +- r-igraph +- r-iterators +- r-logging +- r-ppcor +update_on: +- regex: SPONGE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SPONGE diff --git a/prepare/r-spp/PKGBUILD b/prepare/r-spp/PKGBUILD new file mode 100644 index 0000000000..7dfc60530b --- /dev/null +++ b/prepare/r-spp/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spp +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ChIP-Seq Processing Pipeline' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bh + r-catools + r-rcpp + r-rsamtools +) +optdepends=( + r-methods +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spp/lilac.py b/prepare/r-spp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spp/lilac.yaml b/prepare/r-spp/lilac.yaml new file mode 100644 index 0000000000..2b6528bd53 --- /dev/null +++ b/prepare/r-spp/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-catools +- r-rcpp +- r-rsamtools +update_on: +- regex: spp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=spp diff --git a/prepare/r-spqn/PKGBUILD b/prepare/r-spqn/PKGBUILD new file mode 100644 index 0000000000..2ed4e5e741 --- /dev/null +++ b/prepare/r-spqn/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spqn +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Spatial quantile normalization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-ggplot2 + r-ggridges + r-matrixstats + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-runit + r-spqndata + r-tools +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spqn/lilac.py b/prepare/r-spqn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spqn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spqn/lilac.yaml b/prepare/r-spqn/lilac.yaml new file mode 100644 index 0000000000..687f0523f2 --- /dev/null +++ b/prepare/r-spqn/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-ggplot2 +- r-ggridges +- r-matrixstats +- r-summarizedexperiment +update_on: +- regex: spqn_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/spqn diff --git a/prepare/r-spscomps/PKGBUILD b/prepare/r-spscomps/PKGBUILD new file mode 100644 index 0000000000..da4177c86c --- /dev/null +++ b/prepare/r-spscomps/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spsComps +_pkgver=0.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'systemPipeShiny' UI and Server Components" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-crayon + r-glue + r-htmltools + r-magrittr + r-r6 + r-shiny + r-shinyace + r-shinytoastr + r-stringr +) +optdepends=( + r-shinyjqui + r-spsutil + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spscomps/lilac.py b/prepare/r-spscomps/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spscomps/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spscomps/lilac.yaml b/prepare/r-spscomps/lilac.yaml new file mode 100644 index 0000000000..f6d43ed8b3 --- /dev/null +++ b/prepare/r-spscomps/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-crayon +- r-glue +- r-htmltools +- r-magrittr +- r-r6 +- r-shiny +- r-shinyace +- r-shinytoastr +- r-stringr +update_on: +- regex: spsComps_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=spsComps diff --git a/prepare/r-spsimseq/PKGBUILD b/prepare/r-spsimseq/PKGBUILD new file mode 100644 index 0000000000..a9e9b6c4b8 --- /dev/null +++ b/prepare/r-spsimseq/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SPsimSeq +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Semi-parametric simulation tool for bulk and single-cell RNA sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-edger + r-fitdistrplus + r-hmisc + r-limma + r-mvtnorm + r-phyloseq + r-singlecellexperiment + r-wgcna +) +optdepends=( + r-biocstyle + r-knitr + r-lsd + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spsimseq/lilac.py b/prepare/r-spsimseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spsimseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spsimseq/lilac.yaml b/prepare/r-spsimseq/lilac.yaml new file mode 100644 index 0000000000..64e0fdefb4 --- /dev/null +++ b/prepare/r-spsimseq/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-edger +- r-fitdistrplus +- r-hmisc +- r-limma +- r-mvtnorm +- r-phyloseq +- r-singlecellexperiment +- r-wgcna +update_on: +- regex: SPsimSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SPsimSeq diff --git a/prepare/r-spsutil/PKGBUILD b/prepare/r-spsutil/PKGBUILD new file mode 100644 index 0000000000..229d377647 --- /dev/null +++ b/prepare/r-spsutil/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=spsUtil +_pkgver=0.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'systemPipeShiny' Utility Functions" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-crayon + r-glue + r-httr + r-magrittr + r-r6 + r-stringr +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-spsutil/lilac.py b/prepare/r-spsutil/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-spsutil/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-spsutil/lilac.yaml b/prepare/r-spsutil/lilac.yaml new file mode 100644 index 0000000000..8befaca8d8 --- /dev/null +++ b/prepare/r-spsutil/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-crayon +- r-glue +- r-httr +- r-magrittr +- r-r6 +- r-stringr +update_on: +- regex: spsUtil_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=spsUtil diff --git a/prepare/r-sqldataframe/PKGBUILD b/prepare/r-sqldataframe/PKGBUILD new file mode 100644 index 0000000000..d8f577419a --- /dev/null +++ b/prepare/r-sqldataframe/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SQLDataFrame +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Representation of SQL database in DataFrame metaphor' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-dbi + r-dbplyr + r-dplyr + r-lazyeval + r-rsqlite + r-s4vectors + r-tibble +) +optdepends=( + r-bigrquery + r-delayedarray + r-knitr + r-rmarkdown + r-rmysql + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sqldataframe/lilac.py b/prepare/r-sqldataframe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sqldataframe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sqldataframe/lilac.yaml b/prepare/r-sqldataframe/lilac.yaml new file mode 100644 index 0000000000..dba191f71a --- /dev/null +++ b/prepare/r-sqldataframe/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-dbi +- r-dbplyr +- r-dplyr +- r-lazyeval +- r-rsqlite +- r-s4vectors +- r-tibble +update_on: +- regex: SQLDataFrame_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SQLDataFrame diff --git a/prepare/r-sqldf/PKGBUILD b/prepare/r-sqldf/PKGBUILD new file mode 100644 index 0000000000..26a8694893 --- /dev/null +++ b/prepare/r-sqldf/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sqldf +_pkgver=0.4-11 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Manipulate R Data Frames Using SQL' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-chron + r-dbi + r-gsubfn + r-proto + r-rsqlite +) +optdepends=( + r-mass + r-rh2 + r-rmysql + r-rpostgresql + r-svunit + r-tcltk +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sqldf/lilac.py b/prepare/r-sqldf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sqldf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sqldf/lilac.yaml b/prepare/r-sqldf/lilac.yaml new file mode 100644 index 0000000000..1e3da998c2 --- /dev/null +++ b/prepare/r-sqldf/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-chron +- r-dbi +- r-gsubfn +- r-proto +- r-rsqlite +update_on: +- regex: sqldf_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sqldf diff --git a/prepare/r-squadd/PKGBUILD b/prepare/r-squadd/PKGBUILD new file mode 100644 index 0000000000..55488553f2 --- /dev/null +++ b/prepare/r-squadd/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SQUADD +_pkgver=1.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Add-on of the SQUAD Software' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rcolorbrewer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-squadd/lilac.py b/prepare/r-squadd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-squadd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-squadd/lilac.yaml b/prepare/r-squadd/lilac.yaml new file mode 100644 index 0000000000..86bd36cf14 --- /dev/null +++ b/prepare/r-squadd/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcolorbrewer +update_on: +- regex: SQUADD_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SQUADD diff --git a/prepare/r-squarem/PKGBUILD b/prepare/r-squarem/PKGBUILD new file mode 100644 index 0000000000..09e95d0152 --- /dev/null +++ b/prepare/r-squarem/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SQUAREM +_pkgver=2021.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-setrng +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-squarem/lilac.py b/prepare/r-squarem/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-squarem/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-squarem/lilac.yaml b/prepare/r-squarem/lilac.yaml new file mode 100644 index 0000000000..023129dde0 --- /dev/null +++ b/prepare/r-squarem/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: SQUAREM_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=SQUAREM diff --git a/prepare/r-squash/PKGBUILD b/prepare/r-squash/PKGBUILD new file mode 100644 index 0000000000..6cb847b70a --- /dev/null +++ b/prepare/r-squash/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=squash +_pkgver=1.0.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Color-Based Plots for Multivariate Visualization' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-squash/lilac.py b/prepare/r-squash/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-squash/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-squash/lilac.yaml b/prepare/r-squash/lilac.yaml new file mode 100644 index 0000000000..d137c87cb2 --- /dev/null +++ b/prepare/r-squash/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: squash_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=squash diff --git a/prepare/r-sracipe/PKGBUILD b/prepare/r-sracipe/PKGBUILD new file mode 100644 index 0000000000..7a180c9601 --- /dev/null +++ b/prepare/r-sracipe/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sRACIPE +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Systems biology tool to simulate gene regulatory circuits' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-ggplot2 + r-gplots + r-gridextra + r-htmlwidgets + r-rcolorbrewer + r-rcpp + r-reshape2 + r-s4vectors + r-summarizedexperiment + r-umap + r-visnetwork +) +optdepends=( + r-biocstyle + r-dofuture + r-knitr + r-rmarkdown + r-tinytest +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sracipe/lilac.py b/prepare/r-sracipe/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sracipe/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sracipe/lilac.yaml b/prepare/r-sracipe/lilac.yaml new file mode 100644 index 0000000000..64bc442b9e --- /dev/null +++ b/prepare/r-sracipe/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-ggplot2 +- r-gplots +- r-gridextra +- r-htmlwidgets +- r-rcolorbrewer +- r-rcpp +- r-reshape2 +- r-s4vectors +- r-summarizedexperiment +- r-umap +- r-visnetwork +update_on: +- regex: sRACIPE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sRACIPE diff --git a/prepare/r-sradb/PKGBUILD b/prepare/r-sradb/PKGBUILD new file mode 100644 index 0000000000..62fa5ee08a --- /dev/null +++ b/prepare/r-sradb/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SRAdb +_pkgver=1.56.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A compilation of metadata from NCBI SRA and tools' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-geoquery + r-graph + r-rcurl + r-rsqlite +) +optdepends=( + r-rgraphviz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sradb/lilac.py b/prepare/r-sradb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sradb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sradb/lilac.yaml b/prepare/r-sradb/lilac.yaml new file mode 100644 index 0000000000..bdee9e226e --- /dev/null +++ b/prepare/r-sradb/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-geoquery +- r-graph +- r-rcurl +- r-rsqlite +update_on: +- regex: SRAdb_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SRAdb diff --git a/prepare/r-srgnet/PKGBUILD b/prepare/r-srgnet/PKGBUILD new file mode 100644 index 0000000000..e76dec0f00 --- /dev/null +++ b/prepare/r-srgnet/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SRGnet +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package for studying synergistic response to gene mutations from transcriptomics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ebcoexpress + r-mass + r-igraph + r-pvclust + r-gdm + r-limma + r-matrixstats + r-hmisc +) +makedepends=( + git + tar +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("git+https://git.bioconductor.org/packages/${_pkgname}.git") +sha256sums=('SKIP') + +build() { + tar -zcvf ${_pkgname}.tar.gz ${_pkgname} + R CMD INSTALL ${_pkgname}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: + diff --git a/prepare/r-srgnet/lilac.py b/prepare/r-srgnet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-srgnet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-srgnet/lilac.yaml b/prepare/r-srgnet/lilac.yaml new file mode 100644 index 0000000000..e5e1680fe5 --- /dev/null +++ b/prepare/r-srgnet/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ebcoexpress +- r-mass +- r-igraph +- r-pvclust +- r-gdm +- r-limma +- r-matrixstats +- r-hmisc +update_on: +- regex: Version(\d+.\d+.\d+) + source: regex + url: https://bioconductor.org/packages/SRGnet diff --git a/prepare/r-srnadiff/PKGBUILD b/prepare/r-srnadiff/PKGBUILD new file mode 100644 index 0000000000..a8bcde2019 --- /dev/null +++ b/prepare/r-srnadiff/PKGBUILD @@ -0,0 +1,52 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=srnadiff +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Finding differentially expressed unannotated genomic regions from RNA-seq data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bayseq + r-biocmanager + r-biocparallel + r-biocstyle + r-deseq2 + r-devtools + r-edger + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-gviz + r-iranges + r-rcpp + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocmanager + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-srnadiff/lilac.py b/prepare/r-srnadiff/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-srnadiff/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-srnadiff/lilac.yaml b/prepare/r-srnadiff/lilac.yaml new file mode 100644 index 0000000000..75b0e81e62 --- /dev/null +++ b/prepare/r-srnadiff/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bayseq +- r-biocmanager +- r-biocparallel +- r-biocstyle +- r-deseq2 +- r-devtools +- r-edger +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-gviz +- r-iranges +- r-rcpp +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: srnadiff_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/srnadiff diff --git a/prepare/r-sscore/PKGBUILD b/prepare/r-sscore/PKGBUILD new file mode 100644 index 0000000000..b6e4af52d2 --- /dev/null +++ b/prepare/r-sscore/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sscore +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='S-Score Algorithm for Affymetrix Oligonucleotide Microarrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-affyio +) +optdepends=( + r-affydata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sscore/lilac.py b/prepare/r-sscore/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sscore/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sscore/lilac.yaml b/prepare/r-sscore/lilac.yaml new file mode 100644 index 0000000000..542a825659 --- /dev/null +++ b/prepare/r-sscore/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-affyio +update_on: +- regex: sscore_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sscore diff --git a/prepare/r-sscu/PKGBUILD b/prepare/r-sscu/PKGBUILD new file mode 100644 index 0000000000..e08404fdd4 --- /dev/null +++ b/prepare/r-sscu/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sscu +_pkgver=2.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Strength of Selected Codon Usage' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-seqinr +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sscu/lilac.py b/prepare/r-sscu/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sscu/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sscu/lilac.yaml b/prepare/r-sscu/lilac.yaml new file mode 100644 index 0000000000..1bdb4d9fe5 --- /dev/null +++ b/prepare/r-sscu/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-seqinr +update_on: +- regex: sscu_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sscu diff --git a/prepare/r-sseq/PKGBUILD b/prepare/r-sseq/PKGBUILD new file mode 100644 index 0000000000..cc1adaafac --- /dev/null +++ b/prepare/r-sseq/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sSeq +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-catools + r-rcolorbrewer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sseq/lilac.py b/prepare/r-sseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sseq/lilac.yaml b/prepare/r-sseq/lilac.yaml new file mode 100644 index 0000000000..2a1821c26c --- /dev/null +++ b/prepare/r-sseq/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-catools +- r-rcolorbrewer +update_on: +- regex: sSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sSeq diff --git a/prepare/r-ssize/PKGBUILD b/prepare/r-ssize/PKGBUILD new file mode 100644 index 0000000000..23758c701e --- /dev/null +++ b/prepare/r-ssize/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ssize +_pkgver=1.68.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimate Microarray Sample Size' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-gdata + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ssize/lilac.py b/prepare/r-ssize/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ssize/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ssize/lilac.yaml b/prepare/r-ssize/lilac.yaml new file mode 100644 index 0000000000..6f2177bf18 --- /dev/null +++ b/prepare/r-ssize/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gdata +- r-xtable +update_on: +- regex: ssize_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ssize diff --git a/prepare/r-sspaths/PKGBUILD b/prepare/r-sspaths/PKGBUILD new file mode 100644 index 0000000000..2a2b8fc74d --- /dev/null +++ b/prepare/r-sspaths/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ssPATHS +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ssPATHS: Single Sample PATHway Score' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-dml + r-mess + r-rocr + r-summarizedexperiment +) +optdepends=( + r-ggplot2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sspaths/lilac.py b/prepare/r-sspaths/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sspaths/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sspaths/lilac.yaml b/prepare/r-sspaths/lilac.yaml new file mode 100644 index 0000000000..b4833c818e --- /dev/null +++ b/prepare/r-sspaths/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dml +- r-mess +- r-rocr +- r-summarizedexperiment +update_on: +- regex: ssPATHS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ssPATHS diff --git a/prepare/r-ssrch/PKGBUILD b/prepare/r-ssrch/PKGBUILD new file mode 100644 index 0000000000..0cfff56ea3 --- /dev/null +++ b/prepare/r-ssrch/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ssrch +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='a simple search engine' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-dt + r-shiny +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ssrch/lilac.py b/prepare/r-ssrch/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ssrch/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ssrch/lilac.yaml b/prepare/r-ssrch/lilac.yaml new file mode 100644 index 0000000000..4f955177da --- /dev/null +++ b/prepare/r-ssrch/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dt +- r-shiny +update_on: +- regex: ssrch_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ssrch diff --git a/prepare/r-ssviz/PKGBUILD b/prepare/r-ssviz/PKGBUILD new file mode 100644 index 0000000000..1a9b7b4fbc --- /dev/null +++ b/prepare/r-ssviz/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ssviz +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A small RNA-seq visualizer and analysis toolkit' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-ggplot2 + r-rcolorbrewer + r-reshape + r-rsamtools +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ssviz/lilac.py b/prepare/r-ssviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ssviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ssviz/lilac.yaml b/prepare/r-ssviz/lilac.yaml new file mode 100644 index 0000000000..58e4cc71fa --- /dev/null +++ b/prepare/r-ssviz/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-ggplot2 +- r-rcolorbrewer +- r-reshape +- r-rsamtools +update_on: +- regex: ssviz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ssviz diff --git a/prepare/r-stable/PKGBUILD b/prepare/r-stable/PKGBUILD new file mode 100644 index 0000000000..559e7aa32e --- /dev/null +++ b/prepare/r-stable/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=stable +_pkgver=1.1.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Probability Functions and Generalized Regression Models for Stable Distributions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rmutil + r-stabledist +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-stable/lilac.py b/prepare/r-stable/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-stable/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-stable/lilac.yaml b/prepare/r-stable/lilac.yaml new file mode 100644 index 0000000000..d07040221d --- /dev/null +++ b/prepare/r-stable/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rmutil +- r-stabledist +update_on: +- regex: stable_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=stable diff --git a/prepare/r-stabledist/PKGBUILD b/prepare/r-stabledist/PKGBUILD new file mode 100644 index 0000000000..c06a81d356 --- /dev/null +++ b/prepare/r-stabledist/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=stabledist +_pkgver=0.7-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Stable Distribution Functions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-fbasics + r-fmstable + r-matrix + r-rmpfr + r-runit + r-sfsmisc +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-stabledist/lilac.py b/prepare/r-stabledist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-stabledist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-stabledist/lilac.yaml b/prepare/r-stabledist/lilac.yaml new file mode 100644 index 0000000000..a90cd0e21b --- /dev/null +++ b/prepare/r-stabledist/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: stabledist_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=stabledist diff --git a/prepare/r-stabs/PKGBUILD b/prepare/r-stabs/PKGBUILD new file mode 100644 index 0000000000..050c5e5a68 --- /dev/null +++ b/prepare/r-stabs/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=stabs +_pkgver=0.6-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Stability Selection with Error Control' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-gamboostlss + r-glmnet + r-hdi + r-knitr + r-lars + r-mboost + r-rmarkdown + r-testthat + r-th.data +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-stabs/lilac.py b/prepare/r-stabs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-stabs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-stabs/lilac.yaml b/prepare/r-stabs/lilac.yaml new file mode 100644 index 0000000000..50a4bb4317 --- /dev/null +++ b/prepare/r-stabs/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: stabs_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=stabs diff --git a/prepare/r-stager/PKGBUILD b/prepare/r-stager/PKGBUILD new file mode 100644 index 0000000000..d57759a539 --- /dev/null +++ b/prepare/r-stager/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=stageR +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='stageR: stage-wise analysis of high throughput gene expression data in R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-summarizedexperiment +) +optdepends=( + r-biobase + r-biocstyle + r-dexseq + r-edger + r-knitr + r-limma + r-methods + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-stager/lilac.py b/prepare/r-stager/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-stager/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-stager/lilac.yaml b/prepare/r-stager/lilac.yaml new file mode 100644 index 0000000000..3e03a483cb --- /dev/null +++ b/prepare/r-stager/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-summarizedexperiment +update_on: +- regex: stageR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/stageR diff --git a/prepare/r-stan/PKGBUILD b/prepare/r-stan/PKGBUILD new file mode 100644 index 0000000000..11ae350fee --- /dev/null +++ b/prepare/r-stan/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=STAN +_pkgver=2.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The Genomic STate ANnotation Package' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-genomeinfodb + r-genomicranges + r-gviz + r-iranges + r-poilog + r-rsolnp + r-s4vectors +) +optdepends=( + r-biocstyle + r-gplots + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-stan/lilac.py b/prepare/r-stan/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-stan/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-stan/lilac.yaml b/prepare/r-stan/lilac.yaml new file mode 100644 index 0000000000..abce24fd59 --- /dev/null +++ b/prepare/r-stan/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomeinfodb +- r-genomicranges +- r-gviz +- r-iranges +- r-poilog +- r-rsolnp +- r-s4vectors +update_on: +- regex: STAN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/STAN diff --git a/prepare/r-stanheaders/PKGBUILD b/prepare/r-stanheaders/PKGBUILD new file mode 100644 index 0000000000..6ab942fff4 --- /dev/null +++ b/prepare/r-stanheaders/PKGBUILD @@ -0,0 +1,42 @@ +# system requirements: pandoc +# Maintainer: Guoyi Zhang + +_pkgname=StanHeaders +_pkgver=2.21.0-7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='C++ Header Files for Stan' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-rcppeigen + r-rcppparallel +) +optdepends=( + r-bh + r-knitr + r-matrix + r-methods + r-rcpp + r-rmarkdown + r-rstan +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-stanheaders/lilac.py b/prepare/r-stanheaders/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-stanheaders/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-stanheaders/lilac.yaml b/prepare/r-stanheaders/lilac.yaml new file mode 100644 index 0000000000..afa2673dfa --- /dev/null +++ b/prepare/r-stanheaders/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcppeigen +- r-rcppparallel +update_on: +- regex: StanHeaders_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=StanHeaders diff --git a/prepare/r-starank/PKGBUILD b/prepare/r-starank/PKGBUILD new file mode 100644 index 0000000000..52aed1ea1f --- /dev/null +++ b/prepare/r-starank/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=staRank +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Stability Ranking' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cellhts2 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-starank/lilac.py b/prepare/r-starank/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-starank/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-starank/lilac.yaml b/prepare/r-starank/lilac.yaml new file mode 100644 index 0000000000..cb9d0244ed --- /dev/null +++ b/prepare/r-starank/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cellhts2 +update_on: +- regex: staRank_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/staRank diff --git a/prepare/r-starbiotrek/PKGBUILD b/prepare/r-starbiotrek/PKGBUILD new file mode 100644 index 0000000000..028d38d8cb --- /dev/null +++ b/prepare/r-starbiotrek/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=StarBioTrek +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='StarBioTrek' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-e1071 + r-ggplot2 + r-graphite + r-igraph + r-mlmetrics + r-reshape2 + r-rocr + r-spidermir +) +optdepends=( + r-biocstyle + r-devtools + r-grid + r-knitr + r-png + r-qgraph + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-starbiotrek/lilac.py b/prepare/r-starbiotrek/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-starbiotrek/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-starbiotrek/lilac.yaml b/prepare/r-starbiotrek/lilac.yaml new file mode 100644 index 0000000000..705be923ad --- /dev/null +++ b/prepare/r-starbiotrek/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-e1071 +- r-ggplot2 +- r-graphite +- r-igraph +- r-mlmetrics +- r-reshape2 +- r-rocr +- r-spidermir +update_on: +- regex: StarBioTrek_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/StarBioTrek diff --git a/prepare/r-startupmsg/PKGBUILD b/prepare/r-startupmsg/PKGBUILD new file mode 100644 index 0000000000..3c6977a306 --- /dev/null +++ b/prepare/r-startupmsg/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=startupmsg +_pkgver=0.9.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities for Start-Up Messages' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-startupmsg/lilac.py b/prepare/r-startupmsg/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-startupmsg/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-startupmsg/lilac.yaml b/prepare/r-startupmsg/lilac.yaml new file mode 100644 index 0000000000..5da59a8bae --- /dev/null +++ b/prepare/r-startupmsg/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: startupmsg_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=startupmsg diff --git a/prepare/r-stategra/PKGBUILD b/prepare/r-stategra/PKGBUILD new file mode 100644 index 0000000000..a7762a6d31 --- /dev/null +++ b/prepare/r-stategra/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=STATegRa +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Classes and methods for multi-omics data integration' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-biobase + r-calibrate + r-edger + r-foreach + r-ggplot2 + r-gplots + r-gridextra + r-limma +) +optdepends=( + r-biocgenerics + r-biocstyle + r-dosnow + r-knitr + r-rmarkdown + r-roxygen2 + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-stategra/lilac.py b/prepare/r-stategra/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-stategra/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-stategra/lilac.yaml b/prepare/r-stategra/lilac.yaml new file mode 100644 index 0000000000..88ecc7bc73 --- /dev/null +++ b/prepare/r-stategra/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +- r-calibrate +- r-edger +- r-foreach +- r-ggplot2 +- r-gplots +- r-gridextra +- r-limma +update_on: +- regex: STATegRa_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/STATegRa diff --git a/prepare/r-statip/PKGBUILD b/prepare/r-statip/PKGBUILD new file mode 100644 index 0000000000..677424e2c5 --- /dev/null +++ b/prepare/r-statip/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=statip +_pkgver=0.2.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Functions for Probability Distributions and Regression' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-clue +) +optdepends=( + r-knitr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-statip/lilac.py b/prepare/r-statip/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-statip/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-statip/lilac.yaml b/prepare/r-statip/lilac.yaml new file mode 100644 index 0000000000..50ca0bb02a --- /dev/null +++ b/prepare/r-statip/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clue +update_on: +- regex: statip_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=statip diff --git a/prepare/r-statmod/PKGBUILD b/prepare/r-statmod/PKGBUILD new file mode 100644 index 0000000000..74d88c270f --- /dev/null +++ b/prepare/r-statmod/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=statmod +_pkgver=1.4.36 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Modeling' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-mass + r-tweedie +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-statmod/lilac.py b/prepare/r-statmod/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-statmod/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-statmod/lilac.yaml b/prepare/r-statmod/lilac.yaml new file mode 100644 index 0000000000..dbbf2393a6 --- /dev/null +++ b/prepare/r-statmod/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: statmod_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=statmod diff --git a/prepare/r-statnet.common/PKGBUILD b/prepare/r-statnet.common/PKGBUILD new file mode 100644 index 0000000000..16a7d87b4b --- /dev/null +++ b/prepare/r-statnet.common/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=statnet.common +_pkgver=4.5.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Common R Scripts and Utilities Used by the Statnet Project Software' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-coda +) +optdepends=( + r-covr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-statnet.common/lilac.py b/prepare/r-statnet.common/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-statnet.common/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-statnet.common/lilac.yaml b/prepare/r-statnet.common/lilac.yaml new file mode 100644 index 0000000000..a22c2e01ab --- /dev/null +++ b/prepare/r-statnet.common/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-coda +update_on: +- regex: statnet.common_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=statnet.common diff --git a/prepare/r-stattarget/PKGBUILD b/prepare/r-stattarget/PKGBUILD new file mode 100644 index 0000000000..1512b1f4b2 --- /dev/null +++ b/prepare/r-stattarget/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=statTarget +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Analysis of Molecular Profiles' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-impute + r-pdist + r-pls + r-plyr + r-randomforest + r-roc + r-rrcov +) +optdepends=( + r-biocstyle + r-gwidgets2 + r-gwidgets2rgtk2 + r-knitr + r-rgtk2 + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-stattarget/lilac.py b/prepare/r-stattarget/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-stattarget/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-stattarget/lilac.yaml b/prepare/r-stattarget/lilac.yaml new file mode 100644 index 0000000000..a5ce7a9143 --- /dev/null +++ b/prepare/r-stattarget/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-impute +- r-pdist +- r-pls +- r-plyr +- r-randomforest +- r-roc +- r-rrcov +update_on: +- regex: statTarget_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/statTarget diff --git a/prepare/r-stemhypoxia/PKGBUILD b/prepare/r-stemhypoxia/PKGBUILD new file mode 100644 index 0000000000..458b8b4dc0 --- /dev/null +++ b/prepare/r-stemhypoxia/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=stemHypoxia +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Differentiation of Human Embryonic Stem Cells under Hypoxia gene expression dataset by Prado-Lopez et al. (2010)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-stemhypoxia/lilac.py b/prepare/r-stemhypoxia/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-stemhypoxia/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-stemhypoxia/lilac.yaml b/prepare/r-stemhypoxia/lilac.yaml new file mode 100644 index 0000000000..1d075c358f --- /dev/null +++ b/prepare/r-stemhypoxia/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: stemHypoxia_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/stemHypoxia diff --git a/prepare/r-stepnorm/PKGBUILD b/prepare/r-stepnorm/PKGBUILD new file mode 100644 index 0000000000..0c821cd27d --- /dev/null +++ b/prepare/r-stepnorm/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=stepNorm +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Stepwise normalization functions for cDNA microarrays' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-marray +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-stepnorm/lilac.py b/prepare/r-stepnorm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-stepnorm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-stepnorm/lilac.yaml b/prepare/r-stepnorm/lilac.yaml new file mode 100644 index 0000000000..fe8c96962d --- /dev/null +++ b/prepare/r-stepnorm/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-marray +update_on: +- regex: stepNorm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/stepNorm diff --git a/prepare/r-stopwords/PKGBUILD b/prepare/r-stopwords/PKGBUILD new file mode 100644 index 0000000000..587082406e --- /dev/null +++ b/prepare/r-stopwords/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=stopwords +_pkgver=2.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multilingual Stopword Lists' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-isocodes +) +optdepends=( + r-covr + r-quanteda + r-spelling + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-stopwords/lilac.py b/prepare/r-stopwords/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-stopwords/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-stopwords/lilac.yaml b/prepare/r-stopwords/lilac.yaml new file mode 100644 index 0000000000..e8e5b2f3bd --- /dev/null +++ b/prepare/r-stopwords/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-isocodes +update_on: +- regex: stopwords_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=stopwords diff --git a/prepare/r-strandcheckr/PKGBUILD b/prepare/r-strandcheckr/PKGBUILD new file mode 100644 index 0000000000..257ab1d6c4 --- /dev/null +++ b/prepare/r-strandcheckr/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=strandCheckR +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Calculate strandness information of a bam file' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-dplyr + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-gridextra + r-iranges + r-magrittr + r-reshape2 + r-rmarkdown + r-rsamtools + r-s4vectors + r-stringr + r-txdb.hsapiens.ucsc.hg38.knowngene +) +optdepends=( + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-strandcheckr/lilac.py b/prepare/r-strandcheckr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-strandcheckr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-strandcheckr/lilac.yaml b/prepare/r-strandcheckr/lilac.yaml new file mode 100644 index 0000000000..4310c13d5a --- /dev/null +++ b/prepare/r-strandcheckr/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-dplyr +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-gridextra +- r-iranges +- r-magrittr +- r-reshape2 +- r-rmarkdown +- r-rsamtools +- r-s4vectors +- r-stringr +- r-txdb.hsapiens.ucsc.hg38.knowngene +update_on: +- regex: strandCheckR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/strandCheckR diff --git a/prepare/r-strawr/PKGBUILD b/prepare/r-strawr/PKGBUILD new file mode 100644 index 0000000000..39c320ff4f --- /dev/null +++ b/prepare/r-strawr/PKGBUILD @@ -0,0 +1,29 @@ +# system requirements: libcurl: libcurl-devel (rpm) orlibcurl4-openssl-dev (deb) +# Maintainer: Guoyi Zhang + +_pkgname=strawr +_pkgver=0.0.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast Implementation of Reading/Dump for .hic Files' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-rcpp +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-strawr/lilac.py b/prepare/r-strawr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-strawr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-strawr/lilac.yaml b/prepare/r-strawr/lilac.yaml new file mode 100644 index 0000000000..959d24afbe --- /dev/null +++ b/prepare/r-strawr/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: strawr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=strawr diff --git a/prepare/r-streamer/PKGBUILD b/prepare/r-streamer/PKGBUILD new file mode 100644 index 0000000000..93d72224ac --- /dev/null +++ b/prepare/r-streamer/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Streamer +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Enabling stream processing of large files' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-graph + r-rbgl +) +optdepends=( + r-genomicalignments + r-rgraphviz + r-rsamtools + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-streamer/lilac.py b/prepare/r-streamer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-streamer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-streamer/lilac.yaml b/prepare/r-streamer/lilac.yaml new file mode 100644 index 0000000000..44daa61e6d --- /dev/null +++ b/prepare/r-streamer/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-graph +- r-rbgl +update_on: +- regex: Streamer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Streamer diff --git a/prepare/r-stringdb/PKGBUILD b/prepare/r-stringdb/PKGBUILD new file mode 100644 index 0000000000..852b566062 --- /dev/null +++ b/prepare/r-stringdb/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=STRINGdb +_pkgver=2.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='STRINGdb (Search Tool for the Retrieval of Interacting proteins database)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-gplots + r-hash + r-igraph + r-plotrix + r-plyr + r-png + r-rcolorbrewer + r-rcurl + r-sqldf +) +optdepends=( + r-biocgenerics + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-stringdb/lilac.py b/prepare/r-stringdb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-stringdb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-stringdb/lilac.yaml b/prepare/r-stringdb/lilac.yaml new file mode 100644 index 0000000000..2fbe58a446 --- /dev/null +++ b/prepare/r-stringdb/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gplots +- r-hash +- r-igraph +- r-plotrix +- r-plyr +- r-png +- r-rcolorbrewer +- r-rcurl +- r-sqldf +update_on: +- regex: STRINGdb_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/STRINGdb diff --git a/prepare/r-stringdist/PKGBUILD b/prepare/r-stringdist/PKGBUILD new file mode 100644 index 0000000000..7ad7a1d02a --- /dev/null +++ b/prepare/r-stringdist/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=stringdist +_pkgver=0.9.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Approximate String Matching, Fuzzy Text Search, and String Distance Functions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-stringdist/lilac.py b/prepare/r-stringdist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-stringdist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-stringdist/lilac.yaml b/prepare/r-stringdist/lilac.yaml new file mode 100644 index 0000000000..b5c1dcfd95 --- /dev/null +++ b/prepare/r-stringdist/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: stringdist_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=stringdist diff --git a/prepare/r-stringfish/PKGBUILD b/prepare/r-stringfish/PKGBUILD new file mode 100644 index 0000000000..24b2d0e0c2 --- /dev/null +++ b/prepare/r-stringfish/PKGBUILD @@ -0,0 +1,38 @@ +# system requirements: C++11, GNU make +# Maintainer: Guoyi Zhang + +_pkgname=stringfish +_pkgver=0.15.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Alt String Implementation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp + r-rcppparallel +) +optdepends=( + r-dplyr + r-knitr + r-qs + r-rlang + r-rmarkdown + r-stringr + r-usethis +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-stringfish/lilac.py b/prepare/r-stringfish/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-stringfish/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-stringfish/lilac.yaml b/prepare/r-stringfish/lilac.yaml new file mode 100644 index 0000000000..4c76d7eb5e --- /dev/null +++ b/prepare/r-stringfish/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-rcppparallel +update_on: +- regex: stringfish_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=stringfish diff --git a/prepare/r-stroma4/PKGBUILD b/prepare/r-stroma4/PKGBUILD new file mode 100644 index 0000000000..7b8a01aa46 --- /dev/null +++ b/prepare/r-stroma4/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=STROMA4 +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assign Properties to TNBC Patients' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocparallel + r-matrixstats +) +optdepends=( + r-breastcancermainz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-stroma4/lilac.py b/prepare/r-stroma4/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-stroma4/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-stroma4/lilac.yaml b/prepare/r-stroma4/lilac.yaml new file mode 100644 index 0000000000..f68bf58632 --- /dev/null +++ b/prepare/r-stroma4/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocparallel +- r-matrixstats +update_on: +- regex: STROMA4_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/STROMA4 diff --git a/prepare/r-strucchange/PKGBUILD b/prepare/r-strucchange/PKGBUILD new file mode 100644 index 0000000000..c25aba1b2e --- /dev/null +++ b/prepare/r-strucchange/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=strucchange +_pkgver=1.5-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Testing, Monitoring, and Dating Structural Changes' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-sandwich + r-zoo +) +optdepends=( + r-car + r-dynlm + r-e1071 + r-foreach + r-lmtest + r-mvtnorm + r-stats4 + r-tseries +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-strucchange/lilac.py b/prepare/r-strucchange/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-strucchange/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-strucchange/lilac.yaml b/prepare/r-strucchange/lilac.yaml new file mode 100644 index 0000000000..9f2cb6a70a --- /dev/null +++ b/prepare/r-strucchange/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-sandwich +- r-zoo +update_on: +- regex: strucchange_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=strucchange diff --git a/prepare/r-struct/PKGBUILD b/prepare/r-struct/PKGBUILD new file mode 100644 index 0000000000..ff8720f5ca --- /dev/null +++ b/prepare/r-struct/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=struct +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistics in R Using Class-based Templates' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-knitr + r-ontologyindex + r-rols + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-covr + r-ggplot2 + r-magick + r-openxlsx + r-rmarkdown + r-rstudioapi + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-struct/lilac.py b/prepare/r-struct/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-struct/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-struct/lilac.yaml b/prepare/r-struct/lilac.yaml new file mode 100644 index 0000000000..acde060264 --- /dev/null +++ b/prepare/r-struct/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-knitr +- r-ontologyindex +- r-rols +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: struct_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/struct diff --git a/prepare/r-structstrings/PKGBUILD b/prepare/r-structstrings/PKGBUILD new file mode 100644 index 0000000000..3467187ada --- /dev/null +++ b/prepare/r-structstrings/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Structstrings +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Implementation of the dot bracket annotations with Biostrings' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biostrings + r-crayon + r-iranges + r-s4vectors + r-stringi + r-stringr + r-xvector +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat + r-trnascanimport +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-structstrings/lilac.py b/prepare/r-structstrings/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-structstrings/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-structstrings/lilac.yaml b/prepare/r-structstrings/lilac.yaml new file mode 100644 index 0000000000..14f1df1718 --- /dev/null +++ b/prepare/r-structstrings/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-crayon +- r-iranges +- r-s4vectors +- r-stringi +- r-stringr +- r-xvector +update_on: +- regex: Structstrings_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Structstrings diff --git a/prepare/r-structtoolbox/PKGBUILD b/prepare/r-structtoolbox/PKGBUILD new file mode 100644 index 0000000000..1e75038578 --- /dev/null +++ b/prepare/r-structtoolbox/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=structToolbox +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data processing & analysis tools for Metabolomics and other omics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-ggthemes + r-gridextra + r-scales + r-sp + r-struct +) +optdepends=( + r-agricolae + r-biocfilecache + r-biocstyle + r-car + r-covr + r-cowplot + r-e1071 + r-emmeans + r-ggdendro + r-knitr + r-magick + r-nlme + r-openxlsx + r-pls + r-pmp + r-rappdirs + r-reshape2 + r-rmarkdown + r-ropls + r-rtsne + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-structtoolbox/lilac.py b/prepare/r-structtoolbox/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-structtoolbox/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-structtoolbox/lilac.yaml b/prepare/r-structtoolbox/lilac.yaml new file mode 100644 index 0000000000..02f33820f3 --- /dev/null +++ b/prepare/r-structtoolbox/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-ggthemes +- r-gridextra +- r-scales +- r-sp +- r-struct +update_on: +- regex: structToolbox_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/structToolbox diff --git a/prepare/r-structuralvariantannotation/PKGBUILD b/prepare/r-structuralvariantannotation/PKGBUILD new file mode 100644 index 0000000000..118398f6ad --- /dev/null +++ b/prepare/r-structuralvariantannotation/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=StructuralVariantAnnotation +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Variant annotations for structural variants' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-biocgenerics + r-biostrings + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-rlang + r-rtracklayer + r-s4vectors + r-stringr + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-biovizbase + r-bsgenome.hsapiens.ucsc.hg19 + r-devtools + r-ggbio + r-ggplot2 + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat + r-tidyverse + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-structuralvariantannotation/lilac.py b/prepare/r-structuralvariantannotation/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-structuralvariantannotation/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-structuralvariantannotation/lilac.yaml b/prepare/r-structuralvariantannotation/lilac.yaml new file mode 100644 index 0000000000..126ed2dfce --- /dev/null +++ b/prepare/r-structuralvariantannotation/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biocgenerics +- r-biostrings +- r-dplyr +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-rlang +- r-rtracklayer +- r-s4vectors +- r-stringr +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: StructuralVariantAnnotation_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/StructuralVariantAnnotation diff --git a/prepare/r-styler/PKGBUILD b/prepare/r-styler/PKGBUILD new file mode 100644 index 0000000000..e7728d5a39 --- /dev/null +++ b/prepare/r-styler/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=styler +_pkgver=1.6.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Non-Invasive Pretty Printing of R Code' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-backports + r-cli + r-glue + r-magrittr + r-purrr + r-r.cache + r-rematch2 + r-rlang + r-rprojroot + r-tibble + r-withr + r-xfun +) +optdepends=( + r-data.tree + r-digest + r-dplyr + r-here + r-knitr + r-prettycode + r-rmarkdown + r-roxygen2 + r-rstudioapi + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-styler/lilac.py b/prepare/r-styler/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-styler/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-styler/lilac.yaml b/prepare/r-styler/lilac.yaml new file mode 100644 index 0000000000..2b2b977cec --- /dev/null +++ b/prepare/r-styler/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-backports +- r-cli +- r-glue +- r-magrittr +- r-purrr +- r-r.cache +- r-rematch2 +- r-rlang +- r-rprojroot +- r-tibble +- r-withr +- r-xfun +update_on: +- regex: styler_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=styler diff --git a/prepare/r-subcellbarcode/PKGBUILD b/prepare/r-subcellbarcode/PKGBUILD new file mode 100644 index 0000000000..5e08c0933e --- /dev/null +++ b/prepare/r-subcellbarcode/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SubCellBarCode +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-caret + r-e1071 + r-ggplot2 + r-ggrepel + r-gridextra + r-networkd3 + r-org.hs.eg.db + r-rtsne + r-scatterplot3d +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-subcellbarcode/lilac.py b/prepare/r-subcellbarcode/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-subcellbarcode/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-subcellbarcode/lilac.yaml b/prepare/r-subcellbarcode/lilac.yaml new file mode 100644 index 0000000000..0b2b9362b7 --- /dev/null +++ b/prepare/r-subcellbarcode/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-caret +- r-e1071 +- r-ggplot2 +- r-ggrepel +- r-gridextra +- r-networkd3 +- r-org.hs.eg.db +- r-rtsne +- r-scatterplot3d +update_on: +- regex: SubCellBarCode_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SubCellBarCode diff --git a/prepare/r-subseq/PKGBUILD b/prepare/r-subseq/PKGBUILD new file mode 100644 index 0000000000..0459254f92 --- /dev/null +++ b/prepare/r-subseq/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=subSeq +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Subsampling of high-throughput sequencing count data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-data.table + r-digest + r-dplyr + r-ggplot2 + r-magrittr + r-qvalue + r-tidyr +) +optdepends=( + r-deseq2 + r-dexseq + r-edger + r-knitr + r-limma + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-subseq/lilac.py b/prepare/r-subseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-subseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-subseq/lilac.yaml b/prepare/r-subseq/lilac.yaml new file mode 100644 index 0000000000..1ef20cd1d8 --- /dev/null +++ b/prepare/r-subseq/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-data.table +- r-digest +- r-dplyr +- r-ggplot2 +- r-magrittr +- r-qvalue +- r-tidyr +update_on: +- regex: subSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/subSeq diff --git a/prepare/r-subspace/PKGBUILD b/prepare/r-subspace/PKGBUILD new file mode 100644 index 0000000000..200d6416e5 --- /dev/null +++ b/prepare/r-subspace/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: Java (>= 6) +# Maintainer: Guoyi Zhang + +_pkgname=subspace +_pkgver=1.0.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interface to OpenSubspace' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-colorspace + r-ggvis + r-rjava + r-stringr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-subspace/lilac.py b/prepare/r-subspace/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-subspace/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-subspace/lilac.yaml b/prepare/r-subspace/lilac.yaml new file mode 100644 index 0000000000..a7757bfffc --- /dev/null +++ b/prepare/r-subspace/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colorspace +- r-ggvis +- r-rjava +- r-stringr +update_on: +- regex: subspace_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=subspace diff --git a/prepare/r-summarizedbenchmark/PKGBUILD b/prepare/r-summarizedbenchmark/PKGBUILD new file mode 100644 index 0000000000..12360359b6 --- /dev/null +++ b/prepare/r-summarizedbenchmark/PKGBUILD @@ -0,0 +1,61 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SummarizedBenchmark +_pkgver=2.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Classes and methods for performing benchmark comparisons' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-crayon + r-digest + r-dplyr + r-ggplot2 + r-mclust + r-rlang + r-s4vectors + r-sessioninfo + r-stringr + r-summarizedexperiment + r-tibble + r-tidyr + r-upsetr +) +optdepends=( + r-biocstyle + r-biomart + r-deseq2 + r-edger + r-icobra + r-ihw + r-knitr + r-limma + r-magrittr + r-qvalue + r-readr + r-rmarkdown + r-rnaseqcomp + r-scater + r-scrnaseq + r-splatter + r-testthat + r-tximport +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-summarizedbenchmark/lilac.py b/prepare/r-summarizedbenchmark/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-summarizedbenchmark/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-summarizedbenchmark/lilac.yaml b/prepare/r-summarizedbenchmark/lilac.yaml new file mode 100644 index 0000000000..eb59ad14be --- /dev/null +++ b/prepare/r-summarizedbenchmark/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-crayon +- r-digest +- r-dplyr +- r-ggplot2 +- r-mclust +- r-rlang +- r-s4vectors +- r-sessioninfo +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-tidyr +- r-upsetr +update_on: +- regex: SummarizedBenchmark_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SummarizedBenchmark diff --git a/prepare/r-summarizedexperiment/PKGBUILD b/prepare/r-summarizedexperiment/PKGBUILD new file mode 100644 index 0000000000..fbbd9517d3 --- /dev/null +++ b/prepare/r-summarizedexperiment/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SummarizedExperiment +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SummarizedExperiment container' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-delayedarray + r-genomeinfodb + r-genomicranges + r-iranges + r-matrixgenerics + r-s4vectors +) +optdepends=( + r-airway + r-annotate + r-annotationdbi + r-biocstyle + r-digest + r-genomicfeatures + r-hdf5array + r-hgu95av2.db + r-jsonlite + r-knitr + r-rhdf5 + r-rmarkdown + r-runit + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-summarizedexperiment/lilac.py b/prepare/r-summarizedexperiment/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-summarizedexperiment/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-summarizedexperiment/lilac.yaml b/prepare/r-summarizedexperiment/lilac.yaml new file mode 100644 index 0000000000..84cc3c120d --- /dev/null +++ b/prepare/r-summarizedexperiment/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-delayedarray +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-matrixgenerics +- r-s4vectors +update_on: +- regex: SummarizedExperiment_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SummarizedExperiment diff --git a/prepare/r-summarytools/PKGBUILD b/prepare/r-summarytools/PKGBUILD new file mode 100644 index 0000000000..06d37b9a25 --- /dev/null +++ b/prepare/r-summarytools/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=summarytools +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools to Quickly and Neatly Summarize Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-base64enc + r-checkmate + r-dplyr + r-htmltools + r-lubridate + r-magick + r-matrixstats + r-pander + r-pryr + r-rapportools + r-tibble + r-tidyr +) +optdepends=( + r-forcats + r-formatr + r-kableextra + r-knitr + r-magrittr + r-rmarkdown + r-rstudioapi +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-summarytools/lilac.py b/prepare/r-summarytools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-summarytools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-summarytools/lilac.yaml b/prepare/r-summarytools/lilac.yaml new file mode 100644 index 0000000000..b243eea4cb --- /dev/null +++ b/prepare/r-summarytools/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-checkmate +- r-dplyr +- r-htmltools +- r-lubridate +- r-magick +- r-matrixstats +- r-pander +- r-pryr +- r-rapportools +- r-tibble +- r-tidyr +update_on: +- regex: summarytools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=summarytools diff --git a/prepare/r-summix/PKGBUILD b/prepare/r-summix/PKGBUILD new file mode 100644 index 0000000000..cbbdcc3cef --- /dev/null +++ b/prepare/r-summix/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Summix +_pkgver=2.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Summix: A method to estimate and adjust for population structure in genetic summary data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-nloptr +) +optdepends=( + r-knitr + r-markdown + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-summix/lilac.py b/prepare/r-summix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-summix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-summix/lilac.yaml b/prepare/r-summix/lilac.yaml new file mode 100644 index 0000000000..cfada346aa --- /dev/null +++ b/prepare/r-summix/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-nloptr +update_on: +- regex: Summix_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Summix diff --git a/prepare/r-superheat/PKGBUILD b/prepare/r-superheat/PKGBUILD new file mode 100644 index 0000000000..7237b99df2 --- /dev/null +++ b/prepare/r-superheat/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=superheat +_pkgver=0.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Graphical Tool for Exploring Complex Datasets Using Heatmaps' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('CC0') +depends=( + r + r-dplyr + r-ggdendro + r-ggplot2 + r-gtable + r-magrittr + r-plyr + r-scales +) +optdepends=( + r-knitr + r-rcolorbrewer + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-superheat/lilac.py b/prepare/r-superheat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-superheat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-superheat/lilac.yaml b/prepare/r-superheat/lilac.yaml new file mode 100644 index 0000000000..1d51222b85 --- /dev/null +++ b/prepare/r-superheat/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggdendro +- r-ggplot2 +- r-gtable +- r-magrittr +- r-plyr +- r-scales +update_on: +- regex: superheat_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=superheat diff --git a/prepare/r-superlearner/PKGBUILD b/prepare/r-superlearner/PKGBUILD new file mode 100644 index 0000000000..87f597cc69 --- /dev/null +++ b/prepare/r-superlearner/PKGBUILD @@ -0,0 +1,71 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SuperLearner +_pkgver=2.0-28 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Super Learner Prediction' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-cvauc + r-gam + r-nnls +) +optdepends=( + r-arm + r-bartmachine + r-biglasso + r-bigmemory + r-caret + r-class + r-devtools + r-e1071 + r-earth + r-extratrees + r-gbm + r-genefilter + r-ggplot2 + r-glmnet + r-ipred + r-kernelknn + r-kernlab + r-knitr + r-lattice + r-logicreg + r-mass + r-mlbench + r-nloptr + r-nnet + r-party + r-polspline + r-prettydoc + r-quadprog + r-randomforest + r-ranger + r-rhpcblasctl + r-rmarkdown + r-rocr + r-rpart + r-sis + r-speedglm + r-spls + r-sva + r-testthat + r-xgboost +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-superlearner/lilac.py b/prepare/r-superlearner/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-superlearner/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-superlearner/lilac.yaml b/prepare/r-superlearner/lilac.yaml new file mode 100644 index 0000000000..f5382918d9 --- /dev/null +++ b/prepare/r-superlearner/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cvauc +- r-gam +- r-nnls +update_on: +- regex: SuperLearner_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=SuperLearner diff --git a/prepare/r-supersigs/PKGBUILD b/prepare/r-supersigs/PKGBUILD new file mode 100644 index 0000000000..7918041d0c --- /dev/null +++ b/prepare/r-supersigs/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=supersigs +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Supervised mutational signatures' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-biostrings + r-caret + r-dplyr + r-rlang + r-rsample + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.hsapiens.ucsc.hg38 + r-ggplot2 + r-knitr + r-rmarkdown + r-testthat + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-supersigs/lilac.py b/prepare/r-supersigs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-supersigs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-supersigs/lilac.yaml b/prepare/r-supersigs/lilac.yaml new file mode 100644 index 0000000000..cd34d264fb --- /dev/null +++ b/prepare/r-supersigs/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biostrings +- r-caret +- r-dplyr +- r-rlang +- r-rsample +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: supersigs_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/supersigs diff --git a/prepare/r-suppdists/PKGBUILD b/prepare/r-suppdists/PKGBUILD new file mode 100644 index 0000000000..205446caa6 --- /dev/null +++ b/prepare/r-suppdists/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SuppDists +_pkgver=1.1-9.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Supplementary Distributions' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-rcppziggurat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-suppdists/lilac.py b/prepare/r-suppdists/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-suppdists/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-suppdists/lilac.yaml b/prepare/r-suppdists/lilac.yaml new file mode 100644 index 0000000000..5abf1d4fe0 --- /dev/null +++ b/prepare/r-suppdists/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: SuppDists_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=SuppDists diff --git a/prepare/r-suprahex/PKGBUILD b/prepare/r-suprahex/PKGBUILD new file mode 100644 index 0000000000..eeca50c4d2 --- /dev/null +++ b/prepare/r-suprahex/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=supraHex +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='supraHex: a supra-hexagonal map for analysing tabular omics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-dplyr + r-hexbin + r-igraph + r-magrittr + r-purrr + r-readr + r-stringr + r-tibble + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-suprahex/lilac.py b/prepare/r-suprahex/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-suprahex/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-suprahex/lilac.yaml b/prepare/r-suprahex/lilac.yaml new file mode 100644 index 0000000000..0914a965f5 --- /dev/null +++ b/prepare/r-suprahex/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-dplyr +- r-hexbin +- r-igraph +- r-magrittr +- r-purrr +- r-readr +- r-stringr +- r-tibble +- r-tidyr +update_on: +- regex: supraHex_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/supraHex diff --git a/prepare/r-surfaltr/PKGBUILD b/prepare/r-surfaltr/PKGBUILD new file mode 100644 index 0000000000..f4bafcf66f --- /dev/null +++ b/prepare/r-surfaltr/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=surfaltr +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biomart + r-biostrings + r-dplyr + r-ggplot2 + r-httr + r-msa + r-protr + r-readr + r-seqinr + r-stringr + r-testthat + r-xml2 +) +optdepends=( + r-devtools + r-kableextra + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-surfaltr/lilac.py b/prepare/r-surfaltr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-surfaltr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-surfaltr/lilac.yaml b/prepare/r-surfaltr/lilac.yaml new file mode 100644 index 0000000000..fa27ee5d28 --- /dev/null +++ b/prepare/r-surfaltr/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-biostrings +- r-dplyr +- r-ggplot2 +- r-httr +- r-msa +- r-protr +- r-readr +- r-seqinr +- r-stringr +- r-testthat +- r-xml2 +update_on: +- regex: surfaltr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/surfaltr diff --git a/prepare/r-survcomp/PKGBUILD b/prepare/r-survcomp/PKGBUILD new file mode 100644 index 0000000000..b1e0a2588b --- /dev/null +++ b/prepare/r-survcomp/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=survcomp +_pkgver=1.44.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Performance Assessment and Comparison for Survival Analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-bootstrap + r-ipred + r-prodlim + r-rmeta + r-suppdists + r-survivalroc +) +optdepends=( + r-biobase + r-biocmanager + r-clinfun + r-hmisc + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-survcomp/lilac.py b/prepare/r-survcomp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-survcomp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-survcomp/lilac.yaml b/prepare/r-survcomp/lilac.yaml new file mode 100644 index 0000000000..cdd144711a --- /dev/null +++ b/prepare/r-survcomp/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bootstrap +- r-ipred +- r-prodlim +- r-rmeta +- r-suppdists +- r-survivalroc +update_on: +- regex: survcomp_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/survcomp diff --git a/prepare/r-survey/PKGBUILD b/prepare/r-survey/PKGBUILD new file mode 100644 index 0000000000..4a13f8e4b7 --- /dev/null +++ b/prepare/r-survey/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=survey +_pkgver=4.1-1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Complex Survey Samples' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-minqa + r-mitools + r-numderiv +) +optdepends=( + r-aer + r-compquadform + r-dbi + r-foreign + r-hexbin + r-kernsmooth + r-mass + r-parallel + r-quantreg + r-rsqlite +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-survey/lilac.py b/prepare/r-survey/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-survey/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-survey/lilac.yaml b/prepare/r-survey/lilac.yaml new file mode 100644 index 0000000000..0a3ebee130 --- /dev/null +++ b/prepare/r-survey/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-minqa +- r-mitools +- r-numderiv +update_on: +- regex: survey_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=survey diff --git a/prepare/r-survivalroc/PKGBUILD b/prepare/r-survivalroc/PKGBUILD new file mode 100644 index 0000000000..4a11950f58 --- /dev/null +++ b/prepare/r-survivalroc/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=survivalROC +_pkgver=1.0.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Time-dependent ROC curve estimation from censored survival data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-survivalroc/lilac.py b/prepare/r-survivalroc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-survivalroc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-survivalroc/lilac.yaml b/prepare/r-survivalroc/lilac.yaml new file mode 100644 index 0000000000..0aeaf5c355 --- /dev/null +++ b/prepare/r-survivalroc/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: survivalROC_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=survivalROC diff --git a/prepare/r-survivalsvm/PKGBUILD b/prepare/r-survivalsvm/PKGBUILD new file mode 100644 index 0000000000..f6c0e2f3ef --- /dev/null +++ b/prepare/r-survivalsvm/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=survivalsvm +_pkgver=0.0.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Survival Support Vector Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-hmisc + r-kernlab + r-pracma + r-quadprog +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-survivalsvm/lilac.py b/prepare/r-survivalsvm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-survivalsvm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-survivalsvm/lilac.yaml b/prepare/r-survivalsvm/lilac.yaml new file mode 100644 index 0000000000..7bf4ba3781 --- /dev/null +++ b/prepare/r-survivalsvm/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-hmisc +- r-kernlab +- r-pracma +- r-quadprog +update_on: +- regex: survivalsvm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=survivalsvm diff --git a/prepare/r-survminer/PKGBUILD b/prepare/r-survminer/PKGBUILD new file mode 100644 index 0000000000..bb17819ddb --- /dev/null +++ b/prepare/r-survminer/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=survminer +_pkgver=0.4.9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Drawing Survival Curves using 'ggplot2'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-broom + r-dplyr + r-ggplot2 + r-ggpubr + r-ggtext + r-gridextra + r-magrittr + r-maxstat + r-purrr + r-rlang + r-scales + r-survmisc + r-tibble + r-tidyr +) +optdepends=( + r-cmprsk + r-flexsurv + r-knitr + r-markdown + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-survminer/lilac.py b/prepare/r-survminer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-survminer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-survminer/lilac.yaml b/prepare/r-survminer/lilac.yaml new file mode 100644 index 0000000000..1decc19102 --- /dev/null +++ b/prepare/r-survminer/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-broom +- r-dplyr +- r-ggplot2 +- r-ggpubr +- r-ggtext +- r-gridextra +- r-magrittr +- r-maxstat +- r-purrr +- r-rlang +- r-scales +- r-survmisc +- r-tibble +- r-tidyr +update_on: +- regex: survminer_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=survminer diff --git a/prepare/r-survmisc/PKGBUILD b/prepare/r-survmisc/PKGBUILD new file mode 100644 index 0000000000..d0785bd3fc --- /dev/null +++ b/prepare/r-survmisc/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=survMisc +_pkgver=0.5.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Miscellaneous Functions for Survival Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-ggplot2 + r-gridextra + r-km.ci + r-kmsurv + r-knitr + r-xtable + r-zoo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-survmisc/lilac.py b/prepare/r-survmisc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-survmisc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-survmisc/lilac.yaml b/prepare/r-survmisc/lilac.yaml new file mode 100644 index 0000000000..89e4ab788a --- /dev/null +++ b/prepare/r-survmisc/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-ggplot2 +- r-gridextra +- r-km.ci +- r-kmsurv +- r-knitr +- r-xtable +- r-zoo +update_on: +- regex: survMisc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=survMisc diff --git a/prepare/r-survtype/PKGBUILD b/prepare/r-survtype/PKGBUILD new file mode 100644 index 0000000000..07d5f667c4 --- /dev/null +++ b/prepare/r-survtype/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=survtype +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Subtype Identification with Survival Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-clustvarsel + r-pheatmap + r-summarizedexperiment + r-survminer +) +optdepends=( + r-knitr + r-maftools + r-rmarkdown + r-scales +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-survtype/lilac.py b/prepare/r-survtype/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-survtype/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-survtype/lilac.yaml b/prepare/r-survtype/lilac.yaml new file mode 100644 index 0000000000..8d3b2675fe --- /dev/null +++ b/prepare/r-survtype/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-clustvarsel +- r-pheatmap +- r-summarizedexperiment +- r-survminer +update_on: +- regex: survtype_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/survtype diff --git a/prepare/r-sushi/PKGBUILD b/prepare/r-sushi/PKGBUILD new file mode 100644 index 0000000000..4d8d8d5cc4 --- /dev/null +++ b/prepare/r-sushi/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Sushi +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for visualizing genomics data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-zoo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sushi/lilac.py b/prepare/r-sushi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sushi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sushi/lilac.yaml b/prepare/r-sushi/lilac.yaml new file mode 100644 index 0000000000..b21d38dcf1 --- /dev/null +++ b/prepare/r-sushi/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-zoo +update_on: +- regex: Sushi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Sushi diff --git a/prepare/r-sva/PKGBUILD b/prepare/r-sva/PKGBUILD new file mode 100644 index 0000000000..7ccb953504 --- /dev/null +++ b/prepare/r-sva/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sva +_pkgver=3.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Surrogate Variable Analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-edger + r-genefilter + r-limma + r-matrixstats +) +optdepends=( + r-biocstyle + r-bladderbatch + r-pamr + r-testthat + r-zebrafishrnaseq +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sva/lilac.py b/prepare/r-sva/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sva/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sva/lilac.yaml b/prepare/r-sva/lilac.yaml new file mode 100644 index 0000000000..6b3aa6feca --- /dev/null +++ b/prepare/r-sva/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-edger +- r-genefilter +- r-limma +- r-matrixstats +update_on: +- regex: sva_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/sva diff --git a/prepare/r-svanumt/PKGBUILD b/prepare/r-svanumt/PKGBUILD new file mode 100644 index 0000000000..a4c591bd12 --- /dev/null +++ b/prepare/r-svanumt/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=svaNUMT +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='NUMT detection from structural variant calls' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-biocgenerics + r-biostrings + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-rlang + r-rtracklayer + r-s4vectors + r-stringr + r-structuralvariantannotation + r-variantannotation +) +optdepends=( + r-circlize + r-devtools + r-ggplot2 + r-iranges + r-knitr + r-plyranges + r-rmarkdown + r-roxygen2 + r-summarizedexperiment + r-testthat + r-tictoc + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-svanumt/lilac.py b/prepare/r-svanumt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-svanumt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-svanumt/lilac.yaml b/prepare/r-svanumt/lilac.yaml new file mode 100644 index 0000000000..56e8a081d4 --- /dev/null +++ b/prepare/r-svanumt/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biocgenerics +- r-biostrings +- r-dplyr +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-rlang +- r-rtracklayer +- r-s4vectors +- r-stringr +- r-structuralvariantannotation +- r-variantannotation +update_on: +- regex: svaNUMT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/svaNUMT diff --git a/prepare/r-svaretro/PKGBUILD b/prepare/r-svaretro/PKGBUILD new file mode 100644 index 0000000000..65c685a6d2 --- /dev/null +++ b/prepare/r-svaretro/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=svaRetro +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Retrotransposed transcript detection from structural variants' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-biocgenerics + r-biostrings + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-rlang + r-rtracklayer + r-s4vectors + r-stringr + r-structuralvariantannotation + r-variantannotation +) +optdepends=( + r-biocstyle + r-circlize + r-devtools + r-ggplot2 + r-iranges + r-knitr + r-plyranges + r-rmarkdown + r-roxygen2 + r-stats + r-summarizedexperiment + r-testthat + r-tictoc + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-svaretro/lilac.py b/prepare/r-svaretro/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-svaretro/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-svaretro/lilac.yaml b/prepare/r-svaretro/lilac.yaml new file mode 100644 index 0000000000..945588c238 --- /dev/null +++ b/prepare/r-svaretro/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biocgenerics +- r-biostrings +- r-dplyr +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-rlang +- r-rtracklayer +- r-s4vectors +- r-stringr +- r-structuralvariantannotation +- r-variantannotation +update_on: +- regex: svaRetro_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/svaRetro diff --git a/prepare/r-svd/PKGBUILD b/prepare/r-svd/PKGBUILD new file mode 100644 index 0000000000..5c5411394b --- /dev/null +++ b/prepare/r-svd/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=svd +_pkgver=0.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interfaces to Various State-of-Art SVD and Eigensolvers' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +optdepends=( + r-testthat +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-svd/lilac.py b/prepare/r-svd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-svd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-svd/lilac.yaml b/prepare/r-svd/lilac.yaml new file mode 100644 index 0000000000..03a501ecd9 --- /dev/null +++ b/prepare/r-svd/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: svd_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=svd diff --git a/prepare/r-svdialogs/PKGBUILD b/prepare/r-svdialogs/PKGBUILD new file mode 100644 index 0000000000..01606d7cc1 --- /dev/null +++ b/prepare/r-svdialogs/PKGBUILD @@ -0,0 +1,36 @@ +# system requirements: zenity, yad +# Maintainer: Guoyi Zhang + +_pkgname=svDialogs +_pkgver=1.0.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SciViews - Standard Dialog Boxes for Windows, MacOS and Linuxes' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rstudioapi + r-svgui +) +optdepends=( + r-covr + r-knitr + r-markdown + r-spelling + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-svdialogs/lilac.py b/prepare/r-svdialogs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-svdialogs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-svdialogs/lilac.yaml b/prepare/r-svdialogs/lilac.yaml new file mode 100644 index 0000000000..a7a6f3a6fe --- /dev/null +++ b/prepare/r-svdialogs/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rstudioapi +- r-svgui +update_on: +- regex: svDialogs_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=svDialogs diff --git a/prepare/r-svglite/PKGBUILD b/prepare/r-svglite/PKGBUILD new file mode 100644 index 0000000000..83ed1027c0 --- /dev/null +++ b/prepare/r-svglite/PKGBUILD @@ -0,0 +1,38 @@ +# system requirements: C++11, libpng +# Maintainer: Guoyi Zhang + +_pkgname=svglite +_pkgver=2.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="An 'SVG' Graphics Device" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-cpp11 + r-systemfonts +) +optdepends=( + r-covr + r-fontquiver + r-htmltools + r-knitr + r-rmarkdown + r-testthat + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-svglite/lilac.py b/prepare/r-svglite/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-svglite/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-svglite/lilac.yaml b/prepare/r-svglite/lilac.yaml new file mode 100644 index 0000000000..f8645df11d --- /dev/null +++ b/prepare/r-svglite/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cpp11 +- r-systemfonts +update_on: +- regex: svglite_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=svglite diff --git a/prepare/r-svgpanzoom/PKGBUILD b/prepare/r-svgpanzoom/PKGBUILD new file mode 100644 index 0000000000..8f560b761a --- /dev/null +++ b/prepare/r-svgpanzoom/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=svgPanZoom +_pkgver=0.3.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="R 'Htmlwidget' to Add Pan and Zoom to Almost any R Graphic" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmlwidgets +) +optdepends=( + r-gridsvg + r-htmltools + r-knitr + r-svglite + r-xml + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-svgpanzoom/lilac.py b/prepare/r-svgpanzoom/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-svgpanzoom/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-svgpanzoom/lilac.yaml b/prepare/r-svgpanzoom/lilac.yaml new file mode 100644 index 0000000000..28445ddd4d --- /dev/null +++ b/prepare/r-svgpanzoom/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmlwidgets +update_on: +- regex: svgPanZoom_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=svgPanZoom diff --git a/prepare/r-svgui/PKGBUILD b/prepare/r-svgui/PKGBUILD new file mode 100644 index 0000000000..f351a4ef2a --- /dev/null +++ b/prepare/r-svgui/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=svGUI +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SciViews - Manage GUIs in R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-covr + r-knitr + r-markdown + r-spelling + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-svgui/lilac.py b/prepare/r-svgui/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-svgui/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-svgui/lilac.yaml b/prepare/r-svgui/lilac.yaml new file mode 100644 index 0000000000..9b4dfab711 --- /dev/null +++ b/prepare/r-svgui/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: svGUI_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=svGUI diff --git a/prepare/r-svmisc/PKGBUILD b/prepare/r-svmisc/PKGBUILD new file mode 100644 index 0000000000..ba254410dd --- /dev/null +++ b/prepare/r-svmisc/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=svMisc +_pkgver=1.2.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'SciViews' - Miscellaneous Functions" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-covr + r-knitr + r-markdown + r-rjava + r-rmarkdown + r-spelling + r-tcltk + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-svmisc/lilac.py b/prepare/r-svmisc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-svmisc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-svmisc/lilac.yaml b/prepare/r-svmisc/lilac.yaml new file mode 100644 index 0000000000..6edfd200ca --- /dev/null +++ b/prepare/r-svmisc/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: svMisc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=svMisc diff --git a/prepare/r-svunit/PKGBUILD b/prepare/r-svunit/PKGBUILD new file mode 100644 index 0000000000..8eb139127d --- /dev/null +++ b/prepare/r-svunit/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=svUnit +_pkgver=1.0.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'SciViews' - Unit, Integration and System Testing" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-covr + r-datasets + r-knitr + r-markdown + r-runit + r-spelling + r-svgui + r-xml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-svunit/lilac.py b/prepare/r-svunit/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-svunit/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-svunit/lilac.yaml b/prepare/r-svunit/lilac.yaml new file mode 100644 index 0000000000..d26b1d7cce --- /dev/null +++ b/prepare/r-svunit/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: svUnit_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=svUnit diff --git a/prepare/r-swamp/PKGBUILD b/prepare/r-swamp/PKGBUILD new file mode 100644 index 0000000000..b120323485 --- /dev/null +++ b/prepare/r-swamp/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=swamp +_pkgver=1.5.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization, Analysis and Adjustment of High-Dimensional Data in Respect to Sample Annotations' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-amap + r-gplots + r-impute +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-swamp/lilac.py b/prepare/r-swamp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-swamp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-swamp/lilac.yaml b/prepare/r-swamp/lilac.yaml new file mode 100644 index 0000000000..8faf515871 --- /dev/null +++ b/prepare/r-swamp/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-amap +- r-gplots +- r-impute +update_on: +- regex: swamp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=swamp diff --git a/prepare/r-swath2stats/PKGBUILD b/prepare/r-swath2stats/PKGBUILD new file mode 100644 index 0000000000..f3076ea888 --- /dev/null +++ b/prepare/r-swath2stats/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SWATH2stats +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Transform and Filter SWATH Data for Statistical Packages' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-data.table + r-ggplot2 + r-reshape2 +) +optdepends=( + r-alfq + r-knitr + r-msstats + r-peca + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-swath2stats/lilac.py b/prepare/r-swath2stats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-swath2stats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-swath2stats/lilac.yaml b/prepare/r-swath2stats/lilac.yaml new file mode 100644 index 0000000000..885fb37d4a --- /dev/null +++ b/prepare/r-swath2stats/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-data.table +- r-ggplot2 +- r-reshape2 +update_on: +- regex: SWATH2stats_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SWATH2stats diff --git a/prepare/r-swathxtend/PKGBUILD b/prepare/r-swathxtend/PKGBUILD new file mode 100644 index 0000000000..51e5658dd2 --- /dev/null +++ b/prepare/r-swathxtend/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SwathXtend +_pkgver=2.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SWATH extended library generation and statistical data analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-e1071 + r-openxlsx + r-venndiagram +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-swathxtend/lilac.py b/prepare/r-swathxtend/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-swathxtend/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-swathxtend/lilac.yaml b/prepare/r-swathxtend/lilac.yaml new file mode 100644 index 0000000000..e4ee74289a --- /dev/null +++ b/prepare/r-swathxtend/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-e1071 +- r-openxlsx +- r-venndiagram +update_on: +- regex: SwathXtend_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SwathXtend diff --git a/prepare/r-swfdr/PKGBUILD b/prepare/r-swfdr/PKGBUILD new file mode 100644 index 0000000000..01192c0374 --- /dev/null +++ b/prepare/r-swfdr/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=swfdr +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimation of the science-wise false discovery rate and the false discovery rate conditional on covariates' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biocstyle + r-dplyr + r-ggplot2 + r-knitr + r-qvalue + r-reshape2 + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-swfdr/lilac.py b/prepare/r-swfdr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-swfdr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-swfdr/lilac.yaml b/prepare/r-swfdr/lilac.yaml new file mode 100644 index 0000000000..4e47adc50b --- /dev/null +++ b/prepare/r-swfdr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: swfdr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/swfdr diff --git a/prepare/r-swimr/PKGBUILD b/prepare/r-swimr/PKGBUILD new file mode 100644 index 0000000000..82cb8c5a48 --- /dev/null +++ b/prepare/r-swimr/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SwimR +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Suite of Analytical Tools for Quantification of C. elegans Swimming Behavior' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-gplots + r-signal + r-r2html +) +makedepends=( + git + tar +) +source=("git+https://git.bioconductor.org/packages/${_pkgname}.git") +sha256sums=('SKIP') + +build() { + tar -zcvf ${_pkgname}.tar.gz ${_pkgname} + R CMD INSTALL ${_pkgname}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: + diff --git a/prepare/r-swimr/lilac.py b/prepare/r-swimr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-swimr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-swimr/lilac.yaml b/prepare/r-swimr/lilac.yaml new file mode 100644 index 0000000000..0c404037cf --- /dev/null +++ b/prepare/r-swimr/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gplots +- r-signal +- r-r2html +update_on: +- regex: Version(\d+.\d+.\d+) + source: regex + url: https://bioconductor.org/packages/SwimR diff --git a/prepare/r-switchbox/PKGBUILD b/prepare/r-switchbox/PKGBUILD new file mode 100644 index 0000000000..25a31be404 --- /dev/null +++ b/prepare/r-switchbox/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=switchBox +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-gplots + r-proc +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-switchbox/lilac.py b/prepare/r-switchbox/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-switchbox/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-switchbox/lilac.yaml b/prepare/r-switchbox/lilac.yaml new file mode 100644 index 0000000000..137cbd2f52 --- /dev/null +++ b/prepare/r-switchbox/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gplots +- r-proc +update_on: +- regex: switchBox_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/switchBox diff --git a/prepare/r-switchde/PKGBUILD b/prepare/r-switchde/PKGBUILD new file mode 100644 index 0000000000..96ede732ef --- /dev/null +++ b/prepare/r-switchde/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=switchde +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Switch-like differential expression across single-cell trajectories' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-ggplot2 + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-numderiv + r-rmarkdown + r-testthat + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-switchde/lilac.py b/prepare/r-switchde/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-switchde/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-switchde/lilac.yaml b/prepare/r-switchde/lilac.yaml new file mode 100644 index 0000000000..7326905ddf --- /dev/null +++ b/prepare/r-switchde/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: switchde_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/switchde diff --git a/prepare/r-sylly.en/PKGBUILD b/prepare/r-sylly.en/PKGBUILD new file mode 100644 index 0000000000..124a33789d --- /dev/null +++ b/prepare/r-sylly.en/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sylly.en +_pkgver=0.1-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Language Support for 'sylly' Package: English" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-sylly +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sylly.en/lilac.py b/prepare/r-sylly.en/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sylly.en/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sylly.en/lilac.yaml b/prepare/r-sylly.en/lilac.yaml new file mode 100644 index 0000000000..5e2dc45ca2 --- /dev/null +++ b/prepare/r-sylly.en/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-sylly +update_on: +- regex: sylly.en_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sylly.en diff --git a/prepare/r-sylly/PKGBUILD b/prepare/r-sylly/PKGBUILD new file mode 100644 index 0000000000..e8d05e6848 --- /dev/null +++ b/prepare/r-sylly/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=sylly +_pkgver=0.1-6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Hyphenation and Syllable Counting for Text Analysis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-rmarkdown + r-sylly.de + r-sylly.en + r-sylly.es + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-sylly/lilac.py b/prepare/r-sylly/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-sylly/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-sylly/lilac.yaml b/prepare/r-sylly/lilac.yaml new file mode 100644 index 0000000000..52743d2eb2 --- /dev/null +++ b/prepare/r-sylly/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: sylly_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=sylly diff --git a/prepare/r-synapsis/PKGBUILD b/prepare/r-synapsis/PKGBUILD new file mode 100644 index 0000000000..e06d326543 --- /dev/null +++ b/prepare/r-synapsis/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=synapsis +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R package to automate the analysis of double-strand break repair during meiosis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-ebimage +) +optdepends=( + r-biocstyle + r-ggplot2 + r-knitr + r-rmarkdown + r-testthat + r-tidyverse +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-synapsis/lilac.py b/prepare/r-synapsis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-synapsis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-synapsis/lilac.yaml b/prepare/r-synapsis/lilac.yaml new file mode 100644 index 0000000000..009060c04f --- /dev/null +++ b/prepare/r-synapsis/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ebimage +update_on: +- regex: synapsis_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/synapsis diff --git a/prepare/r-synapter/PKGBUILD b/prepare/r-synapter/PKGBUILD new file mode 100644 index 0000000000..5fd3da27db --- /dev/null +++ b/prepare/r-synapter/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=synapter +_pkgver=2.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Label-free data analysis pipeline for optimal identification and quantitation' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rcolorbrewer + r-lattice + r-qvalue + r-multtest + r-biobase + r-knitr + r-biostrings + r-cleaver + r-readr + r-rmarkdown + r-msnbase +) +makedepends=( + git + tar +) +optdepends=( + r-synapterdata + r-xtable + r-testthat + r-brain + r-biocstyle +) +source=("git+https://git.bioconductor.org/packages/${_pkgname}.git") +sha256sums=('SKIP') + +build() { + tar -zcvf ${_pkgname}.tar.gz ${_pkgname} + R CMD INSTALL ${_pkgname}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: + diff --git a/prepare/r-synapter/lilac.py b/prepare/r-synapter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-synapter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-synapter/lilac.yaml b/prepare/r-synapter/lilac.yaml new file mode 100644 index 0000000000..a178022add --- /dev/null +++ b/prepare/r-synapter/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcolorbrewer +- r-lattice +- r-qvalue +- r-multtest +- r-biobase +- r-knitr +- r-biostrings +- r-cleaver +- r-readr +- r-rmarkdown +- r-msnbase +update_on: +- regex: Version(\d+.\d+.\d+) + source: regex + url: https://bioconductor.org/packages/synapter diff --git a/prepare/r-synergyfinder/PKGBUILD b/prepare/r-synergyfinder/PKGBUILD new file mode 100644 index 0000000000..6ae5d18845 --- /dev/null +++ b/prepare/r-synergyfinder/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Guoyi Zhang + +_pkgname=synergyfinder +_pkgver=3.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Calculate and Visualize Synergy Scores for Drug Combinations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MPL2') +depends=( + r + r-dplyr + r-drc + r-furrr + r-future + r-ggforce + r-ggplot2 + r-ggrepel + r-gstat + r-kriging + r-magrittr + r-metr + r-mice + r-nleqslv + r-pbapply + r-plotly + r-purrr + r-reshape2 + r-sp + r-spatialextremes + r-stringr + r-tidyr + r-tidyverse + r-vegan +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-synergyfinder/lilac.py b/prepare/r-synergyfinder/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-synergyfinder/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-synergyfinder/lilac.yaml b/prepare/r-synergyfinder/lilac.yaml new file mode 100644 index 0000000000..bde3ea0728 --- /dev/null +++ b/prepare/r-synergyfinder/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-drc +- r-furrr +- r-future +- r-ggforce +- r-ggplot2 +- r-ggrepel +- r-gstat +- r-kriging +- r-magrittr +- r-metr +- r-mice +- r-nleqslv +- r-pbapply +- r-plotly +- r-purrr +- r-reshape2 +- r-sp +- r-spatialextremes +- r-stringr +- r-tidyr +- r-tidyverse +- r-vegan +update_on: +- regex: synergyfinder_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/synergyfinder diff --git a/prepare/r-synextend/PKGBUILD b/prepare/r-synextend/PKGBUILD new file mode 100644 index 0000000000..6e40fa1611 --- /dev/null +++ b/prepare/r-synextend/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SynExtend +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Working With Synteny Objects' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-decipher + r-iranges + r-s4vectors +) +optdepends=( + r-biocstyle + r-igraph + r-knitr + r-markdown + r-rmarkdown + r-rtracklayer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-synextend/lilac.py b/prepare/r-synextend/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-synextend/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-synextend/lilac.yaml b/prepare/r-synextend/lilac.yaml new file mode 100644 index 0000000000..4b5b06b5cd --- /dev/null +++ b/prepare/r-synextend/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-decipher +- r-iranges +- r-s4vectors +update_on: +- regex: SynExtend_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SynExtend diff --git a/prepare/r-synlet/PKGBUILD b/prepare/r-synlet/PKGBUILD new file mode 100644 index 0000000000..9bc815fb13 --- /dev/null +++ b/prepare/r-synlet/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=synlet +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Hits Selection for Synthetic Lethal RNAi Screen Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-doby + r-dplyr + r-ggplot2 + r-magrittr + r-rankprod + r-rcolorbrewer + r-reshape2 +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-synlet/lilac.py b/prepare/r-synlet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-synlet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-synlet/lilac.yaml b/prepare/r-synlet/lilac.yaml new file mode 100644 index 0000000000..e96f0574de --- /dev/null +++ b/prepare/r-synlet/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doby +- r-dplyr +- r-ggplot2 +- r-magrittr +- r-rankprod +- r-rcolorbrewer +- r-reshape2 +update_on: +- regex: synlet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/synlet diff --git a/prepare/r-synmut/PKGBUILD b/prepare/r-synmut/PKGBUILD new file mode 100644 index 0000000000..0c80b618d8 --- /dev/null +++ b/prepare/r-synmut/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=SynMut +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-seqinr + r-stringr +) +optdepends=( + r-biocmanager + r-devtools + r-glue + r-knitr + r-prettydoc + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-synmut/lilac.py b/prepare/r-synmut/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-synmut/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-synmut/lilac.yaml b/prepare/r-synmut/lilac.yaml new file mode 100644 index 0000000000..5d5c3f98ea --- /dev/null +++ b/prepare/r-synmut/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-seqinr +- r-stringr +update_on: +- regex: SynMut_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/SynMut diff --git a/prepare/r-systemfonts/PKGBUILD b/prepare/r-systemfonts/PKGBUILD new file mode 100644 index 0000000000..99f39aedd4 --- /dev/null +++ b/prepare/r-systemfonts/PKGBUILD @@ -0,0 +1,36 @@ +# system requirements: c("C++11", "\n fontconfig", "\n freetype2"), C++11 +# Maintainer: Guoyi Zhang + +_pkgname=systemfonts +_pkgver=1.0.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='System Native Font Finding' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-cpp11 +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-testthat + r-tools +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-systemfonts/lilac.py b/prepare/r-systemfonts/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-systemfonts/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-systemfonts/lilac.yaml b/prepare/r-systemfonts/lilac.yaml new file mode 100644 index 0000000000..75fb32a7cc --- /dev/null +++ b/prepare/r-systemfonts/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cpp11 +update_on: +- regex: systemfonts_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=systemfonts diff --git a/prepare/r-systempiper/PKGBUILD b/prepare/r-systempiper/PKGBUILD new file mode 100644 index 0000000000..2904f06723 --- /dev/null +++ b/prepare/r-systempiper/PKGBUILD @@ -0,0 +1,65 @@ +# system requirements: systemPipeR can be used to run externalcommand-line software (e.g. short read aligners), but thecorresponding tool needs to be installed on a system. +# Maintainer: Guoyi Zhang + +_pkgname=systemPipeR +_pkgver=2.0.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='systemPipeR: NGS workflow and report generation environment' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-biostrings + r-crayon + r-genomicranges + r-ggplot2 + r-htmlwidgets + r-magrittr + r-rsamtools + r-s4vectors + r-shortread + r-stringr + r-summarizedexperiment + r-yaml +) +optdepends=( + r-annotate + r-annotationdbi + r-batchtools + r-biocstyle + r-deseq2 + r-dplyr + r-dt + r-edger + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-go.db + r-grid + r-iranges + r-kableextra + r-knitr + r-limma + r-rjson + r-rmarkdown + r-rtracklayer + r-systempiperdata + r-testthat + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-systempiper/lilac.py b/prepare/r-systempiper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-systempiper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-systempiper/lilac.yaml b/prepare/r-systempiper/lilac.yaml new file mode 100644 index 0000000000..e91da37548 --- /dev/null +++ b/prepare/r-systempiper/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-crayon +- r-genomicranges +- r-ggplot2 +- r-htmlwidgets +- r-magrittr +- r-rsamtools +- r-s4vectors +- r-shortread +- r-stringr +- r-summarizedexperiment +- r-yaml +update_on: +- regex: systemPipeR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/systemPipeR diff --git a/prepare/r-systempiperdata/PKGBUILD b/prepare/r-systempiperdata/PKGBUILD new file mode 100644 index 0000000000..cd6c867917 --- /dev/null +++ b/prepare/r-systempiperdata/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=systemPipeRdata +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='systemPipeRdata: Workflow templates and sample data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-genomicfeatures + r-genomicranges + r-iranges + r-jsonlite + r-remotes + r-rsamtools + r-rtracklayer + r-shortread +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-runit + r-systempiper +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-systempiperdata/lilac.py b/prepare/r-systempiperdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-systempiperdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-systempiperdata/lilac.yaml b/prepare/r-systempiperdata/lilac.yaml new file mode 100644 index 0000000000..8f4a3beb40 --- /dev/null +++ b/prepare/r-systempiperdata/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-jsonlite +- r-remotes +- r-rsamtools +- r-rtracklayer +- r-shortread +update_on: +- regex: systemPipeRdata_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/systemPipeRdata diff --git a/prepare/r-systempipeshiny/PKGBUILD b/prepare/r-systempipeshiny/PKGBUILD new file mode 100644 index 0000000000..cd6e81cd9d --- /dev/null +++ b/prepare/r-systempipeshiny/PKGBUILD @@ -0,0 +1,84 @@ +# Maintainer: Guoyi Zhang + +_pkgname=systemPipeShiny +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='systemPipeShiny: An Interactive Framework for Workflow Management and Visualization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-bsplus + r-crayon + r-dplyr + r-drawer + r-dt + r-ggplot2 + r-glue + r-htmltools + r-magrittr + r-openssl + r-plotly + r-r6 + r-rlang + r-rsqlite + r-rstudioapi + r-shiny + r-shinyace + r-shinydashboard + r-shinydashboardplus + r-shinyfiles + r-shinyjqui + r-shinyjs + r-shinytoastr + r-shinywidgets + r-spscomps + r-spsutil + r-stringr + r-styler + r-tibble + r-vroom + r-yaml +) +optdepends=( + r-ape + r-biocstyle + r-callr + r-cicerone + r-deseq2 + r-esquisse + r-fs + r-glmpca + r-grid + r-knitr + r-pheatmap + r-pushbar + r-r.utils + r-readr + r-rhandsontable + r-rmarkdown + r-rtsne + r-summarizedexperiment + r-systempiper + r-systempiperdata + r-testthat + r-tidyr + r-upsetr + r-zip +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-systempipeshiny/lilac.py b/prepare/r-systempipeshiny/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-systempipeshiny/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-systempipeshiny/lilac.yaml b/prepare/r-systempipeshiny/lilac.yaml new file mode 100644 index 0000000000..1ec9ddbb55 --- /dev/null +++ b/prepare/r-systempipeshiny/lilac.yaml @@ -0,0 +1,41 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-bsplus +- r-crayon +- r-dplyr +- r-drawer +- r-dt +- r-ggplot2 +- r-glue +- r-htmltools +- r-magrittr +- r-openssl +- r-plotly +- r-r6 +- r-rlang +- r-rsqlite +- r-rstudioapi +- r-shiny +- r-shinyace +- r-shinydashboard +- r-shinydashboardplus +- r-shinyfiles +- r-shinyjqui +- r-shinyjs +- r-shinytoastr +- r-shinywidgets +- r-spscomps +- r-spsutil +- r-stringr +- r-styler +- r-tibble +- r-vroom +- r-yaml +update_on: +- regex: systemPipeShiny_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/systemPipeShiny diff --git a/prepare/r-systempipetools/PKGBUILD b/prepare/r-systempipetools/PKGBUILD new file mode 100644 index 0000000000..f74bf81a6a --- /dev/null +++ b/prepare/r-systempipetools/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=systemPipeTools +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for data visualization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ape + r-deseq2 + r-dplyr + r-dt + r-ggally + r-ggplot2 + r-ggrepel + r-ggtree + r-glmpca + r-magrittr + r-pheatmap + r-plotly + r-rtsne + r-summarizedexperiment + r-tibble +) +optdepends=( + r-biocgenerics + r-biocstyle + r-biostrings + r-knitr + r-methods + r-rmarkdown + r-systempiper + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-systempipetools/lilac.py b/prepare/r-systempipetools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-systempipetools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-systempipetools/lilac.yaml b/prepare/r-systempipetools/lilac.yaml new file mode 100644 index 0000000000..238cebb2ef --- /dev/null +++ b/prepare/r-systempipetools/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-deseq2 +- r-dplyr +- r-dt +- r-ggally +- r-ggplot2 +- r-ggrepel +- r-ggtree +- r-glmpca +- r-magrittr +- r-pheatmap +- r-plotly +- r-rtsne +- r-summarizedexperiment +- r-tibble +update_on: +- regex: systemPipeTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/systemPipeTools diff --git a/prepare/r-syuzhet/PKGBUILD b/prepare/r-syuzhet/PKGBUILD new file mode 100644 index 0000000000..8923e2bfd1 --- /dev/null +++ b/prepare/r-syuzhet/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=syuzhet +_pkgver=1.0.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Extracts Sentiment and Sentiment-Derived Plot Arcs from Text' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-dtt + r-nlp + r-rlang + r-textshape + r-tidyr + r-zoo +) +optdepends=( + r-devtools + r-knitr + r-pander + r-parallel + r-readxl + r-rmarkdown + r-stringr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-syuzhet/lilac.py b/prepare/r-syuzhet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-syuzhet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-syuzhet/lilac.yaml b/prepare/r-syuzhet/lilac.yaml new file mode 100644 index 0000000000..862eb31e33 --- /dev/null +++ b/prepare/r-syuzhet/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-dtt +- r-nlp +- r-rlang +- r-textshape +- r-tidyr +- r-zoo +update_on: +- regex: syuzhet_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=syuzhet diff --git a/prepare/r-tadcompare/PKGBUILD b/prepare/r-tadcompare/PKGBUILD new file mode 100644 index 0000000000..83abfd6bb0 --- /dev/null +++ b/prepare/r-tadcompare/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TADCompare +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='TADCompare: Identification and characterization of differential TADs' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-cowplot + r-dplyr + r-ggplot2 + r-ggpubr + r-hiccompare + r-magrittr + r-primme + r-rcolorbrewer + r-reshape2 + r-tidyr +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-microbenchmark + r-pheatmap + r-rgreat + r-rmarkdown + r-spectraltad + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tadcompare/lilac.py b/prepare/r-tadcompare/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tadcompare/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tadcompare/lilac.yaml b/prepare/r-tadcompare/lilac.yaml new file mode 100644 index 0000000000..e43a5516cc --- /dev/null +++ b/prepare/r-tadcompare/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cowplot +- r-dplyr +- r-ggplot2 +- r-ggpubr +- r-hiccompare +- r-magrittr +- r-primme +- r-rcolorbrewer +- r-reshape2 +- r-tidyr +update_on: +- regex: TADCompare_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TADCompare diff --git a/prepare/r-tagcloud/PKGBUILD b/prepare/r-tagcloud/PKGBUILD new file mode 100644 index 0000000000..efcb966d00 --- /dev/null +++ b/prepare/r-tagcloud/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tagcloud +_pkgver=0.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tag Clouds' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcolorbrewer + r-rcpp +) +optdepends=( + r-extrafont + r-knitr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tagcloud/lilac.py b/prepare/r-tagcloud/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tagcloud/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tagcloud/lilac.yaml b/prepare/r-tagcloud/lilac.yaml new file mode 100644 index 0000000000..099df6666c --- /dev/null +++ b/prepare/r-tagcloud/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcolorbrewer +- r-rcpp +update_on: +- regex: tagcloud_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tagcloud diff --git a/prepare/r-tanggle/PKGBUILD b/prepare/r-tanggle/PKGBUILD new file mode 100644 index 0000000000..3fde22ec04 --- /dev/null +++ b/prepare/r-tanggle/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tanggle +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization of Phylogenetic Networks' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ape + r-ggplot2 + r-ggtree + r-phangorn +) +optdepends=( + r-biocstyle + r-ggimage + r-knitr + r-rmarkdown + r-tinytest +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tanggle/lilac.py b/prepare/r-tanggle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tanggle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tanggle/lilac.yaml b/prepare/r-tanggle/lilac.yaml new file mode 100644 index 0000000000..3cdd2b6163 --- /dev/null +++ b/prepare/r-tanggle/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-ggplot2 +- r-ggtree +- r-phangorn +update_on: +- regex: tanggle_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tanggle diff --git a/prepare/r-tapseq/PKGBUILD b/prepare/r-tapseq/PKGBUILD new file mode 100644 index 0000000000..5f3a76a3c1 --- /dev/null +++ b/prepare/r-tapseq/PKGBUILD @@ -0,0 +1,53 @@ +# system requirements: Primer3 (>= 2.5.0), BLAST+ (>=2.6.0) +# Maintainer: Guoyi Zhang + +_pkgname=TAPseq +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Targeted scRNA-seq primer design for TAP-seq' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-dplyr + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-s4vectors + r-tidyr +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg38 + r-cowplot + r-ggplot2 + r-glmnet + r-knitr + r-matrix + r-rmarkdown + r-rtracklayer + r-seurat + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tapseq/lilac.py b/prepare/r-tapseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tapseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tapseq/lilac.yaml b/prepare/r-tapseq/lilac.yaml new file mode 100644 index 0000000000..50e5bcdbfa --- /dev/null +++ b/prepare/r-tapseq/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-dplyr +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-s4vectors +- r-tidyr +update_on: +- regex: TAPseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TAPseq diff --git a/prepare/r-target/PKGBUILD b/prepare/r-target/PKGBUILD new file mode 100644 index 0000000000..a3fe99c70d --- /dev/null +++ b/prepare/r-target/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=target +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Predict Combined Function of Transcription Factors' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-genomicranges + r-iranges + r-matrixstats + r-shiny +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-shinybs + r-shinytest + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-target/lilac.py b/prepare/r-target/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-target/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-target/lilac.yaml b/prepare/r-target/lilac.yaml new file mode 100644 index 0000000000..c1ee4e4055 --- /dev/null +++ b/prepare/r-target/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomicranges +- r-iranges +- r-matrixstats +- r-shiny +update_on: +- regex: target_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/target diff --git a/prepare/r-targetdecoy/PKGBUILD b/prepare/r-targetdecoy/PKGBUILD new file mode 100644 index 0000000000..96575398d6 --- /dev/null +++ b/prepare/r-targetdecoy/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TargetDecoy +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Diagnostic Plots to Evaluate the Target Decoy Approach' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ggplot2 + r-ggpubr + r-mzid + r-mzr +) +optdepends=( + r-biocstyle + r-covr + r-gridextra + r-knitr + r-msdata + r-rmarkdown + r-sessioninfo + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-targetdecoy/lilac.py b/prepare/r-targetdecoy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-targetdecoy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-targetdecoy/lilac.yaml b/prepare/r-targetdecoy/lilac.yaml new file mode 100644 index 0000000000..afb9168353 --- /dev/null +++ b/prepare/r-targetdecoy/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-ggpubr +- r-mzid +- r-mzr +update_on: +- regex: TargetDecoy_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TargetDecoy diff --git a/prepare/r-targetscore/PKGBUILD b/prepare/r-targetscore/PKGBUILD new file mode 100644 index 0000000000..055d288613 --- /dev/null +++ b/prepare/r-targetscore/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TargetScore +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-pracma +) +optdepends=( + r-biobase + r-geoquery + r-gplots + r-targetscoredata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-targetscore/lilac.py b/prepare/r-targetscore/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-targetscore/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-targetscore/lilac.yaml b/prepare/r-targetscore/lilac.yaml new file mode 100644 index 0000000000..5bcf16bc4f --- /dev/null +++ b/prepare/r-targetscore/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-pracma +update_on: +- regex: TargetScore_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TargetScore diff --git a/prepare/r-targetsearch/PKGBUILD b/prepare/r-targetsearch/PKGBUILD new file mode 100644 index 0000000000..c85fe98fc9 --- /dev/null +++ b/prepare/r-targetsearch/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TargetSearch +_pkgver=1.50.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A package for the analysis of GC-MS metabolite profiling data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-assertthat + r-ncdf4 +) +optdepends=( + r-biocstyle + r-knitr + r-targetsearchdata + r-tinytest +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-targetsearch/lilac.py b/prepare/r-targetsearch/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-targetsearch/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-targetsearch/lilac.yaml b/prepare/r-targetsearch/lilac.yaml new file mode 100644 index 0000000000..9162744827 --- /dev/null +++ b/prepare/r-targetsearch/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-ncdf4 +update_on: +- regex: TargetSearch_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TargetSearch diff --git a/prepare/r-tarifx/PKGBUILD b/prepare/r-tarifx/PKGBUILD new file mode 100644 index 0000000000..b442ade4ed --- /dev/null +++ b/prepare/r-tarifx/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=taRifx +_pkgver=1.0.6.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Collection of Utility and Convenience Functions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-plyr + r-reshape2 +) +optdepends=( + r-catools + r-data.table + r-gdata + r-ggplot2 + r-grid + r-lattice + r-pspline + r-rsqlite + r-stringr + r-xtable +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tarifx/lilac.py b/prepare/r-tarifx/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tarifx/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tarifx/lilac.yaml b/prepare/r-tarifx/lilac.yaml new file mode 100644 index 0000000000..4bdfb7a199 --- /dev/null +++ b/prepare/r-tarifx/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-plyr +- r-reshape2 +update_on: +- regex: taRifx_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=taRifx diff --git a/prepare/r-tarseqqc/PKGBUILD b/prepare/r-tarseqqc/PKGBUILD new file mode 100644 index 0000000000..94c9f95d26 --- /dev/null +++ b/prepare/r-tarseqqc/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TarSeqQC +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='TARgeted SEQuencing Experiment Quality Control' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biocparallel + r-biostrings + r-cowplot + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-hmisc + r-iranges + r-openxlsx + r-plyr + r-reshape2 + r-rsamtools + r-s4vectors +) +optdepends=( + r-biocmanager + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tarseqqc/lilac.py b/prepare/r-tarseqqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tarseqqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tarseqqc/lilac.yaml b/prepare/r-tarseqqc/lilac.yaml new file mode 100644 index 0000000000..07dd74648d --- /dev/null +++ b/prepare/r-tarseqqc/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-cowplot +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-hmisc +- r-iranges +- r-openxlsx +- r-plyr +- r-reshape2 +- r-rsamtools +- r-s4vectors +update_on: +- regex: TarSeqQC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TarSeqQC diff --git a/prepare/r-tbsignatureprofiler/PKGBUILD b/prepare/r-tbsignatureprofiler/PKGBUILD new file mode 100644 index 0000000000..edfd495d3b --- /dev/null +++ b/prepare/r-tbsignatureprofiler/PKGBUILD @@ -0,0 +1,68 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TBSignatureProfiler +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Profile RNA-Seq Data Using TB Pathway Signatures' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-assign + r-biocgenerics + r-biocparallel + r-complexheatmap + r-deseq2 + r-dt + r-edger + r-gdata + r-ggplot2 + r-gsva + r-magrittr + r-rcolorbrewer + r-reshape2 + r-rlang + r-rocit + r-s4vectors + r-singscore + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-caret + r-circlize + r-class + r-covr + r-dplyr + r-e1071 + r-glmnet + r-hgnchelper + r-impute + r-knitr + r-lintr + r-mass + r-plyr + r-proc + r-randomforest + r-rmarkdown + r-shiny + r-spelling + r-sva + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tbsignatureprofiler/lilac.py b/prepare/r-tbsignatureprofiler/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tbsignatureprofiler/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tbsignatureprofiler/lilac.yaml b/prepare/r-tbsignatureprofiler/lilac.yaml new file mode 100644 index 0000000000..4f906ec5d1 --- /dev/null +++ b/prepare/r-tbsignatureprofiler/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assign +- r-biocgenerics +- r-biocparallel +- r-complexheatmap +- r-deseq2 +- r-dt +- r-edger +- r-gdata +- r-ggplot2 +- r-gsva +- r-magrittr +- r-rcolorbrewer +- r-reshape2 +- r-rlang +- r-rocit +- r-s4vectors +- r-singscore +- r-summarizedexperiment +update_on: +- regex: TBSignatureProfiler_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TBSignatureProfiler diff --git a/prepare/r-tbx20bamsubset/PKGBUILD b/prepare/r-tbx20bamsubset/PKGBUILD new file mode 100644 index 0000000000..4142b0e2d1 --- /dev/null +++ b/prepare/r-tbx20bamsubset/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TBX20BamSubset +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Subset of BAM files from the "TBX20" experiment' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-rsamtools + r-xtable +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tbx20bamsubset/lilac.py b/prepare/r-tbx20bamsubset/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tbx20bamsubset/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tbx20bamsubset/lilac.yaml b/prepare/r-tbx20bamsubset/lilac.yaml new file mode 100644 index 0000000000..7ad75739bb --- /dev/null +++ b/prepare/r-tbx20bamsubset/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rsamtools +- r-xtable +update_on: +- regex: TBX20BamSubset_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TBX20BamSubset diff --git a/prepare/r-tcc/PKGBUILD b/prepare/r-tcc/PKGBUILD new file mode 100644 index 0000000000..d73c084bcf --- /dev/null +++ b/prepare/r-tcc/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TCC +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='TCC: Differential expression analysis for tag count data with robust normalization strategies' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bayseq + r-deseq2 + r-edger + r-roc +) +optdepends=( + r-biocgenerics + r-runit + r-snow +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tcc/lilac.py b/prepare/r-tcc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tcc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tcc/lilac.yaml b/prepare/r-tcc/lilac.yaml new file mode 100644 index 0000000000..58a6865d89 --- /dev/null +++ b/prepare/r-tcc/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bayseq +- r-deseq2 +- r-edger +- r-roc +update_on: +- regex: TCC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TCC diff --git a/prepare/r-tcgabiolinks/PKGBUILD b/prepare/r-tcgabiolinks/PKGBUILD new file mode 100644 index 0000000000..707f3411e9 --- /dev/null +++ b/prepare/r-tcgabiolinks/PKGBUILD @@ -0,0 +1,85 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TCGAbiolinks +_pkgver=2.22.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-data.table + r-downloader + r-dplyr + r-genomicranges + r-ggplot2 + r-httr + r-iranges + r-jsonlite + r-knitr + r-plyr + r-purrr + r-r.utils + r-readr + r-rvest + r-s4vectors + r-stringr + r-summarizedexperiment + r-tcgabiolinksgui.data + r-tibble + r-tidyr + r-xml + r-xml2 +) +optdepends=( + r-affy + r-biobase + r-biocstyle + r-c3net + r-circlize + r-clusterprofiler + r-complexheatmap + r-consensusclusterplus + r-devtools + r-dnet + r-doparallel + r-edaseq + r-edger + r-genefilter + r-ggrepel + r-grid + r-gridextra + r-igraph + r-jpeg + r-limma + r-maftools + r-minet + r-parallel + r-parmigene + r-pathview + r-png + r-rmarkdown + r-scales + r-sesame + r-suprahex + r-survival + r-survminer + r-sva + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tcgabiolinks/lilac.py b/prepare/r-tcgabiolinks/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tcgabiolinks/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tcgabiolinks/lilac.yaml b/prepare/r-tcgabiolinks/lilac.yaml new file mode 100644 index 0000000000..37cb0512aa --- /dev/null +++ b/prepare/r-tcgabiolinks/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-data.table +- r-downloader +- r-dplyr +- r-genomicranges +- r-ggplot2 +- r-httr +- r-iranges +- r-jsonlite +- r-knitr +- r-plyr +- r-purrr +- r-r.utils +- r-readr +- r-rvest +- r-s4vectors +- r-stringr +- r-summarizedexperiment +- r-tcgabiolinksgui.data +- r-tibble +- r-tidyr +- r-xml +- r-xml2 +update_on: +- regex: TCGAbiolinks_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TCGAbiolinks diff --git a/prepare/r-tcgabiolinksgui.data/PKGBUILD b/prepare/r-tcgabiolinksgui.data/PKGBUILD new file mode 100644 index 0000000000..2429bfc675 --- /dev/null +++ b/prepare/r-tcgabiolinksgui.data/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TCGAbiolinksGUI.data +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Data for the TCGAbiolinksGUI package' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biocstyle + r-dt + r-knitr + r-readr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tcgabiolinksgui.data/lilac.py b/prepare/r-tcgabiolinksgui.data/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tcgabiolinksgui.data/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tcgabiolinksgui.data/lilac.yaml b/prepare/r-tcgabiolinksgui.data/lilac.yaml new file mode 100644 index 0000000000..7c63bb28d7 --- /dev/null +++ b/prepare/r-tcgabiolinksgui.data/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: TCGAbiolinksGUI.data_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TCGAbiolinksGUI.data diff --git a/prepare/r-tcgabiolinksgui/PKGBUILD b/prepare/r-tcgabiolinksgui/PKGBUILD new file mode 100644 index 0000000000..bae6095e92 --- /dev/null +++ b/prepare/r-tcgabiolinksgui/PKGBUILD @@ -0,0 +1,62 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TCGAbiolinksGUI +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-caret + r-clusterprofiler + r-colourpicker + r-data.table + r-downloader + r-dt + r-elmer + r-ggplot2 + r-ggrepel + r-maftools + r-pathview + r-plotly + r-readr + r-sesame + r-shiny + r-shinybs + r-shinydashboard + r-shinyfiles + r-shinyjs + r-stringr + r-summarizedexperiment + r-tcgabiolinks + r-tcgabiolinksgui.data +) +optdepends=( + r-animation + r-biocstyle + r-devtools + r-dplyr + r-knitr + r-pander + r-rmarkdown + r-roxygen2 + r-rvest + r-testthat + r-xml2 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tcgabiolinksgui/lilac.py b/prepare/r-tcgabiolinksgui/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tcgabiolinksgui/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tcgabiolinksgui/lilac.yaml b/prepare/r-tcgabiolinksgui/lilac.yaml new file mode 100644 index 0000000000..54bd7860f3 --- /dev/null +++ b/prepare/r-tcgabiolinksgui/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-caret +- r-clusterprofiler +- r-colourpicker +- r-data.table +- r-downloader +- r-dt +- r-elmer +- r-ggplot2 +- r-ggrepel +- r-maftools +- r-pathview +- r-plotly +- r-readr +- r-sesame +- r-shiny +- r-shinybs +- r-shinydashboard +- r-shinyfiles +- r-shinyjs +- r-stringr +- r-summarizedexperiment +- r-tcgabiolinks +- r-tcgabiolinksgui.data +update_on: +- regex: TCGAbiolinksGUI_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TCGAbiolinksGUI diff --git a/prepare/r-tcgautils/PKGBUILD b/prepare/r-tcgautils/PKGBUILD new file mode 100644 index 0000000000..438940318a --- /dev/null +++ b/prepare/r-tcgautils/PKGBUILD @@ -0,0 +1,63 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TCGAutils +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='TCGA utility functions for data management' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biocgenerics + r-genomeinfodb + r-genomicdatacommons + r-genomicfeatures + r-genomicranges + r-iranges + r-multiassayexperiment + r-raggedexperiment + r-rvest + r-s4vectors + r-stringr + r-summarizedexperiment + r-xml2 +) +optdepends=( + r-biocfilecache + r-biocstyle + r-complexheatmap + r-curatedtcgadata + r-devtools + r-dplyr + r-illuminahumanmethylation450kanno.ilmn12.hg19 + r-impute + r-knitr + r-magrittr + r-mirbase.db + r-org.hs.eg.db + r-r.utils + r-rcolorbrewer + r-readr + r-rmarkdown + r-rtcgatoolbox + r-rtracklayer + r-testthat + r-txdb.hsapiens.ucsc.hg18.knowngene + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tcgautils/lilac.py b/prepare/r-tcgautils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tcgautils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tcgautils/lilac.yaml b/prepare/r-tcgautils/lilac.yaml new file mode 100644 index 0000000000..78f358d177 --- /dev/null +++ b/prepare/r-tcgautils/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-genomeinfodb +- r-genomicdatacommons +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-multiassayexperiment +- r-raggedexperiment +- r-rvest +- r-s4vectors +- r-stringr +- r-summarizedexperiment +- r-xml2 +update_on: +- regex: TCGAutils_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TCGAutils diff --git a/prepare/r-tcltk2/PKGBUILD b/prepare/r-tcltk2/PKGBUILD new file mode 100644 index 0000000000..a6b8f5e4af --- /dev/null +++ b/prepare/r-tcltk2/PKGBUILD @@ -0,0 +1,30 @@ +# system requirements: Tcl/Tk (>= 8.5), Tktable (>= 2.9, optional) +# Maintainer: Guoyi Zhang + +_pkgname=tcltk2 +_pkgver=1.2-11 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tcl/Tk Additions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r +) +optdepends=( + r-utils +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tcltk2/lilac.py b/prepare/r-tcltk2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tcltk2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tcltk2/lilac.yaml b/prepare/r-tcltk2/lilac.yaml new file mode 100644 index 0000000000..407af1c7de --- /dev/null +++ b/prepare/r-tcltk2/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: tcltk2_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tcltk2 diff --git a/prepare/r-tcseq/PKGBUILD b/prepare/r-tcseq/PKGBUILD new file mode 100644 index 0000000000..fcec25c62e --- /dev/null +++ b/prepare/r-tcseq/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TCseq +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Time course sequencing data analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-e1071 + r-edger + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-locfit + r-reshape2 + r-rsamtools + r-summarizedexperiment +) +optdepends=( + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tcseq/lilac.py b/prepare/r-tcseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tcseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tcseq/lilac.yaml b/prepare/r-tcseq/lilac.yaml new file mode 100644 index 0000000000..f485fd6bc0 --- /dev/null +++ b/prepare/r-tcseq/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-e1071 +- r-edger +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-locfit +- r-reshape2 +- r-rsamtools +- r-summarizedexperiment +update_on: +- regex: TCseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TCseq diff --git a/prepare/r-tdaracne/PKGBUILD b/prepare/r-tdaracne/PKGBUILD new file mode 100644 index 0000000000..04515dd788 --- /dev/null +++ b/prepare/r-tdaracne/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TDARACNE +_pkgver=1.44.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Network reverse engineering from time course data.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-genkern + r-rgraphviz +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tdaracne/lilac.py b/prepare/r-tdaracne/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tdaracne/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tdaracne/lilac.yaml b/prepare/r-tdaracne/lilac.yaml new file mode 100644 index 0000000000..a8d35ad3be --- /dev/null +++ b/prepare/r-tdaracne/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-genkern +- r-rgraphviz +update_on: +- regex: TDARACNE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TDARACNE diff --git a/prepare/r-teachingdemos/PKGBUILD b/prepare/r-teachingdemos/PKGBUILD new file mode 100644 index 0000000000..328c5ecd4e --- /dev/null +++ b/prepare/r-teachingdemos/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TeachingDemos +_pkgver=2.12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Demonstrations for Teaching and Learning' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-ggplot2 + r-lattice + r-logspline + r-manipulate + r-maptools + r-mass + r-png + r-r2wd + r-rgl + r-tcltk + r-tcltk2 + r-tkrplot +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-teachingdemos/lilac.py b/prepare/r-teachingdemos/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-teachingdemos/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-teachingdemos/lilac.yaml b/prepare/r-teachingdemos/lilac.yaml new file mode 100644 index 0000000000..0df0ea1f60 --- /dev/null +++ b/prepare/r-teachingdemos/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: TeachingDemos_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=TeachingDemos diff --git a/prepare/r-tensor/PKGBUILD b/prepare/r-tensor/PKGBUILD new file mode 100644 index 0000000000..e622e0f983 --- /dev/null +++ b/prepare/r-tensor/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tensor +_pkgver=1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tensor product of arrays' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tensor/lilac.py b/prepare/r-tensor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tensor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tensor/lilac.yaml b/prepare/r-tensor/lilac.yaml new file mode 100644 index 0000000000..7922c8b137 --- /dev/null +++ b/prepare/r-tensor/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: tensor_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tensor diff --git a/prepare/r-tensora/PKGBUILD b/prepare/r-tensora/PKGBUILD new file mode 100644 index 0000000000..390317c797 --- /dev/null +++ b/prepare/r-tensora/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tensorA +_pkgver=0.36.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Advanced Tensor Arithmetic with Named Indices' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tensora/lilac.py b/prepare/r-tensora/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tensora/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tensora/lilac.yaml b/prepare/r-tensora/lilac.yaml new file mode 100644 index 0000000000..62b0f680ff --- /dev/null +++ b/prepare/r-tensora/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: tensorA_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tensorA diff --git a/prepare/r-tensorflow/PKGBUILD b/prepare/r-tensorflow/PKGBUILD new file mode 100644 index 0000000000..e91f2dc458 --- /dev/null +++ b/prepare/r-tensorflow/PKGBUILD @@ -0,0 +1,39 @@ +# system requirements: TensorFlow (https://www.tensorflow.org/) +# Maintainer: Guoyi Zhang + +_pkgname=tensorflow +_pkgver=2.7.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="R Interface to 'TensorFlow'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-config + r-processx + r-reticulate + r-rstudioapi + r-tfautograph + r-tfruns + r-yaml +) +optdepends=( + r-callr + r-keras + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tensorflow/lilac.py b/prepare/r-tensorflow/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tensorflow/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tensorflow/lilac.yaml b/prepare/r-tensorflow/lilac.yaml new file mode 100644 index 0000000000..3b7a2ba711 --- /dev/null +++ b/prepare/r-tensorflow/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-config +- r-processx +- r-reticulate +- r-rstudioapi +- r-tfautograph +- r-tfruns +- r-yaml +update_on: +- regex: tensorflow_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tensorflow diff --git a/prepare/r-tenxpbmcdata/PKGBUILD b/prepare/r-tenxpbmcdata/PKGBUILD new file mode 100644 index 0000000000..4f40c218a5 --- /dev/null +++ b/prepare/r-tenxpbmcdata/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TENxPBMCData +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='PBMC data from 10X Genomics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('CCPL:by-nc-sa') +depends=( + r + r-annotationhub + r-experimenthub + r-hdf5array + r-singlecellexperiment +) +optdepends=( + r-biocfilecache + r-biocparallel + r-biocstyle + r-knitr + r-rmarkdown + r-snow +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tenxpbmcdata/lilac.py b/prepare/r-tenxpbmcdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tenxpbmcdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tenxpbmcdata/lilac.yaml b/prepare/r-tenxpbmcdata/lilac.yaml new file mode 100644 index 0000000000..1e7776d898 --- /dev/null +++ b/prepare/r-tenxpbmcdata/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-experimenthub +- r-hdf5array +- r-singlecellexperiment +update_on: +- regex: TENxPBMCData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TENxPBMCData diff --git a/prepare/r-tenxplore/PKGBUILD b/prepare/r-tenxplore/PKGBUILD new file mode 100644 index 0000000000..e9f9b2028c --- /dev/null +++ b/prepare/r-tenxplore/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tenXplore +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-matrixstats + r-ontoproc + r-org.mm.eg.db + r-restfulse + r-shiny + r-summarizedexperiment +) +optdepends=( + r-knitr + r-org.hs.eg.db + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tenxplore/lilac.py b/prepare/r-tenxplore/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tenxplore/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tenxplore/lilac.yaml b/prepare/r-tenxplore/lilac.yaml new file mode 100644 index 0000000000..77cdde6aba --- /dev/null +++ b/prepare/r-tenxplore/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-matrixstats +- r-ontoproc +- r-org.mm.eg.db +- r-restfulse +- r-shiny +- r-summarizedexperiment +update_on: +- regex: tenXplore_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tenXplore diff --git a/prepare/r-teqc/PKGBUILD b/prepare/r-teqc/PKGBUILD new file mode 100644 index 0000000000..44c874bcd3 --- /dev/null +++ b/prepare/r-teqc/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TEQC +_pkgver=4.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quality control for target capture experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-hwriter + r-iranges + r-rsamtools +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-teqc/lilac.py b/prepare/r-teqc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-teqc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-teqc/lilac.yaml b/prepare/r-teqc/lilac.yaml new file mode 100644 index 0000000000..f889ba0ead --- /dev/null +++ b/prepare/r-teqc/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-hwriter +- r-iranges +- r-rsamtools +update_on: +- regex: TEQC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TEQC diff --git a/prepare/r-ternarynet/PKGBUILD b/prepare/r-ternarynet/PKGBUILD new file mode 100644 index 0000000000..e7e916f65d --- /dev/null +++ b/prepare/r-ternarynet/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ternarynet +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Ternary Network Estimation' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-igraph +) +optdepends=( + r-rmpi + r-snow + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ternarynet/lilac.py b/prepare/r-ternarynet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ternarynet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ternarynet/lilac.yaml b/prepare/r-ternarynet/lilac.yaml new file mode 100644 index 0000000000..db0614e0a9 --- /dev/null +++ b/prepare/r-ternarynet/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-igraph +update_on: +- regex: ternarynet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ternarynet diff --git a/prepare/r-terra/PKGBUILD b/prepare/r-terra/PKGBUILD new file mode 100644 index 0000000000..3f03e29e54 --- /dev/null +++ b/prepare/r-terra/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: C++11, GDAL (>= 2.2.3), GEOS (>= 3.4.0), PROJ (>=4.9.3), sqlite3 +# Maintainer: Guoyi Zhang + +_pkgname=terra +_pkgver=1.4-22 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Spatial Data Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-deldir + r-ncdf4 + r-parallel + r-raster + r-sf + r-tinytest + r-xml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-terra/lilac.py b/prepare/r-terra/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-terra/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-terra/lilac.yaml b/prepare/r-terra/lilac.yaml new file mode 100644 index 0000000000..fc9557b579 --- /dev/null +++ b/prepare/r-terra/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: terra_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=terra diff --git a/prepare/r-tester/PKGBUILD b/prepare/r-tester/PKGBUILD new file mode 100644 index 0000000000..60af0472c1 --- /dev/null +++ b/prepare/r-tester/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tester +_pkgver=0.1.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tests and checks characteristics of R objects' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tester/lilac.py b/prepare/r-tester/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tester/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tester/lilac.yaml b/prepare/r-tester/lilac.yaml new file mode 100644 index 0000000000..9378950db3 --- /dev/null +++ b/prepare/r-tester/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: tester_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tester diff --git a/prepare/r-testthat/PKGBUILD b/prepare/r-testthat/PKGBUILD new file mode 100644 index 0000000000..a3f72439ee --- /dev/null +++ b/prepare/r-testthat/PKGBUILD @@ -0,0 +1,59 @@ +# Maintainer: Guoyi Zhang + +_pkgname=testthat +_pkgver=3.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Unit Testing for R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-brio + r-callr + r-cli + r-crayon + r-desc + r-digest + r-ellipsis + r-evaluate + r-jsonlite + r-lifecycle + r-magrittr + r-pkgload + r-praise + r-processx + r-ps + r-r6 + r-rlang + r-waldo + r-withr +) +optdepends=( + r-covr + r-curl + r-diffviewer + r-knitr + r-mockery + r-rmarkdown + r-rstudioapi + r-shiny + r-usethis + r-vctrs + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-testthat/lilac.py b/prepare/r-testthat/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-testthat/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-testthat/lilac.yaml b/prepare/r-testthat/lilac.yaml new file mode 100644 index 0000000000..5dc43ef07b --- /dev/null +++ b/prepare/r-testthat/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-brio +- r-callr +- r-cli +- r-crayon +- r-desc +- r-digest +- r-ellipsis +- r-evaluate +- r-jsonlite +- r-lifecycle +- r-magrittr +- r-pkgload +- r-praise +- r-processx +- r-ps +- r-r6 +- r-rlang +- r-waldo +- r-withr +update_on: +- regex: testthat_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=testthat diff --git a/prepare/r-text2vec/PKGBUILD b/prepare/r-text2vec/PKGBUILD new file mode 100644 index 0000000000..c15c1ed5ab --- /dev/null +++ b/prepare/r-text2vec/PKGBUILD @@ -0,0 +1,45 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=text2vec +_pkgver=0.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Modern Text Mining Framework for R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-digest + r-lgr + r-mlapi + r-r6 + r-rcpp + r-rsparse + r-stringi +) +optdepends=( + r-covr + r-glmnet + r-knitr + r-magrittr + r-proxy + r-rmarkdown + r-testthat + r-udpipe +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-text2vec/lilac.py b/prepare/r-text2vec/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-text2vec/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-text2vec/lilac.yaml b/prepare/r-text2vec/lilac.yaml new file mode 100644 index 0000000000..d29212f3eb --- /dev/null +++ b/prepare/r-text2vec/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-digest +- r-lgr +- r-mlapi +- r-r6 +- r-rcpp +- r-rsparse +- r-stringi +update_on: +- regex: text2vec_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=text2vec diff --git a/prepare/r-textclean/PKGBUILD b/prepare/r-textclean/PKGBUILD new file mode 100644 index 0000000000..0be52f34cb --- /dev/null +++ b/prepare/r-textclean/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=textclean +_pkgver=0.9.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Text Cleaning Tools' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-english + r-glue + r-lexicon + r-mgsub + r-qdapregex + r-stringi + r-textshape +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-textclean/lilac.py b/prepare/r-textclean/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-textclean/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-textclean/lilac.yaml b/prepare/r-textclean/lilac.yaml new file mode 100644 index 0000000000..96568caeaf --- /dev/null +++ b/prepare/r-textclean/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-english +- r-glue +- r-lexicon +- r-mgsub +- r-qdapregex +- r-stringi +- r-textshape +update_on: +- regex: textclean_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=textclean diff --git a/prepare/r-textshape/PKGBUILD b/prepare/r-textshape/PKGBUILD new file mode 100644 index 0000000000..d1f6397fd8 --- /dev/null +++ b/prepare/r-textshape/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=textshape +_pkgver=1.7.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Reshaping Text' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-slam + r-stringi +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-textshape/lilac.py b/prepare/r-textshape/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-textshape/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-textshape/lilac.yaml b/prepare/r-textshape/lilac.yaml new file mode 100644 index 0000000000..0b0e9e13de --- /dev/null +++ b/prepare/r-textshape/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-slam +- r-stringi +update_on: +- regex: textshape_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=textshape diff --git a/prepare/r-textshaping/PKGBUILD b/prepare/r-textshaping/PKGBUILD new file mode 100644 index 0000000000..442ce7f5ea --- /dev/null +++ b/prepare/r-textshaping/PKGBUILD @@ -0,0 +1,35 @@ +# system requirements: C++11, freetype2, harfbuzz, fribidi +# Maintainer: Guoyi Zhang + +_pkgname=textshaping +_pkgver=0.3.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text Shaping" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-cpp11 + r-systemfonts +) +optdepends=( + r-covr + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-textshaping/lilac.py b/prepare/r-textshaping/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-textshaping/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-textshaping/lilac.yaml b/prepare/r-textshaping/lilac.yaml new file mode 100644 index 0000000000..02d50e4c6b --- /dev/null +++ b/prepare/r-textshaping/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cpp11 +- r-systemfonts +update_on: +- regex: textshaping_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=textshaping diff --git a/prepare/r-textstem/PKGBUILD b/prepare/r-textstem/PKGBUILD new file mode 100644 index 0000000000..ee55235aab --- /dev/null +++ b/prepare/r-textstem/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=textstem +_pkgver=0.1.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Stemming and Lemmatizing Text' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-hunspell + r-korpus + r-korpus.lang.en + r-lexicon + r-quanteda + r-snowballc + r-stringi + r-textclean + r-textshape +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-textstem/lilac.py b/prepare/r-textstem/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-textstem/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-textstem/lilac.yaml b/prepare/r-textstem/lilac.yaml new file mode 100644 index 0000000000..0f3d542f0f --- /dev/null +++ b/prepare/r-textstem/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-hunspell +- r-korpus +- r-korpus.lang.en +- r-lexicon +- r-quanteda +- r-snowballc +- r-stringi +- r-textclean +- r-textshape +update_on: +- regex: textstem_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=textstem diff --git a/prepare/r-tfarm/PKGBUILD b/prepare/r-tfarm/PKGBUILD new file mode 100644 index 0000000000..e8ef5bc243 --- /dev/null +++ b/prepare/r-tfarm/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TFARM +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Transcription Factors Association Rules Miner' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-arules + r-fields + r-genomicranges + r-gplots + r-stringr +) +optdepends=( + r-biocstyle + r-knitr + r-plyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tfarm/lilac.py b/prepare/r-tfarm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tfarm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tfarm/lilac.yaml b/prepare/r-tfarm/lilac.yaml new file mode 100644 index 0000000000..e0bd29b702 --- /dev/null +++ b/prepare/r-tfarm/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-arules +- r-fields +- r-genomicranges +- r-gplots +- r-stringr +update_on: +- regex: TFARM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TFARM diff --git a/prepare/r-tfautograph/PKGBUILD b/prepare/r-tfautograph/PKGBUILD new file mode 100644 index 0000000000..04becd0b6a --- /dev/null +++ b/prepare/r-tfautograph/PKGBUILD @@ -0,0 +1,34 @@ +# system requirements: TensorFlow (https://www.tensorflow.org/) +# Maintainer: Guoyi Zhang + +_pkgname=tfautograph +_pkgver=0.3.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Autograph R for 'Tensorflow'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-backports + r-reticulate +) +optdepends=( + r-rlang + r-tensorflow + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tfautograph/lilac.py b/prepare/r-tfautograph/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tfautograph/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tfautograph/lilac.yaml b/prepare/r-tfautograph/lilac.yaml new file mode 100644 index 0000000000..bc653cc978 --- /dev/null +++ b/prepare/r-tfautograph/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-backports +- r-reticulate +update_on: +- regex: tfautograph_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tfautograph diff --git a/prepare/r-tfbstools/PKGBUILD b/prepare/r-tfbstools/PKGBUILD new file mode 100644 index 0000000000..80b6b36d7f --- /dev/null +++ b/prepare/r-tfbstools/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TFBSTools +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Software Package for Transcription Factor Binding Site (TFBS) Analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-catools + r-cner + r-dbi + r-dirichletmultinomial + r-genomeinfodb + r-genomicranges + r-gtools + r-iranges + r-rsqlite + r-rtracklayer + r-s4vectors + r-seqlogo + r-tfmpvalue + r-xml + r-xvector +) +optdepends=( + r-biocstyle + r-jaspar2014 + r-jaspar2016 + r-jaspar2018 + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tfbstools/lilac.py b/prepare/r-tfbstools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tfbstools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tfbstools/lilac.yaml b/prepare/r-tfbstools/lilac.yaml new file mode 100644 index 0000000000..a9e6f0ab70 --- /dev/null +++ b/prepare/r-tfbstools/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-catools +- r-cner +- r-dbi +- r-dirichletmultinomial +- r-genomeinfodb +- r-genomicranges +- r-gtools +- r-iranges +- r-rsqlite +- r-rtracklayer +- r-s4vectors +- r-seqlogo +- r-tfmpvalue +- r-xml +- r-xvector +update_on: +- regex: TFBSTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TFBSTools diff --git a/prepare/r-tfea.chip/PKGBUILD b/prepare/r-tfea.chip/PKGBUILD new file mode 100644 index 0000000000..997d886e4f --- /dev/null +++ b/prepare/r-tfea.chip/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TFEA.ChIP +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analyze Transcription Factor Enrichment' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biomart + r-dplyr + r-genomicfeatures + r-genomicranges + r-iranges + r-org.hs.eg.db + r-r.utils +) +optdepends=( + r-biocgenerics + r-deseq2 + r-ggplot2 + r-ggrepel + r-gseabase + r-knitr + r-plotly + r-rcompanion + r-rmarkdown + r-s4vectors + r-scales + r-tidyr + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tfea.chip/lilac.py b/prepare/r-tfea.chip/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tfea.chip/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tfea.chip/lilac.yaml b/prepare/r-tfea.chip/lilac.yaml new file mode 100644 index 0000000000..c836ff3aac --- /dev/null +++ b/prepare/r-tfea.chip/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-dplyr +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-org.hs.eg.db +- r-r.utils +update_on: +- regex: TFEA.ChIP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TFEA.ChIP diff --git a/prepare/r-tfhaz/PKGBUILD b/prepare/r-tfhaz/PKGBUILD new file mode 100644 index 0000000000..04629574d7 --- /dev/null +++ b/prepare/r-tfhaz/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TFHAZ +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Transcription Factor High Accumulation Zones' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-genomicranges + r-iranges + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tfhaz/lilac.py b/prepare/r-tfhaz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tfhaz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tfhaz/lilac.yaml b/prepare/r-tfhaz/lilac.yaml new file mode 100644 index 0000000000..4210e77c50 --- /dev/null +++ b/prepare/r-tfhaz/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-iranges +- r-s4vectors +update_on: +- regex: TFHAZ_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TFHAZ diff --git a/prepare/r-tfisher/PKGBUILD b/prepare/r-tfisher/PKGBUILD new file mode 100644 index 0000000000..9e9c3584c0 --- /dev/null +++ b/prepare/r-tfisher/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TFisher +_pkgver=0.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Optimal Thresholding Fisher's P-Value Combination Method" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-mvtnorm + r-sn +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tfisher/lilac.py b/prepare/r-tfisher/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tfisher/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tfisher/lilac.yaml b/prepare/r-tfisher/lilac.yaml new file mode 100644 index 0000000000..db516ce8b1 --- /dev/null +++ b/prepare/r-tfisher/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-mvtnorm +- r-sn +update_on: +- regex: TFisher_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=TFisher diff --git a/prepare/r-tfmpvalue/PKGBUILD b/prepare/r-tfmpvalue/PKGBUILD new file mode 100644 index 0000000000..7cf8f5f36b --- /dev/null +++ b/prepare/r-tfmpvalue/PKGBUILD @@ -0,0 +1,31 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=TFMPvalue +_pkgver=0.0.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Efficient and Accurate P-Value Computation for Position Weight Matrices' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tfmpvalue/lilac.py b/prepare/r-tfmpvalue/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tfmpvalue/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tfmpvalue/lilac.yaml b/prepare/r-tfmpvalue/lilac.yaml new file mode 100644 index 0000000000..2e04a4a974 --- /dev/null +++ b/prepare/r-tfmpvalue/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: TFMPvalue_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=TFMPvalue diff --git a/prepare/r-tfruns/PKGBUILD b/prepare/r-tfruns/PKGBUILD new file mode 100644 index 0000000000..ee5ef8684e --- /dev/null +++ b/prepare/r-tfruns/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tfruns +_pkgver=1.5.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Training Run Tools for 'TensorFlow'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-base64enc + r-config + r-jsonlite + r-magrittr + r-reticulate + r-rlang + r-rstudioapi + r-tidyselect + r-whisker + r-yaml +) +optdepends=( + r-here + r-knitr + r-rmarkdown + r-testthat + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tfruns/lilac.py b/prepare/r-tfruns/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tfruns/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tfruns/lilac.yaml b/prepare/r-tfruns/lilac.yaml new file mode 100644 index 0000000000..6e0cb838b6 --- /dev/null +++ b/prepare/r-tfruns/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-config +- r-jsonlite +- r-magrittr +- r-reticulate +- r-rlang +- r-rstudioapi +- r-tidyselect +- r-whisker +- r-yaml +update_on: +- regex: tfruns_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tfruns diff --git a/prepare/r-tfutils/PKGBUILD b/prepare/r-tfutils/PKGBUILD new file mode 100644 index 0000000000..400f5f7838 --- /dev/null +++ b/prepare/r-tfutils/PKGBUILD @@ -0,0 +1,66 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TFutils +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='TFutils' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biocfilecache + r-dplyr + r-dt + r-gseabase + r-httr + r-magrittr + r-miniui + r-org.hs.eg.db + r-readxl + r-rjson + r-rsamtools + r-shiny +) +optdepends=( + r-annotationfilter + r-biobase + r-biocparallel + r-biocstyle + r-data.table + r-ensdb.hsapiens.v75 + r-genomeinfodb + r-genomicfeatures + r-genomicfiles + r-genomicranges + r-ggplot2 + r-go.db + r-gviz + r-gwascat + r-iranges + r-knitr + r-motifdb + r-motifstack + r-png + r-rcolorbrewer + r-rmarkdown + r-s4vectors + r-summarizedexperiment + r-testthat + r-upsetr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tfutils/lilac.py b/prepare/r-tfutils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tfutils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tfutils/lilac.yaml b/prepare/r-tfutils/lilac.yaml new file mode 100644 index 0000000000..c8646cabc5 --- /dev/null +++ b/prepare/r-tfutils/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocfilecache +- r-dplyr +- r-dt +- r-gseabase +- r-httr +- r-magrittr +- r-miniui +- r-org.hs.eg.db +- r-readxl +- r-rjson +- r-rsamtools +- r-shiny +update_on: +- regex: TFutils_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TFutils diff --git a/prepare/r-th.data/PKGBUILD b/prepare/r-th.data/PKGBUILD new file mode 100644 index 0000000000..5913307625 --- /dev/null +++ b/prepare/r-th.data/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TH.data +_pkgver=1.1-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="TH's Data Archive" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-atr + r-coin + r-colorspace + r-dplyr + r-gdata + r-gridextra + r-knitr + r-lattice + r-multcomp + r-plyr + r-rms + r-tram + r-trtf + r-vcd +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-th.data/lilac.py b/prepare/r-th.data/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-th.data/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-th.data/lilac.yaml b/prepare/r-th.data/lilac.yaml new file mode 100644 index 0000000000..f7bccbdc13 --- /dev/null +++ b/prepare/r-th.data/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: TH.data_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=TH.data diff --git a/prepare/r-threejs/PKGBUILD b/prepare/r-threejs/PKGBUILD new file mode 100644 index 0000000000..9aa13e9ad9 --- /dev/null +++ b/prepare/r-threejs/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=threejs +_pkgver=0.3.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive 3D Scatter Plots, Networks and Globes' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-base64enc + r-crosstalk + r-htmlwidgets + r-igraph +) +optdepends=( + r-knitr + r-maps + r-shiny +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-threejs/lilac.py b/prepare/r-threejs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-threejs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-threejs/lilac.yaml b/prepare/r-threejs/lilac.yaml new file mode 100644 index 0000000000..e232e7c5b2 --- /dev/null +++ b/prepare/r-threejs/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-crosstalk +- r-htmlwidgets +- r-igraph +update_on: +- regex: threejs_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=threejs diff --git a/prepare/r-tictoc/PKGBUILD b/prepare/r-tictoc/PKGBUILD new file mode 100644 index 0000000000..e1e53d939d --- /dev/null +++ b/prepare/r-tictoc/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tictoc +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for Timing R Scripts, as Well as Implementations of Stack and List Structures' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tictoc/lilac.py b/prepare/r-tictoc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tictoc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tictoc/lilac.yaml b/prepare/r-tictoc/lilac.yaml new file mode 100644 index 0000000000..fef6c8aa15 --- /dev/null +++ b/prepare/r-tictoc/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: tictoc_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tictoc diff --git a/prepare/r-tidybayes/PKGBUILD b/prepare/r-tidybayes/PKGBUILD new file mode 100644 index 0000000000..e7b0f83a0b --- /dev/null +++ b/prepare/r-tidybayes/PKGBUILD @@ -0,0 +1,73 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tidybayes +_pkgver=3.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Tidy Data and 'Geoms' for Bayesian Models" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-arrayhelpers + r-coda + r-dplyr + r-ggdist + r-ggplot2 + r-magrittr + r-posterior + r-rlang + r-tibble + r-tidyr + r-tidyselect + r-vctrs + r-withr +) +optdepends=( + r-bayesplot + r-bindrcpp + r-brms + r-broom + r-covr + r-cowplot + r-distributional + r-dotwhisker + r-emmeans + r-forcats + r-gdtools + r-gganimate + r-ggrepel + r-gifski + r-jagsui + r-knitr + r-mcmcglmm + r-modelr + r-pkgdown + r-png + r-purrr + r-rcolorbrewer + r-rjags + r-rmarkdown + r-rstan + r-rstanarm + r-rstantools + r-runjags + r-svglite + r-testthat + r-transformr + r-vdiffr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tidybayes/lilac.py b/prepare/r-tidybayes/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tidybayes/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tidybayes/lilac.yaml b/prepare/r-tidybayes/lilac.yaml new file mode 100644 index 0000000000..0b7bb7c83c --- /dev/null +++ b/prepare/r-tidybayes/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-arrayhelpers +- r-coda +- r-dplyr +- r-ggdist +- r-ggplot2 +- r-magrittr +- r-posterior +- r-rlang +- r-tibble +- r-tidyr +- r-tidyselect +- r-vctrs +- r-withr +update_on: +- regex: tidybayes_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tidybayes diff --git a/prepare/r-tidybulk/PKGBUILD b/prepare/r-tidybulk/PKGBUILD new file mode 100644 index 0000000000..58c3be97d3 --- /dev/null +++ b/prepare/r-tidybulk/PKGBUILD @@ -0,0 +1,81 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tidybulk +_pkgver=1.6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Brings transcriptomics to the tidyverse' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-genomicranges + r-lifecycle + r-magrittr + r-preprocesscore + r-purrr + r-readr + r-rlang + r-scales + r-stringi + r-stringr + r-summarizedexperiment + r-tibble + r-tidyr + r-tidyselect +) +optdepends=( + r-annotationdbi + r-betareg + r-biocmanager + r-biocstyle + r-boot + r-broom + r-clusterprofiler + r-covr + r-deseq2 + r-devtools + r-e1071 + r-edger + r-functional + r-ggally + r-ggplot2 + r-ggrepel + r-kernsmooth + r-knitr + r-limma + r-markdown + r-msigdbr + r-org.hs.eg.db + r-org.mm.eg.db + r-pasilla + r-qpdf + r-rsubread + r-rtsne + r-s4vectors + r-seurat + r-survival + r-survminer + r-sva + r-testthat + r-tidyheatmap + r-tidysummarizedexperiment + r-uwot + r-vctrs + r-widyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tidybulk/lilac.py b/prepare/r-tidybulk/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tidybulk/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tidybulk/lilac.yaml b/prepare/r-tidybulk/lilac.yaml new file mode 100644 index 0000000000..45a21f25e6 --- /dev/null +++ b/prepare/r-tidybulk/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-genomicranges +- r-lifecycle +- r-magrittr +- r-preprocesscore +- r-purrr +- r-readr +- r-rlang +- r-scales +- r-stringi +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-tidyr +- r-tidyselect +update_on: +- regex: tidybulk_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tidybulk diff --git a/prepare/r-tidygraph/PKGBUILD b/prepare/r-tidygraph/PKGBUILD new file mode 100644 index 0000000000..0cf481bb1e --- /dev/null +++ b/prepare/r-tidygraph/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tidygraph +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Tidy API for Graph Manipulation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-igraph + r-magrittr + r-pillar + r-r6 + r-rcpp + r-rlang + r-tibble + r-tidyr +) +optdepends=( + r-ape + r-covr + r-data.tree + r-graph + r-influencer + r-methods + r-netrankr + r-netswan + r-network + r-seriation + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tidygraph/lilac.py b/prepare/r-tidygraph/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tidygraph/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tidygraph/lilac.yaml b/prepare/r-tidygraph/lilac.yaml new file mode 100644 index 0000000000..d3010c2ca4 --- /dev/null +++ b/prepare/r-tidygraph/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-igraph +- r-magrittr +- r-pillar +- r-r6 +- r-rcpp +- r-rlang +- r-tibble +- r-tidyr +update_on: +- regex: tidygraph_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tidygraph diff --git a/prepare/r-tidyr/PKGBUILD b/prepare/r-tidyr/PKGBUILD new file mode 100644 index 0000000000..260cd03c82 --- /dev/null +++ b/prepare/r-tidyr/PKGBUILD @@ -0,0 +1,49 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=tidyr +_pkgver=1.1.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tidy Messy Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-cpp11 + r-dplyr + r-ellipsis + r-glue + r-lifecycle + r-magrittr + r-purrr + r-rlang + r-tibble + r-tidyselect + r-vctrs +) +optdepends=( + r-covr + r-data.table + r-jsonlite + r-knitr + r-readr + r-repurrrsive + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tidyr/lilac.py b/prepare/r-tidyr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tidyr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tidyr/lilac.yaml b/prepare/r-tidyr/lilac.yaml new file mode 100644 index 0000000000..c0a2e98d18 --- /dev/null +++ b/prepare/r-tidyr/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cpp11 +- r-dplyr +- r-ellipsis +- r-glue +- r-lifecycle +- r-magrittr +- r-purrr +- r-rlang +- r-tibble +- r-tidyselect +- r-vctrs +update_on: +- regex: tidyr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tidyr diff --git a/prepare/r-tidysinglecellexperiment/PKGBUILD b/prepare/r-tidysinglecellexperiment/PKGBUILD new file mode 100644 index 0000000000..412d18056c --- /dev/null +++ b/prepare/r-tidysinglecellexperiment/PKGBUILD @@ -0,0 +1,62 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tidySingleCellExperiment +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Brings SingleCellExperiment to the Tidyverse' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cli + r-dplyr + r-ellipsis + r-fansi + r-ggplot2 + r-lifecycle + r-magrittr + r-pillar + r-plotly + r-purrr + r-rlang + r-s4vectors + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-tibble + r-tidyr + r-tidyselect +) +optdepends=( + r-biocstyle + r-celldex + r-dittoseq + r-ensdb.hsapiens.v86 + r-ggally + r-igraph + r-knitr + r-markdown + r-matrix + r-scater + r-scran + r-singlecellsignalr + r-singler + r-testthat + r-tidyheatmap + r-uwot +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tidysinglecellexperiment/lilac.py b/prepare/r-tidysinglecellexperiment/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tidysinglecellexperiment/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tidysinglecellexperiment/lilac.yaml b/prepare/r-tidysinglecellexperiment/lilac.yaml new file mode 100644 index 0000000000..aafaa3ae4d --- /dev/null +++ b/prepare/r-tidysinglecellexperiment/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cli +- r-dplyr +- r-ellipsis +- r-fansi +- r-ggplot2 +- r-lifecycle +- r-magrittr +- r-pillar +- r-plotly +- r-purrr +- r-rlang +- r-s4vectors +- r-singlecellexperiment +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-tidyr +- r-tidyselect +update_on: +- regex: tidySingleCellExperiment_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tidySingleCellExperiment diff --git a/prepare/r-tidysummarizedexperiment/PKGBUILD b/prepare/r-tidysummarizedexperiment/PKGBUILD new file mode 100644 index 0000000000..5477283bcd --- /dev/null +++ b/prepare/r-tidysummarizedexperiment/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tidySummarizedExperiment +_pkgver=1.4.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Brings SummarizedExperiment to the Tidyverse' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cli + r-dplyr + r-ellipsis + r-fansi + r-ggplot2 + r-lifecycle + r-magrittr + r-pillar + r-plotly + r-purrr + r-rlang + r-s4vectors + r-stringr + r-summarizedexperiment + r-tibble + r-tidyr + r-tidyselect +) +optdepends=( + r-biocstyle + r-knitr + r-markdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tidysummarizedexperiment/lilac.py b/prepare/r-tidysummarizedexperiment/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tidysummarizedexperiment/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tidysummarizedexperiment/lilac.yaml b/prepare/r-tidysummarizedexperiment/lilac.yaml new file mode 100644 index 0000000000..3b1c64f8f3 --- /dev/null +++ b/prepare/r-tidysummarizedexperiment/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cli +- r-dplyr +- r-ellipsis +- r-fansi +- r-ggplot2 +- r-lifecycle +- r-magrittr +- r-pillar +- r-plotly +- r-purrr +- r-rlang +- r-s4vectors +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-tidyr +- r-tidyselect +update_on: +- regex: tidySummarizedExperiment_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tidySummarizedExperiment diff --git a/prepare/r-tidytext/PKGBUILD b/prepare/r-tidytext/PKGBUILD new file mode 100644 index 0000000000..3ab16f4430 --- /dev/null +++ b/prepare/r-tidytext/PKGBUILD @@ -0,0 +1,62 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tidytext +_pkgver=0.3.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Text Mining using 'dplyr', 'ggplot2', and Other Tidy Tools" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-generics + r-hunspell + r-janeaustenr + r-lifecycle + r-purrr + r-rlang + r-stringr + r-tibble + r-tokenizers + r-vctrs +) +optdepends=( + r-broom + r-covr + r-data.table + r-ggplot2 + r-knitr + r-mallet + r-nlp + r-quanteda + r-readr + r-reshape2 + r-rmarkdown + r-scales + r-stm + r-stopwords + r-testthat + r-textdata + r-tidyr + r-tm + r-topicmodels + r-vdiffr + r-wordcloud + r-xml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tidytext/lilac.py b/prepare/r-tidytext/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tidytext/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tidytext/lilac.yaml b/prepare/r-tidytext/lilac.yaml new file mode 100644 index 0000000000..bd7b87ab86 --- /dev/null +++ b/prepare/r-tidytext/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-generics +- r-hunspell +- r-janeaustenr +- r-lifecycle +- r-purrr +- r-rlang +- r-stringr +- r-tibble +- r-tokenizers +- r-vctrs +update_on: +- regex: tidytext_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tidytext diff --git a/prepare/r-tidytree/PKGBUILD b/prepare/r-tidytree/PKGBUILD new file mode 100644 index 0000000000..5607e3eabc --- /dev/null +++ b/prepare/r-tidytree/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tidytree +_pkgver=0.3.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Tidy Tool for Phylogenetic Tree Data Manipulation' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ape + r-dplyr + r-lazyeval + r-magrittr + r-rlang + r-tibble + r-tidyr + r-tidyselect + r-yulab.utils +) +optdepends=( + r-knitr + r-pillar + r-prettydoc + r-rmarkdown + r-testthat + r-utils +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tidytree/lilac.py b/prepare/r-tidytree/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tidytree/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tidytree/lilac.yaml b/prepare/r-tidytree/lilac.yaml new file mode 100644 index 0000000000..8373dc2f7a --- /dev/null +++ b/prepare/r-tidytree/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-dplyr +- r-lazyeval +- r-magrittr +- r-rlang +- r-tibble +- r-tidyr +- r-tidyselect +- r-yulab.utils +update_on: +- regex: tidytree_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tidytree diff --git a/prepare/r-tidyverse/PKGBUILD b/prepare/r-tidyverse/PKGBUILD new file mode 100644 index 0000000000..0eeb33e5c8 --- /dev/null +++ b/prepare/r-tidyverse/PKGBUILD @@ -0,0 +1,64 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tidyverse +_pkgver=1.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Easily Install and Load the 'Tidyverse'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-broom + r-cli + r-crayon + r-dbplyr + r-dplyr + r-dtplyr + r-forcats + r-ggplot2 + r-googledrive + r-googlesheets4 + r-haven + r-hms + r-httr + r-jsonlite + r-lubridate + r-magrittr + r-modelr + r-pillar + r-purrr + r-readr + r-readxl + r-reprex + r-rlang + r-rstudioapi + r-rvest + r-stringr + r-tibble + r-tidyr + r-xml2 +) +optdepends=( + r-covr + r-feather + r-glue + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tidyverse/lilac.py b/prepare/r-tidyverse/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tidyverse/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tidyverse/lilac.yaml b/prepare/r-tidyverse/lilac.yaml new file mode 100644 index 0000000000..c56654342d --- /dev/null +++ b/prepare/r-tidyverse/lilac.yaml @@ -0,0 +1,38 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-broom +- r-cli +- r-crayon +- r-dbplyr +- r-dplyr +- r-dtplyr +- r-forcats +- r-ggplot2 +- r-googledrive +- r-googlesheets4 +- r-haven +- r-hms +- r-httr +- r-jsonlite +- r-lubridate +- r-magrittr +- r-modelr +- r-pillar +- r-purrr +- r-readr +- r-readxl +- r-reprex +- r-rlang +- r-rstudioapi +- r-rvest +- r-stringr +- r-tibble +- r-tidyr +- r-xml2 +update_on: +- regex: tidyverse_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tidyverse diff --git a/prepare/r-tiff/PKGBUILD b/prepare/r-tiff/PKGBUILD new file mode 100644 index 0000000000..128558a8c5 --- /dev/null +++ b/prepare/r-tiff/PKGBUILD @@ -0,0 +1,27 @@ +# system requirements: tiff and jpeg libraries +# Maintainer: Guoyi Zhang + +_pkgname=tiff +_pkgver=0.1-10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Read and Write TIFF Images' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tiff/lilac.py b/prepare/r-tiff/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tiff/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tiff/lilac.yaml b/prepare/r-tiff/lilac.yaml new file mode 100644 index 0000000000..50951bebae --- /dev/null +++ b/prepare/r-tiff/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: tiff_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tiff diff --git a/prepare/r-tigre/PKGBUILD b/prepare/r-tigre/PKGBUILD new file mode 100644 index 0000000000..444f6841ec --- /dev/null +++ b/prepare/r-tigre/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tigre +_pkgver=1.48.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Transcription factor Inference through Gaussian process Reconstruction of Expression' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-gplots + r-rsqlite +) +optdepends=( + r-biocmanager + r-biocstyle + r-drosgenome1.db + r-lumi + r-puma +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tigre/lilac.py b/prepare/r-tigre/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tigre/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tigre/lilac.yaml b/prepare/r-tigre/lilac.yaml new file mode 100644 index 0000000000..9d82a8af44 --- /dev/null +++ b/prepare/r-tigre/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-dbi +- r-gplots +- r-rsqlite +update_on: +- regex: tigre_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tigre diff --git a/prepare/r-tiledb/PKGBUILD b/prepare/r-tiledb/PKGBUILD new file mode 100644 index 0000000000..7f0f514ec4 --- /dev/null +++ b/prepare/r-tiledb/PKGBUILD @@ -0,0 +1,43 @@ +# system requirements: A C++17 compiler is required, and on macOScompilation for version 11.14 is required. Optionally cmake(only when TileDB source build selected), git (only when TileDBsource build selected); on x86_64 and M1 platforms pre-builtTileDB Embedded libraries are available at GitHub and are usedif no TileDB installation is detected, and no other option tobuild or download was specified by the user. +# Maintainer: Guoyi Zhang + +_pkgname=tiledb +_pkgver=0.10.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Universal Storage Engine for Sparse and Dense Multidimensional Arrays' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-nanotime + r-rcpp +) +optdepends=( + r-bit64 + r-curl + r-data.table + r-knitr + r-matrix + r-minidown + r-nycflights13 + r-palmerpenguins + r-rmarkdown + r-tibble + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tiledb/lilac.py b/prepare/r-tiledb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tiledb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tiledb/lilac.yaml b/prepare/r-tiledb/lilac.yaml new file mode 100644 index 0000000000..90a92166b5 --- /dev/null +++ b/prepare/r-tiledb/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-nanotime +- r-rcpp +update_on: +- regex: tiledb_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tiledb diff --git a/prepare/r-tiledbarray/PKGBUILD b/prepare/r-tiledbarray/PKGBUILD new file mode 100644 index 0000000000..46d4a475a9 --- /dev/null +++ b/prepare/r-tiledbarray/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TileDBArray +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Using TileDB as a DelayedArray Backend' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-delayedarray + r-rcpp + r-s4vectors + r-tiledb +) +optdepends=( + r-biocparallel + r-biocstyle + r-knitr + r-matrix + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tiledbarray/lilac.py b/prepare/r-tiledbarray/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tiledbarray/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tiledbarray/lilac.yaml b/prepare/r-tiledbarray/lilac.yaml new file mode 100644 index 0000000000..f9831e9a8c --- /dev/null +++ b/prepare/r-tiledbarray/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-delayedarray +- r-rcpp +- r-s4vectors +- r-tiledb +update_on: +- regex: TileDBArray_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TileDBArray diff --git a/prepare/r-tilingarray/PKGBUILD b/prepare/r-tilingarray/PKGBUILD new file mode 100644 index 0000000000..243f513aba --- /dev/null +++ b/prepare/r-tilingarray/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tilingArray +_pkgver=1.72.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Transcript mapping with high-density oligonucleotide tiling arrays' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-affy + r-biobase + r-genefilter + r-pixmap + r-rcolorbrewer + r-strucchange + r-vsn +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tilingarray/lilac.py b/prepare/r-tilingarray/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tilingarray/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tilingarray/lilac.yaml b/prepare/r-tilingarray/lilac.yaml new file mode 100644 index 0000000000..65b01217d7 --- /dev/null +++ b/prepare/r-tilingarray/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +- r-genefilter +- r-pixmap +- r-rcolorbrewer +- r-strucchange +- r-vsn +update_on: +- regex: tilingArray_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tilingArray diff --git a/prepare/r-timecourse/PKGBUILD b/prepare/r-timecourse/PKGBUILD new file mode 100644 index 0000000000..bed67dc837 --- /dev/null +++ b/prepare/r-timecourse/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=timecourse +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical Analysis for Developmental Microarray Time Course Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-limma + r-marray +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-timecourse/lilac.py b/prepare/r-timecourse/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-timecourse/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-timecourse/lilac.yaml b/prepare/r-timecourse/lilac.yaml new file mode 100644 index 0000000000..a7b4ae0c2e --- /dev/null +++ b/prepare/r-timecourse/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-limma +- r-marray +update_on: +- regex: timecourse_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/timecourse diff --git a/prepare/r-timedate/PKGBUILD b/prepare/r-timedate/PKGBUILD new file mode 100644 index 0000000000..56dc1683ba --- /dev/null +++ b/prepare/r-timedate/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=timeDate +_pkgver=3043.102 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Rmetrics - Chronological and Calendar Objects' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-date + r-runit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-timedate/lilac.py b/prepare/r-timedate/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-timedate/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-timedate/lilac.yaml b/prepare/r-timedate/lilac.yaml new file mode 100644 index 0000000000..58defc80b7 --- /dev/null +++ b/prepare/r-timedate/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: timeDate_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=timeDate diff --git a/prepare/r-timeomics/PKGBUILD b/prepare/r-timeomics/PKGBUILD new file mode 100644 index 0000000000..e982d2e173 --- /dev/null +++ b/prepare/r-timeomics/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=timeOmics +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Time-Course Multi-Omics data integration' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-ggplot2 + r-ggrepel + r-lmtest + r-magrittr + r-mixomics + r-plyr + r-propr + r-purrr + r-stringr + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-gplots + r-igraph + r-knitr + r-rmarkdown + r-snow + r-testthat + r-tidyverse +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-timeomics/lilac.py b/prepare/r-timeomics/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-timeomics/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-timeomics/lilac.yaml b/prepare/r-timeomics/lilac.yaml new file mode 100644 index 0000000000..ff4698b01b --- /dev/null +++ b/prepare/r-timeomics/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ggplot2 +- r-ggrepel +- r-lmtest +- r-magrittr +- r-mixomics +- r-plyr +- r-propr +- r-purrr +- r-stringr +- r-tibble +- r-tidyr +update_on: +- regex: timeOmics_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/timeOmics diff --git a/prepare/r-timescape/PKGBUILD b/prepare/r-timescape/PKGBUILD new file mode 100644 index 0000000000..59c67204af --- /dev/null +++ b/prepare/r-timescape/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=timescape +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Patient Clonal Timescapes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-gtools + r-htmlwidgets + r-jsonlite + r-stringr +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-timescape/lilac.py b/prepare/r-timescape/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-timescape/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-timescape/lilac.yaml b/prepare/r-timescape/lilac.yaml new file mode 100644 index 0000000000..89d0d066ae --- /dev/null +++ b/prepare/r-timescape/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-gtools +- r-htmlwidgets +- r-jsonlite +- r-stringr +update_on: +- regex: timescape_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/timescape diff --git a/prepare/r-timeseries/PKGBUILD b/prepare/r-timeseries/PKGBUILD new file mode 100644 index 0000000000..dd48e2e82d --- /dev/null +++ b/prepare/r-timeseries/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=timeSeries +_pkgver=3062.100 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Financial Time Series Objects (Rmetrics)' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-timedate +) +optdepends=( + r-ftrading + r-performanceanalytics + r-robustbase + r-runit + r-xts +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-timeseries/lilac.py b/prepare/r-timeseries/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-timeseries/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-timeseries/lilac.yaml b/prepare/r-timeseries/lilac.yaml new file mode 100644 index 0000000000..2e572fade3 --- /dev/null +++ b/prepare/r-timeseries/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-timedate +update_on: +- regex: timeSeries_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=timeSeries diff --git a/prepare/r-timeseriesexperiment/PKGBUILD b/prepare/r-timeseriesexperiment/PKGBUILD new file mode 100644 index 0000000000..31d98662ec --- /dev/null +++ b/prepare/r-timeseriesexperiment/PKGBUILD @@ -0,0 +1,58 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TimeSeriesExperiment +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis for short time-series data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-deseq2 + r-dplyr + r-dynamictreecut + r-edger + r-ggplot2 + r-hmisc + r-limma + r-magrittr + r-proxy + r-s4vectors + r-summarizedexperiment + r-tibble + r-tidyr + r-vegan + r-viridis +) +optdepends=( + r-biobase + r-biocfilecache + r-circlize + r-complexheatmap + r-go.db + r-grdevices + r-grid + r-knitr + r-mass + r-org.hs.eg.db + r-org.mm.eg.db + r-rcolorbrewer + r-rmarkdown + r-upsetr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-timeseriesexperiment/lilac.py b/prepare/r-timeseriesexperiment/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-timeseriesexperiment/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-timeseriesexperiment/lilac.yaml b/prepare/r-timeseriesexperiment/lilac.yaml new file mode 100644 index 0000000000..18c97c94ad --- /dev/null +++ b/prepare/r-timeseriesexperiment/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-deseq2 +- r-dplyr +- r-dynamictreecut +- r-edger +- r-ggplot2 +- r-hmisc +- r-limma +- r-magrittr +- r-proxy +- r-s4vectors +- r-summarizedexperiment +- r-tibble +- r-tidyr +- r-vegan +- r-viridis +update_on: +- regex: TimeSeriesExperiment_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TimeSeriesExperiment diff --git a/prepare/r-timirgen/PKGBUILD b/prepare/r-timirgen/PKGBUILD new file mode 100644 index 0000000000..7d3a6db425 --- /dev/null +++ b/prepare/r-timirgen/PKGBUILD @@ -0,0 +1,54 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TimiRGeN +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Time sensitive microRNA-mRNA integration, analysis and network generation tool' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-clusterprofiler + r-dplyr + r-freqprof + r-ggdendro + r-gghighlight + r-ggplot2 + r-gplots + r-gtools + r-igraph + r-mfuzz + r-multiassayexperiment + r-rcy3 + r-readxl + r-reshape2 + r-rwikipathways + r-scales + r-stringr + r-tidyr +) +optdepends=( + r-biocmanager + r-kableextra + r-knitr + r-org.hs.eg.db + r-org.mm.eg.db + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-timirgen/lilac.py b/prepare/r-timirgen/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-timirgen/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-timirgen/lilac.yaml b/prepare/r-timirgen/lilac.yaml new file mode 100644 index 0000000000..556be31f29 --- /dev/null +++ b/prepare/r-timirgen/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-clusterprofiler +- r-dplyr +- r-freqprof +- r-ggdendro +- r-gghighlight +- r-ggplot2 +- r-gplots +- r-gtools +- r-igraph +- r-mfuzz +- r-multiassayexperiment +- r-rcy3 +- r-readxl +- r-reshape2 +- r-rwikipathways +- r-scales +- r-stringr +- r-tidyr +update_on: +- regex: TimiRGeN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TimiRGeN diff --git a/prepare/r-timsac/PKGBUILD b/prepare/r-timsac/PKGBUILD new file mode 100644 index 0000000000..d0df540581 --- /dev/null +++ b/prepare/r-timsac/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=timsac +_pkgver=1.3.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Time Series Analysis and Control Package' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-timsac/lilac.py b/prepare/r-timsac/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-timsac/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-timsac/lilac.yaml b/prepare/r-timsac/lilac.yaml new file mode 100644 index 0000000000..a767ab104a --- /dev/null +++ b/prepare/r-timsac/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: timsac_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=timsac diff --git a/prepare/r-tin/PKGBUILD b/prepare/r-tin/PKGBUILD new file mode 100644 index 0000000000..5a29e3ed83 --- /dev/null +++ b/prepare/r-tin/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TIN +_pkgver=1.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Transcriptome instability analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-aroma.affymetrix + r-data.table + r-impute + r-squash + r-stringr + r-wgcna +) +optdepends=( + r-affxparser + r-aroma.light + r-biocgenerics + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tin/lilac.py b/prepare/r-tin/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tin/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tin/lilac.yaml b/prepare/r-tin/lilac.yaml new file mode 100644 index 0000000000..bf4da508c5 --- /dev/null +++ b/prepare/r-tin/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-aroma.affymetrix +- r-data.table +- r-impute +- r-squash +- r-stringr +- r-wgcna +update_on: +- regex: TIN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TIN diff --git a/prepare/r-tinytex/PKGBUILD b/prepare/r-tinytex/PKGBUILD new file mode 100644 index 0000000000..d30d7f5eaa --- /dev/null +++ b/prepare/r-tinytex/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tinytex +_pkgver=0.36 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-xfun +) +optdepends=( + r-rstudioapi + r-testit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tinytex/lilac.py b/prepare/r-tinytex/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tinytex/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tinytex/lilac.yaml b/prepare/r-tinytex/lilac.yaml new file mode 100644 index 0000000000..f630aa5b13 --- /dev/null +++ b/prepare/r-tinytex/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-xfun +update_on: +- regex: tinytex_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tinytex diff --git a/prepare/r-tippy/PKGBUILD b/prepare/r-tippy/PKGBUILD new file mode 100644 index 0000000000..b8373a7f19 --- /dev/null +++ b/prepare/r-tippy/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tippy +_pkgver=0.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Add Tooltips to 'R markdown' Documents or 'Shiny' Apps" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmltools + r-htmlwidgets + r-jsonlite + r-shiny +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tippy/lilac.py b/prepare/r-tippy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tippy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tippy/lilac.yaml b/prepare/r-tippy/lilac.yaml new file mode 100644 index 0000000000..09611a6524 --- /dev/null +++ b/prepare/r-tippy/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-htmlwidgets +- r-jsonlite +- r-shiny +update_on: +- regex: tippy_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tippy diff --git a/prepare/r-tissueenrich/PKGBUILD b/prepare/r-tissueenrich/PKGBUILD new file mode 100644 index 0000000000..cb4dfcf7cc --- /dev/null +++ b/prepare/r-tissueenrich/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TissueEnrich +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tissue-specific gene enrichment analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-ensurer + r-ggplot2 + r-gseabase + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tissueenrich/lilac.py b/prepare/r-tissueenrich/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tissueenrich/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tissueenrich/lilac.yaml b/prepare/r-tissueenrich/lilac.yaml new file mode 100644 index 0000000000..4a50bca3cb --- /dev/null +++ b/prepare/r-tissueenrich/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-ensurer +- r-ggplot2 +- r-gseabase +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: TissueEnrich_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TissueEnrich diff --git a/prepare/r-titancna/PKGBUILD b/prepare/r-titancna/PKGBUILD new file mode 100644 index 0000000000..1643bbc99d --- /dev/null +++ b/prepare/r-titancna/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TitanCNA +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Subclonal copy number and LOH prediction from whole genome sequencing of tumours' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-data.table + r-dplyr + r-foreach + r-genomeinfodb + r-genomicranges + r-iranges + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-titancna/lilac.py b/prepare/r-titancna/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-titancna/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-titancna/lilac.yaml b/prepare/r-titancna/lilac.yaml new file mode 100644 index 0000000000..30905e7f32 --- /dev/null +++ b/prepare/r-titancna/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-data.table +- r-dplyr +- r-foreach +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-variantannotation +update_on: +- regex: TitanCNA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TitanCNA diff --git a/prepare/r-tkrplot/PKGBUILD b/prepare/r-tkrplot/PKGBUILD new file mode 100644 index 0000000000..a4c56d7ed0 --- /dev/null +++ b/prepare/r-tkrplot/PKGBUILD @@ -0,0 +1,27 @@ +# system requirements: Windows or X11 +# Maintainer: Guoyi Zhang + +_pkgname=tkrplot +_pkgver=0.0-26 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='TK Rplot' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tkrplot/lilac.py b/prepare/r-tkrplot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tkrplot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tkrplot/lilac.yaml b/prepare/r-tkrplot/lilac.yaml new file mode 100644 index 0000000000..13ce85abc1 --- /dev/null +++ b/prepare/r-tkrplot/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: tkrplot_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tkrplot diff --git a/prepare/r-tkwidgets/PKGBUILD b/prepare/r-tkwidgets/PKGBUILD new file mode 100644 index 0000000000..1b14700aa1 --- /dev/null +++ b/prepare/r-tkwidgets/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tkWidgets +_pkgver=1.72.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R based tk widgets' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-dyndoc + r-widgettools +) +optdepends=( + r-biobase + r-hgu95av2 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tkwidgets/lilac.py b/prepare/r-tkwidgets/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tkwidgets/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tkwidgets/lilac.yaml b/prepare/r-tkwidgets/lilac.yaml new file mode 100644 index 0000000000..d6d96c40c8 --- /dev/null +++ b/prepare/r-tkwidgets/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dyndoc +- r-widgettools +update_on: +- regex: tkWidgets_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tkWidgets diff --git a/prepare/r-tloh/PKGBUILD b/prepare/r-tloh/PKGBUILD new file mode 100644 index 0000000000..63a2bc5d34 --- /dev/null +++ b/prepare/r-tloh/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tLOH +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-data.table + r-dplyr + r-genomicranges + r-ggplot2 + r-matrixgenerics + r-purrr + r-scales + r-variantannotation +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tloh/lilac.py b/prepare/r-tloh/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tloh/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tloh/lilac.yaml b/prepare/r-tloh/lilac.yaml new file mode 100644 index 0000000000..d1dcf2c831 --- /dev/null +++ b/prepare/r-tloh/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-dplyr +- r-genomicranges +- r-ggplot2 +- r-matrixgenerics +- r-purrr +- r-scales +- r-variantannotation +update_on: +- regex: tLOH_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tLOH diff --git a/prepare/r-tm/PKGBUILD b/prepare/r-tm/PKGBUILD new file mode 100644 index 0000000000..3cfb34d92b --- /dev/null +++ b/prepare/r-tm/PKGBUILD @@ -0,0 +1,44 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=tm +_pkgver=0.7-8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Text Mining Package' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-bh + r-nlp + r-rcpp + r-slam + r-xml2 +) +optdepends=( + r-antiword + r-filehash + r-methods + r-pdftools + r-rcampdf + r-rgraphviz + r-rpoppler + r-snowballc + r-testthat + r-tm.lexicon.generalinquirer +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tm/lilac.py b/prepare/r-tm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tm/lilac.yaml b/prepare/r-tm/lilac.yaml new file mode 100644 index 0000000000..aed46a119f --- /dev/null +++ b/prepare/r-tm/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bh +- r-nlp +- r-rcpp +- r-slam +- r-xml2 +update_on: +- regex: tm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tm diff --git a/prepare/r-tmb/PKGBUILD b/prepare/r-tmb/PKGBUILD new file mode 100644 index 0000000000..19b88fc3bd --- /dev/null +++ b/prepare/r-tmb/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TMB +_pkgver=1.7.22 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Template Model Builder: A General Random Effect Tool Inspired by 'ADMB'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcppeigen +) +optdepends=( + r-numderiv + r-parallel +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tmb/lilac.py b/prepare/r-tmb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tmb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tmb/lilac.yaml b/prepare/r-tmb/lilac.yaml new file mode 100644 index 0000000000..e626f5f07e --- /dev/null +++ b/prepare/r-tmb/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcppeigen +update_on: +- regex: TMB_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=TMB diff --git a/prepare/r-tmixclust/PKGBUILD b/prepare/r-tmixclust/PKGBUILD new file mode 100644 index 0000000000..1d89689000 --- /dev/null +++ b/prepare/r-tmixclust/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TMixClust +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocparallel + r-flexclust + r-gss + r-mvtnorm + r-spem + r-zoo +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tmixclust/lilac.py b/prepare/r-tmixclust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tmixclust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tmixclust/lilac.yaml b/prepare/r-tmixclust/lilac.yaml new file mode 100644 index 0000000000..71a61d3d13 --- /dev/null +++ b/prepare/r-tmixclust/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocparallel +- r-flexclust +- r-gss +- r-mvtnorm +- r-spem +- r-zoo +update_on: +- regex: TMixClust_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TMixClust diff --git a/prepare/r-tmvnsim/PKGBUILD b/prepare/r-tmvnsim/PKGBUILD new file mode 100644 index 0000000000..f21aaba7e3 --- /dev/null +++ b/prepare/r-tmvnsim/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tmvnsim +_pkgver=1.0-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Truncated Multivariate Normal Simulation' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tmvnsim/lilac.py b/prepare/r-tmvnsim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tmvnsim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tmvnsim/lilac.yaml b/prepare/r-tmvnsim/lilac.yaml new file mode 100644 index 0000000000..84649e8e3c --- /dev/null +++ b/prepare/r-tmvnsim/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: tmvnsim_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tmvnsim diff --git a/prepare/r-tmvtnorm/PKGBUILD b/prepare/r-tmvtnorm/PKGBUILD new file mode 100644 index 0000000000..dde7201669 --- /dev/null +++ b/prepare/r-tmvtnorm/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tmvtnorm +_pkgver=1.4-10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Truncated Multivariate Normal and Student t Distribution' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-gmm + r-mvtnorm +) +optdepends=( + r-lattice +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tmvtnorm/lilac.py b/prepare/r-tmvtnorm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tmvtnorm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tmvtnorm/lilac.yaml b/prepare/r-tmvtnorm/lilac.yaml new file mode 100644 index 0000000000..4e61a1a405 --- /dev/null +++ b/prepare/r-tmvtnorm/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-gmm +- r-mvtnorm +update_on: +- regex: tmvtnorm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tmvtnorm diff --git a/prepare/r-tnbc.cms/PKGBUILD b/prepare/r-tnbc.cms/PKGBUILD new file mode 100644 index 0000000000..941a4d2503 --- /dev/null +++ b/prepare/r-tnbc.cms/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TNBC.CMS +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='TNBC.CMS: Prediction of TNBC Consensus Molecular Subtypes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-e1071 + r-forestplot + r-ggally + r-ggplot2 + r-ggpubr + r-gsva + r-pheatmap + r-pracma + r-quadprog + r-r.utils + r-rcolorbrewer + r-summarizedexperiment +) +optdepends=( + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tnbc.cms/lilac.py b/prepare/r-tnbc.cms/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tnbc.cms/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tnbc.cms/lilac.yaml b/prepare/r-tnbc.cms/lilac.yaml new file mode 100644 index 0000000000..31be59ad02 --- /dev/null +++ b/prepare/r-tnbc.cms/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-e1071 +- r-forestplot +- r-ggally +- r-ggplot2 +- r-ggpubr +- r-gsva +- r-pheatmap +- r-pracma +- r-quadprog +- r-r.utils +- r-rcolorbrewer +- r-summarizedexperiment +update_on: +- regex: TNBC.CMS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TNBC.CMS diff --git a/prepare/r-tnt/PKGBUILD b/prepare/r-tnt/PKGBUILD new file mode 100644 index 0000000000..59e0f7febf --- /dev/null +++ b/prepare/r-tnt/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TnT +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive Visualization for Genomic Features' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('AGPL') +depends=( + r + r-biobase + r-data.table + r-genomeinfodb + r-genomicranges + r-htmlwidgets + r-iranges + r-jsonlite + r-knitr + r-s4vectors +) +optdepends=( + r-biocmanager + r-genomicfeatures + r-rmarkdown + r-shiny + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tnt/lilac.py b/prepare/r-tnt/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tnt/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tnt/lilac.yaml b/prepare/r-tnt/lilac.yaml new file mode 100644 index 0000000000..c954705710 --- /dev/null +++ b/prepare/r-tnt/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-data.table +- r-genomeinfodb +- r-genomicranges +- r-htmlwidgets +- r-iranges +- r-jsonlite +- r-knitr +- r-s4vectors +update_on: +- regex: TnT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TnT diff --git a/prepare/r-toast/PKGBUILD b/prepare/r-toast/PKGBUILD new file mode 100644 index 0000000000..e9d1083897 --- /dev/null +++ b/prepare/r-toast/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TOAST +_pkgver=1.7.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for the analysis of heterogeneous tissues' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-corpcor + r-epidish + r-limma + r-nnls + r-reffreeewas + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-cssam + r-gplots + r-knitr + r-matrix + r-matrixstats + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-toast/lilac.py b/prepare/r-toast/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-toast/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-toast/lilac.yaml b/prepare/r-toast/lilac.yaml new file mode 100644 index 0000000000..80eb369234 --- /dev/null +++ b/prepare/r-toast/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-corpcor +- r-epidish +- r-limma +- r-nnls +- r-reffreeewas +- r-summarizedexperiment +update_on: +- regex: TOAST_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TOAST diff --git a/prepare/r-tofsims/PKGBUILD b/prepare/r-tofsims/PKGBUILD new file mode 100644 index 0000000000..3b47a4a190 --- /dev/null +++ b/prepare/r-tofsims/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tofsims +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-als + r-alsace + r-protgenerics + r-rcpp + r-rcpparmadillo + r-signal +) +optdepends=( + r-biocparallel + r-ebimage + r-knitr + r-parallel + r-rcolorbrewer + r-rmarkdown + r-testthat + r-tofsimsdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tofsims/lilac.py b/prepare/r-tofsims/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tofsims/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tofsims/lilac.yaml b/prepare/r-tofsims/lilac.yaml new file mode 100644 index 0000000000..19b232890d --- /dev/null +++ b/prepare/r-tofsims/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-als +- r-alsace +- r-protgenerics +- r-rcpp +- r-rcpparmadillo +- r-signal +update_on: +- regex: tofsims_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tofsims diff --git a/prepare/r-tokenizers/PKGBUILD b/prepare/r-tokenizers/PKGBUILD new file mode 100644 index 0000000000..4b0e8aaa3f --- /dev/null +++ b/prepare/r-tokenizers/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tokenizers +_pkgver=0.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fast, Consistent Tokenization of Natural Language Text' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-rcpp + r-snowballc + r-stringi +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-stopwords + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tokenizers/lilac.py b/prepare/r-tokenizers/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tokenizers/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tokenizers/lilac.yaml b/prepare/r-tokenizers/lilac.yaml new file mode 100644 index 0000000000..0b1e25f9a8 --- /dev/null +++ b/prepare/r-tokenizers/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-snowballc +- r-stringi +update_on: +- regex: tokenizers_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tokenizers diff --git a/prepare/r-tomoda/PKGBUILD b/prepare/r-tomoda/PKGBUILD new file mode 100644 index 0000000000..152689f1ad --- /dev/null +++ b/prepare/r-tomoda/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tomoda +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tomo-seq data analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-ggplot2 + r-ggrepel + r-rcolorbrewer + r-reshape2 + r-rtsne + r-summarizedexperiment + r-umap +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tomoda/lilac.py b/prepare/r-tomoda/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tomoda/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tomoda/lilac.yaml b/prepare/r-tomoda/lilac.yaml new file mode 100644 index 0000000000..7ca583d4a1 --- /dev/null +++ b/prepare/r-tomoda/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-ggrepel +- r-rcolorbrewer +- r-reshape2 +- r-rtsne +- r-summarizedexperiment +- r-umap +update_on: +- regex: tomoda_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tomoda diff --git a/prepare/r-topconfects/PKGBUILD b/prepare/r-topconfects/PKGBUILD new file mode 100644 index 0000000000..1cca1675d1 --- /dev/null +++ b/prepare/r-topconfects/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=topconfects +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Top Confident Effect Sizes' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-assertthat + r-ggplot2 +) +optdepends=( + r-annotationdbi + r-ashr + r-biocstyle + r-deseq2 + r-dplyr + r-edger + r-knitr + r-limma + r-nbpseq + r-org.at.tair.db + r-readr + r-reshape2 + r-rmarkdown + r-statmod + r-testthat + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-topconfects/lilac.py b/prepare/r-topconfects/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-topconfects/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-topconfects/lilac.yaml b/prepare/r-topconfects/lilac.yaml new file mode 100644 index 0000000000..d2428ae03e --- /dev/null +++ b/prepare/r-topconfects/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-ggplot2 +update_on: +- regex: topconfects_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/topconfects diff --git a/prepare/r-topdownr/PKGBUILD b/prepare/r-topdownr/PKGBUILD new file mode 100644 index 0000000000..039e87b7f4 --- /dev/null +++ b/prepare/r-topdownr/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=topdownr +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Investigation of Fragmentation Conditions in Top-Down Proteomics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-biostrings + r-ggplot2 + r-msnbase + r-mzr + r-protgenerics + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-ranger + r-rmarkdown + r-testthat + r-topdownrdata + r-xml2 +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-topdownr/lilac.py b/prepare/r-topdownr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-topdownr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-topdownr/lilac.yaml b/prepare/r-topdownr/lilac.yaml new file mode 100644 index 0000000000..4d29762ed1 --- /dev/null +++ b/prepare/r-topdownr/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biostrings +- r-ggplot2 +- r-msnbase +- r-mzr +- r-protgenerics +- r-s4vectors +update_on: +- regex: topdownr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/topdownr diff --git a/prepare/r-topgo/PKGBUILD b/prepare/r-topgo/PKGBUILD new file mode 100644 index 0000000000..0f9e2c21ce --- /dev/null +++ b/prepare/r-topgo/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=topGO +_pkgver=2.46.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Enrichment Analysis for Gene Ontology' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-go.db + r-graph + r-matrixstats + r-sparsem +) +optdepends=( + r-all + r-genefilter + r-globaltest + r-hgu133a.db + r-hgu95av2.db + r-multtest + r-rgraphviz + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-topgo/lilac.py b/prepare/r-topgo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-topgo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-topgo/lilac.yaml b/prepare/r-topgo/lilac.yaml new file mode 100644 index 0000000000..c04258ee6e --- /dev/null +++ b/prepare/r-topgo/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-dbi +- r-go.db +- r-graph +- r-matrixstats +- r-sparsem +update_on: +- regex: topGO_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/topGO diff --git a/prepare/r-topicmodels/PKGBUILD b/prepare/r-topicmodels/PKGBUILD new file mode 100644 index 0000000000..ca1580788e --- /dev/null +++ b/prepare/r-topicmodels/PKGBUILD @@ -0,0 +1,38 @@ +# system requirements: GNU Scientific Library version >= 1.8, C++11 +# Maintainer: Guoyi Zhang + +_pkgname=topicmodels +_pkgver=0.2-12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Topic Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-modeltools + r-slam + r-tm +) +optdepends=( + r-corpus.jss.papers + r-lasso2 + r-lattice + r-lda + r-oaiharvester + r-snowballc +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-topicmodels/lilac.py b/prepare/r-topicmodels/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-topicmodels/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-topicmodels/lilac.yaml b/prepare/r-topicmodels/lilac.yaml new file mode 100644 index 0000000000..8ac853b159 --- /dev/null +++ b/prepare/r-topicmodels/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-modeltools +- r-slam +- r-tm +update_on: +- regex: topicmodels_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=topicmodels diff --git a/prepare/r-toxicogx/PKGBUILD b/prepare/r-toxicogx/PKGBUILD new file mode 100644 index 0000000000..280aa49a03 --- /dev/null +++ b/prepare/r-toxicogx/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ToxicoGx +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of Large-Scale Toxico-Genomic Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-assertthat + r-biobase + r-biocparallel + r-catools + r-coregx + r-data.table + r-downloader + r-dplyr + r-ggplot2 + r-jsonlite + r-limma + r-magrittr + r-reshape2 + r-s4vectors + r-scales + r-summarizedexperiment + r-tibble + r-tidyr +) +optdepends=( + r-biocstyle + r-devtools + r-knitr + r-markdown + r-pharmacogx + r-rmarkdown + r-testthat + r-tinytex + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-toxicogx/lilac.py b/prepare/r-toxicogx/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-toxicogx/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-toxicogx/lilac.yaml b/prepare/r-toxicogx/lilac.yaml new file mode 100644 index 0000000000..8262ddf2ec --- /dev/null +++ b/prepare/r-toxicogx/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biobase +- r-biocparallel +- r-catools +- r-coregx +- r-data.table +- r-downloader +- r-dplyr +- r-ggplot2 +- r-jsonlite +- r-limma +- r-magrittr +- r-reshape2 +- r-s4vectors +- r-scales +- r-summarizedexperiment +- r-tibble +- r-tidyr +update_on: +- regex: ToxicoGx_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ToxicoGx diff --git a/prepare/r-tpp/PKGBUILD b/prepare/r-tpp/PKGBUILD new file mode 100644 index 0000000000..903e378042 --- /dev/null +++ b/prepare/r-tpp/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TPP +_pkgver=3.22.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analyze thermal proteome profiling (TPP) experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biobroom + r-broom + r-data.table + r-doparallel + r-dplyr + r-foreach + r-futile.logger + r-ggplot2 + r-gridextra + r-knitr + r-limma + r-magrittr + r-mefa + r-nls2 + r-openxlsx + r-plyr + r-purrr + r-rcolorbrewer + r-rcurl + r-reshape2 + r-rmarkdown + r-stringr + r-tibble + r-tidyr + r-venndiagram + r-vgam +) +optdepends=( + r-biocstyle + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tpp/lilac.py b/prepare/r-tpp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tpp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tpp/lilac.yaml b/prepare/r-tpp/lilac.yaml new file mode 100644 index 0000000000..b5e86c435a --- /dev/null +++ b/prepare/r-tpp/lilac.yaml @@ -0,0 +1,36 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biobroom +- r-broom +- r-data.table +- r-doparallel +- r-dplyr +- r-foreach +- r-futile.logger +- r-ggplot2 +- r-gridextra +- r-knitr +- r-limma +- r-magrittr +- r-mefa +- r-nls2 +- r-openxlsx +- r-plyr +- r-purrr +- r-rcolorbrewer +- r-rcurl +- r-reshape2 +- r-rmarkdown +- r-stringr +- r-tibble +- r-tidyr +- r-venndiagram +- r-vgam +update_on: +- regex: TPP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TPP diff --git a/prepare/r-tpp2d/PKGBUILD b/prepare/r-tpp2d/PKGBUILD new file mode 100644 index 0000000000..6aa2bfb4f7 --- /dev/null +++ b/prepare/r-tpp2d/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TPP2D +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-doparallel + r-dplyr + r-foreach + r-ggplot2 + r-limma + r-openxlsx + r-rcurl + r-stringr + r-tidyr +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tpp2d/lilac.py b/prepare/r-tpp2d/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tpp2d/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tpp2d/lilac.yaml b/prepare/r-tpp2d/lilac.yaml new file mode 100644 index 0000000000..15f3ba79f7 --- /dev/null +++ b/prepare/r-tpp2d/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-doparallel +- r-dplyr +- r-foreach +- r-ggplot2 +- r-limma +- r-openxlsx +- r-rcurl +- r-stringr +- r-tidyr +update_on: +- regex: TPP2D_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TPP2D diff --git a/prepare/r-tracktables/PKGBUILD b/prepare/r-tracktables/PKGBUILD new file mode 100644 index 0000000000..673fd83415 --- /dev/null +++ b/prepare/r-tracktables/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tracktables +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Build IGV tracks and HTML reports' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-genomicranges + r-iranges + r-rcolorbrewer + r-rsamtools + r-stringr + r-tractor.base + r-xml + r-xvector +) +optdepends=( + r-biocstyle + r-knitr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tracktables/lilac.py b/prepare/r-tracktables/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tracktables/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tracktables/lilac.yaml b/prepare/r-tracktables/lilac.yaml new file mode 100644 index 0000000000..87f03d3d31 --- /dev/null +++ b/prepare/r-tracktables/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-genomicranges +- r-iranges +- r-rcolorbrewer +- r-rsamtools +- r-stringr +- r-tractor.base +- r-xml +- r-xvector +update_on: +- regex: tracktables_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tracktables diff --git a/prepare/r-trackviewer/PKGBUILD b/prepare/r-trackviewer/PKGBUILD new file mode 100644 index 0000000000..931fce7cc7 --- /dev/null +++ b/prepare/r-trackviewer/PKGBUILD @@ -0,0 +1,58 @@ +# Maintainer: Guoyi Zhang + +_pkgname=trackViewer +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocgenerics + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-graph + r-grimport + r-gviz + r-htmlwidgets + r-interactionset + r-iranges + r-plotrix + r-rcpp + r-rgraphviz + r-rhdf5 + r-rsamtools + r-rtracklayer + r-s4vectors + r-scales +) +optdepends=( + r-biocstyle + r-biomart + r-htmltools + r-httr + r-knitr + r-org.hs.eg.db + r-rmarkdown + r-runit + r-txdb.hsapiens.ucsc.hg19.knowngene + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-trackviewer/lilac.py b/prepare/r-trackviewer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-trackviewer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-trackviewer/lilac.yaml b/prepare/r-trackviewer/lilac.yaml new file mode 100644 index 0000000000..9b102398cc --- /dev/null +++ b/prepare/r-trackviewer/lilac.yaml @@ -0,0 +1,29 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-graph +- r-grimport +- r-gviz +- r-htmlwidgets +- r-interactionset +- r-iranges +- r-plotrix +- r-rcpp +- r-rgraphviz +- r-rhdf5 +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-scales +update_on: +- regex: trackViewer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/trackViewer diff --git a/prepare/r-tractor.base/PKGBUILD b/prepare/r-tractor.base/PKGBUILD new file mode 100644 index 0000000000..3ef3f326b5 --- /dev/null +++ b/prepare/r-tractor.base/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tractor.base +_pkgver=3.3.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Read, Manipulate and Visualise Magnetic Resonance Images' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ore + r-reportr + r-rnifti + r-shades +) +optdepends=( + r-divest + r-jsonlite + r-loder + r-mmand + r-oro.nifti + r-testthat + r-yaml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tractor.base/lilac.py b/prepare/r-tractor.base/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tractor.base/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tractor.base/lilac.yaml b/prepare/r-tractor.base/lilac.yaml new file mode 100644 index 0000000000..9b67d7c625 --- /dev/null +++ b/prepare/r-tractor.base/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ore +- r-reportr +- r-rnifti +- r-shades +update_on: +- regex: tractor.base_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tractor.base diff --git a/prepare/r-tradeseq/PKGBUILD b/prepare/r-tradeseq/PKGBUILD new file mode 100644 index 0000000000..d2c57889a9 --- /dev/null +++ b/prepare/r-tradeseq/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tradeSeq +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='trajectory-based differential expression analysis for sequencing data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-biocparallel + r-edger + r-ggplot2 + r-igraph + r-magrittr + r-matrixstats + r-pbapply + r-princurve + r-rcolorbrewer + r-s4vectors + r-singlecellexperiment + r-slingshot + r-summarizedexperiment + r-tibble + r-trajectoryutils + r-viridis +) +optdepends=( + r-clusterexperiment + r-covr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tradeseq/lilac.py b/prepare/r-tradeseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tradeseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tradeseq/lilac.yaml b/prepare/r-tradeseq/lilac.yaml new file mode 100644 index 0000000000..d4fa1a6255 --- /dev/null +++ b/prepare/r-tradeseq/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocparallel +- r-edger +- r-ggplot2 +- r-igraph +- r-magrittr +- r-matrixstats +- r-pbapply +- r-princurve +- r-rcolorbrewer +- r-s4vectors +- r-singlecellexperiment +- r-slingshot +- r-summarizedexperiment +- r-tibble +- r-trajectoryutils +- r-viridis +update_on: +- regex: tradeSeq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tradeSeq diff --git a/prepare/r-trajectorygeometry/PKGBUILD b/prepare/r-trajectorygeometry/PKGBUILD new file mode 100644 index 0000000000..c1b693cfc2 --- /dev/null +++ b/prepare/r-trajectorygeometry/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TrajectoryGeometry +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-ggplot2 + r-pracma + r-rgl +) +optdepends=( + r-dplyr + r-knitr + r-rcolorbrewer + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-trajectorygeometry/lilac.py b/prepare/r-trajectorygeometry/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-trajectorygeometry/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-trajectorygeometry/lilac.yaml b/prepare/r-trajectorygeometry/lilac.yaml new file mode 100644 index 0000000000..12041a104a --- /dev/null +++ b/prepare/r-trajectorygeometry/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-pracma +- r-rgl +update_on: +- regex: TrajectoryGeometry_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TrajectoryGeometry diff --git a/prepare/r-trajectoryutils/PKGBUILD b/prepare/r-trajectoryutils/PKGBUILD new file mode 100644 index 0000000000..c562fdd78b --- /dev/null +++ b/prepare/r-trajectoryutils/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TrajectoryUtils +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Single-Cell Trajectory Analysis Utilities' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-igraph + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocneighbors + r-biocparallel + r-biocstyle + r-delayedarray + r-delayedmatrixstats + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-trajectoryutils/lilac.py b/prepare/r-trajectoryutils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-trajectoryutils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-trajectoryutils/lilac.yaml b/prepare/r-trajectoryutils/lilac.yaml new file mode 100644 index 0000000000..bbc0cd968f --- /dev/null +++ b/prepare/r-trajectoryutils/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: TrajectoryUtils_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TrajectoryUtils diff --git a/prepare/r-transcriptogramer/PKGBUILD b/prepare/r-transcriptogramer/PKGBUILD new file mode 100644 index 0000000000..6b6541871d --- /dev/null +++ b/prepare/r-transcriptogramer/PKGBUILD @@ -0,0 +1,46 @@ +# system requirements: Java Runtime Environment (>= 6) +# Maintainer: Guoyi Zhang + +_pkgname=transcriptogramer +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Transcriptional analysis based on transcriptograms' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-data.table + r-dosnow + r-foreach + r-ggplot2 + r-igraph + r-limma + r-progress + r-reder + r-snow + r-tidyr + r-topgo +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-transcriptogramer/lilac.py b/prepare/r-transcriptogramer/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-transcriptogramer/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-transcriptogramer/lilac.yaml b/prepare/r-transcriptogramer/lilac.yaml new file mode 100644 index 0000000000..e68b18ecfa --- /dev/null +++ b/prepare/r-transcriptogramer/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-data.table +- r-dosnow +- r-foreach +- r-ggplot2 +- r-igraph +- r-limma +- r-progress +- r-reder +- r-snow +- r-tidyr +- r-topgo +update_on: +- regex: transcriptogramer_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/transcriptogramer diff --git a/prepare/r-transcriptr/PKGBUILD b/prepare/r-transcriptr/PKGBUILD new file mode 100644 index 0000000000..9a85487393 --- /dev/null +++ b/prepare/r-transcriptr/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=transcriptR +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-caret + r-chipseq + r-e1071 + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-proc + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-transcriptr/lilac.py b/prepare/r-transcriptr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-transcriptr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-transcriptr/lilac.yaml b/prepare/r-transcriptr/lilac.yaml new file mode 100644 index 0000000000..4e4c944d55 --- /dev/null +++ b/prepare/r-transcriptr/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-caret +- r-chipseq +- r-e1071 +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-proc +- r-reshape2 +- r-rsamtools +- r-rtracklayer +- r-s4vectors +update_on: +- regex: transcriptR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/transcriptR diff --git a/prepare/r-transformgampoi/PKGBUILD b/prepare/r-transformgampoi/PKGBUILD new file mode 100644 index 0000000000..fdb0f83860 --- /dev/null +++ b/prepare/r-transformgampoi/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=transformGamPoi +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Variance Stabilizing Transformation for Gamma-Poisson Models' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-delayedarray + r-glmgampoi + r-hdf5array + r-matrixgenerics + r-summarizedexperiment +) +optdepends=( + r-knitr + r-rmarkdown + r-scran + r-tenxpbmcdata + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-transformgampoi/lilac.py b/prepare/r-transformgampoi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-transformgampoi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-transformgampoi/lilac.yaml b/prepare/r-transformgampoi/lilac.yaml new file mode 100644 index 0000000000..29eb7d35ae --- /dev/null +++ b/prepare/r-transformgampoi/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-delayedarray +- r-glmgampoi +- r-hdf5array +- r-matrixgenerics +- r-summarizedexperiment +update_on: +- regex: transformGamPoi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/transformGamPoi diff --git a/prepare/r-transite/PKGBUILD b/prepare/r-transite/PKGBUILD new file mode 100644 index 0000000000..17e8b9538c --- /dev/null +++ b/prepare/r-transite/PKGBUILD @@ -0,0 +1,44 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=transite +_pkgver=1.12.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RNA-binding protein motif analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocgenerics + r-biostrings + r-dplyr + r-genomicranges + r-ggplot2 + r-ggseqlogo + r-gridextra + r-rcpp + r-scales + r-tfmpvalue +) +optdepends=( + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-transite/lilac.py b/prepare/r-transite/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-transite/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-transite/lilac.yaml b/prepare/r-transite/lilac.yaml new file mode 100644 index 0000000000..06dd4777d4 --- /dev/null +++ b/prepare/r-transite/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-dplyr +- r-genomicranges +- r-ggplot2 +- r-ggseqlogo +- r-gridextra +- r-rcpp +- r-scales +- r-tfmpvalue +update_on: +- regex: transite_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/transite diff --git a/prepare/r-translatome/PKGBUILD b/prepare/r-translatome/PKGBUILD new file mode 100644 index 0000000000..b3ffa2416d --- /dev/null +++ b/prepare/r-translatome/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tRanslatome +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Comparison between multiple levels of gene expression' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-anota + r-biobase + r-deseq2 + r-edger + r-gosemsim + r-gplots + r-heatplus + r-limma + r-org.hs.eg.db + r-plotrix + r-rankprod + r-sigpathway + r-topgo +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-translatome/lilac.py b/prepare/r-translatome/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-translatome/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-translatome/lilac.yaml b/prepare/r-translatome/lilac.yaml new file mode 100644 index 0000000000..5b1c2ca257 --- /dev/null +++ b/prepare/r-translatome/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-anota +- r-biobase +- r-deseq2 +- r-edger +- r-gosemsim +- r-gplots +- r-heatplus +- r-limma +- r-org.hs.eg.db +- r-plotrix +- r-rankprod +- r-sigpathway +- r-topgo +update_on: +- regex: tRanslatome_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tRanslatome diff --git a/prepare/r-transomics2cytoscape/PKGBUILD b/prepare/r-transomics2cytoscape/PKGBUILD new file mode 100644 index 0000000000..6fae2d0162 --- /dev/null +++ b/prepare/r-transomics2cytoscape/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: Java 11, Cytoscape 3.8.2, Cy3D >= 1.1.3 +# Maintainer: Guoyi Zhang + +_pkgname=transomics2cytoscape +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A tool set for 3D Trans-Omic network visualization with Cytoscape' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-dplyr + r-keggrest + r-rcy3 +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-roxygen2 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-transomics2cytoscape/lilac.py b/prepare/r-transomics2cytoscape/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-transomics2cytoscape/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-transomics2cytoscape/lilac.yaml b/prepare/r-transomics2cytoscape/lilac.yaml new file mode 100644 index 0000000000..0a2ff5fff9 --- /dev/null +++ b/prepare/r-transomics2cytoscape/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-keggrest +- r-rcy3 +update_on: +- regex: transomics2cytoscape_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/transomics2cytoscape diff --git a/prepare/r-transport/PKGBUILD b/prepare/r-transport/PKGBUILD new file mode 100644 index 0000000000..21a02ec0b0 --- /dev/null +++ b/prepare/r-transport/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=transport +_pkgver=0.12-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Computation of Optimal Transport Plans and Wasserstein Distances' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-data.table + r-rcpp + r-rcppeigen +) +optdepends=( + r-animation + r-ks + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-transport/lilac.py b/prepare/r-transport/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-transport/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-transport/lilac.yaml b/prepare/r-transport/lilac.yaml new file mode 100644 index 0000000000..9ede3442b2 --- /dev/null +++ b/prepare/r-transport/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-rcpp +- r-rcppeigen +update_on: +- regex: transport_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=transport diff --git a/prepare/r-transview/PKGBUILD b/prepare/r-transview/PKGBUILD new file mode 100644 index 0000000000..e8b4d83c01 --- /dev/null +++ b/prepare/r-transview/PKGBUILD @@ -0,0 +1,39 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=TransView +_pkgver=1.38.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-genomicranges + r-gplots + r-iranges + r-rhtslib + r-s4vectors + r-zlibbioc +) +optdepends=( + r-biocmanager + r-pasillabamsubset + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-transview/lilac.py b/prepare/r-transview/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-transview/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-transview/lilac.yaml b/prepare/r-transview/lilac.yaml new file mode 100644 index 0000000000..e5fe863f1d --- /dev/null +++ b/prepare/r-transview/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-genomicranges +- r-gplots +- r-iranges +- r-rhtslib +- r-s4vectors +- r-zlibbioc +update_on: +- regex: TransView_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TransView diff --git a/prepare/r-trare/PKGBUILD b/prepare/r-trare/PKGBUILD new file mode 100644 index 0000000000..65d82a00af --- /dev/null +++ b/prepare/r-trare/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TraRe +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Transcriptional Rewiring' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocparallel + r-dqrng + r-ggplot2 + r-glmnet + r-gplots + r-gtools + r-hash + r-igraph + r-matrixstats + r-pvclust + r-r.utils + r-summarizedexperiment + r-vbsr +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-trare/lilac.py b/prepare/r-trare/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-trare/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-trare/lilac.yaml b/prepare/r-trare/lilac.yaml new file mode 100644 index 0000000000..7d2f9b236d --- /dev/null +++ b/prepare/r-trare/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-dqrng +- r-ggplot2 +- r-glmnet +- r-gplots +- r-gtools +- r-hash +- r-igraph +- r-matrixstats +- r-pvclust +- r-r.utils +- r-summarizedexperiment +- r-vbsr +update_on: +- regex: TraRe_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TraRe diff --git a/prepare/r-traser/PKGBUILD b/prepare/r-traser/PKGBUILD new file mode 100644 index 0000000000..6b53ee2835 --- /dev/null +++ b/prepare/r-traser/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=traseR +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='GWAS trait-associated SNP enrichment analyses in genomic intervals' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bsgenome.hsapiens.ucsc.hg19 + r-genomicranges + r-iranges +) +optdepends=( + r-biocgenerics + r-biocstyle + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-traser/lilac.py b/prepare/r-traser/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-traser/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-traser/lilac.yaml b/prepare/r-traser/lilac.yaml new file mode 100644 index 0000000000..ec22ac7d3e --- /dev/null +++ b/prepare/r-traser/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bsgenome.hsapiens.ucsc.hg19 +- r-genomicranges +- r-iranges +update_on: +- regex: traseR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/traseR diff --git a/prepare/r-travel/PKGBUILD b/prepare/r-travel/PKGBUILD new file mode 100644 index 0000000000..4827425e16 --- /dev/null +++ b/prepare/r-travel/PKGBUILD @@ -0,0 +1,36 @@ +# system requirements: C++11 Windows: Dokan Linux&Mac: fuse, pkg-config +# Maintainer: Guoyi Zhang + +_pkgname=Travel +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An utility to create an ALTREP object with a virtual pointer' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-biocstyle + r-inline + r-knitr + r-parallel + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-travel/lilac.py b/prepare/r-travel/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-travel/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-travel/lilac.yaml b/prepare/r-travel/lilac.yaml new file mode 100644 index 0000000000..086be2c483 --- /dev/null +++ b/prepare/r-travel/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: Travel_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Travel diff --git a/prepare/r-traviz/PKGBUILD b/prepare/r-traviz/PKGBUILD new file mode 100644 index 0000000000..7768970cb5 --- /dev/null +++ b/prepare/r-traviz/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=traviz +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Trajectory functions for visualization and interpretation.' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biobase + r-ggplot2 + r-princurve + r-rcolorbrewer + r-rgl + r-singlecellexperiment + r-slingshot + r-summarizedexperiment + r-viridis +) +optdepends=( + r-covr + r-dplyr + r-knitr + r-rmarkdown + r-s4vectors + r-scater + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-traviz/lilac.py b/prepare/r-traviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-traviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-traviz/lilac.yaml b/prepare/r-traviz/lilac.yaml new file mode 100644 index 0000000000..7fe729a1d9 --- /dev/null +++ b/prepare/r-traviz/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-ggplot2 +- r-princurve +- r-rcolorbrewer +- r-rgl +- r-singlecellexperiment +- r-slingshot +- r-summarizedexperiment +- r-viridis +update_on: +- regex: traviz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/traviz diff --git a/prepare/r-treeandleaf/PKGBUILD b/prepare/r-treeandleaf/PKGBUILD new file mode 100644 index 0000000000..47ca357125 --- /dev/null +++ b/prepare/r-treeandleaf/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TreeAndLeaf +_pkgver=1.6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Displaying binary trees with focus on dendrogram leaves' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ape + r-igraph + r-reder +) +optdepends=( + r-biocgenerics + r-biocstyle + r-dendextend + r-dplyr + r-geneplast + r-ggplot2 + r-ggtree + r-knitr + r-rcolorbrewer + r-rmarkdown + r-runit + r-stringr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-treeandleaf/lilac.py b/prepare/r-treeandleaf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-treeandleaf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-treeandleaf/lilac.yaml b/prepare/r-treeandleaf/lilac.yaml new file mode 100644 index 0000000000..d73d5d2898 --- /dev/null +++ b/prepare/r-treeandleaf/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-igraph +- r-reder +update_on: +- regex: TreeAndLeaf_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TreeAndLeaf diff --git a/prepare/r-treeio/PKGBUILD b/prepare/r-treeio/PKGBUILD new file mode 100644 index 0000000000..e76a2fc052 --- /dev/null +++ b/prepare/r-treeio/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=treeio +_pkgver=1.18.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Base Classes and Functions for Phylogenetic Tree Input and Output' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-ape + r-dplyr + r-jsonlite + r-magrittr + r-rlang + r-tibble + r-tidytree +) +optdepends=( + r-biostrings + r-ggplot2 + r-ggtree + r-igraph + r-knitr + r-phangorn + r-prettydoc + r-rmarkdown + r-testthat + r-tidyr + r-vroom + r-xml2 + r-yaml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-treeio/lilac.py b/prepare/r-treeio/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-treeio/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-treeio/lilac.yaml b/prepare/r-treeio/lilac.yaml new file mode 100644 index 0000000000..c869d824aa --- /dev/null +++ b/prepare/r-treeio/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-dplyr +- r-jsonlite +- r-magrittr +- r-rlang +- r-tibble +- r-tidytree +update_on: +- regex: treeio_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/treeio diff --git a/prepare/r-treekor/PKGBUILD b/prepare/r-treekor/PKGBUILD new file mode 100644 index 0000000000..e59403de41 --- /dev/null +++ b/prepare/r-treekor/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=treekoR +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-data.table + r-diffcyt + r-dplyr + r-edger + r-ggiraph + r-ggplot2 + r-ggtree + r-hopach + r-lme4 + r-multcomp + r-patchwork + r-singlecellexperiment + r-tidyr +) +optdepends=( + r-biocstyle + r-catalyst + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-treekor/lilac.py b/prepare/r-treekor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-treekor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-treekor/lilac.yaml b/prepare/r-treekor/lilac.yaml new file mode 100644 index 0000000000..46d4deae35 --- /dev/null +++ b/prepare/r-treekor/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-data.table +- r-diffcyt +- r-dplyr +- r-edger +- r-ggiraph +- r-ggplot2 +- r-ggtree +- r-hopach +- r-lme4 +- r-multcomp +- r-patchwork +- r-singlecellexperiment +- r-tidyr +update_on: +- regex: treekoR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/treekoR diff --git a/prepare/r-treemap/PKGBUILD b/prepare/r-treemap/PKGBUILD new file mode 100644 index 0000000000..dcbfcdaa5b --- /dev/null +++ b/prepare/r-treemap/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=treemap +_pkgver=2.4-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Treemap Visualization' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-colorspace + r-data.table + r-ggplot2 + r-gridbase + r-igraph + r-rcolorbrewer + r-shiny +) +optdepends=( + r-knitr + r-markdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-treemap/lilac.py b/prepare/r-treemap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-treemap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-treemap/lilac.yaml b/prepare/r-treemap/lilac.yaml new file mode 100644 index 0000000000..c67bb5ae7a --- /dev/null +++ b/prepare/r-treemap/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colorspace +- r-data.table +- r-ggplot2 +- r-gridbase +- r-igraph +- r-rcolorbrewer +- r-shiny +update_on: +- regex: treemap_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=treemap diff --git a/prepare/r-treesummarizedexperiment/PKGBUILD b/prepare/r-treesummarizedexperiment/PKGBUILD new file mode 100644 index 0000000000..9e2b7e4f6b --- /dev/null +++ b/prepare/r-treesummarizedexperiment/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TreeSummarizedExperiment +_pkgver=2.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='TreeSummarizedExperiment: a S4 Class for Data with Tree Structures' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-biocgenerics + r-biocparallel + r-biostrings + r-dplyr + r-iranges + r-rlang + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-treeio +) +optdepends=( + r-biocstyle + r-ggplot2 + r-ggtree + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-treesummarizedexperiment/lilac.py b/prepare/r-treesummarizedexperiment/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-treesummarizedexperiment/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-treesummarizedexperiment/lilac.yaml b/prepare/r-treesummarizedexperiment/lilac.yaml new file mode 100644 index 0000000000..c39ae45fd5 --- /dev/null +++ b/prepare/r-treesummarizedexperiment/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-dplyr +- r-iranges +- r-rlang +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +- r-treeio +update_on: +- regex: TreeSummarizedExperiment_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TreeSummarizedExperiment diff --git a/prepare/r-trena/PKGBUILD b/prepare/r-trena/PKGBUILD new file mode 100644 index 0000000000..4c43aa6854 --- /dev/null +++ b/prepare/r-trena/PKGBUILD @@ -0,0 +1,59 @@ +# Maintainer: Guoyi Zhang + +_pkgname=trena +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Fit transcriptional regulatory networks using gene expression, priors, machine learning' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biomart + r-biostrings + r-bsgenome + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.hsapiens.ucsc.hg38 + r-bsgenome.mmusculus.ucsc.mm10 + r-dbi + r-genomicranges + r-glmnet + r-lassopv + r-motifdb + r-org.hs.eg.db + r-randomforest + r-rmysql + r-rpostgresql + r-rsqlite + r-snplocs.hsapiens.dbsnp150.grch38 + r-vbsr + r-wgcna + r-xgboost +) +optdepends=( + r-biocgenerics + r-biocparallel + r-bsgenome.athaliana.tair.tair9 + r-bsgenome.scerevisiae.ucsc.saccer3 + r-formatr + r-knitr + r-markdown + r-plyr + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-trena/lilac.py b/prepare/r-trena/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-trena/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-trena/lilac.yaml b/prepare/r-trena/lilac.yaml new file mode 100644 index 0000000000..33f2197b1d --- /dev/null +++ b/prepare/r-trena/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biomart +- r-biostrings +- r-bsgenome +- r-bsgenome.hsapiens.ucsc.hg19 +- r-bsgenome.hsapiens.ucsc.hg38 +- r-bsgenome.mmusculus.ucsc.mm10 +- r-dbi +- r-genomicranges +- r-glmnet +- r-lassopv +- r-motifdb +- r-org.hs.eg.db +- r-randomforest +- r-rmysql +- r-rpostgresql +- r-rsqlite +- r-snplocs.hsapiens.dbsnp150.grch38 +- r-vbsr +- r-wgcna +- r-xgboost +update_on: +- regex: trena_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/trena diff --git a/prepare/r-trendy/PKGBUILD b/prepare/r-trendy/PKGBUILD new file mode 100644 index 0000000000..b3de35b7f7 --- /dev/null +++ b/prepare/r-trendy/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Trendy +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Breakpoint analysis of time-course expression data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocparallel + r-dt + r-gplots + r-magrittr + r-s4vectors + r-segmented + r-shiny + r-shinyfiles + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-devtools + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-trendy/lilac.py b/prepare/r-trendy/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-trendy/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-trendy/lilac.yaml b/prepare/r-trendy/lilac.yaml new file mode 100644 index 0000000000..97508377d0 --- /dev/null +++ b/prepare/r-trendy/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-dt +- r-gplots +- r-magrittr +- r-s4vectors +- r-segmented +- r-shiny +- r-shinyfiles +- r-summarizedexperiment +update_on: +- regex: Trendy_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Trendy diff --git a/prepare/r-tress/PKGBUILD b/prepare/r-tress/PKGBUILD new file mode 100644 index 0000000000..c29ccac552 --- /dev/null +++ b/prepare/r-tress/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TRESS +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Toolbox for mRNA epigenetics sequencing analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-genomicfeatures + r-genomicranges + r-iranges + r-matrixstats + r-rsamtools + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tress/lilac.py b/prepare/r-tress/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tress/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tress/lilac.yaml b/prepare/r-tress/lilac.yaml new file mode 100644 index 0000000000..d849b0876c --- /dev/null +++ b/prepare/r-tress/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-matrixstats +- r-rsamtools +- r-rtracklayer +- r-s4vectors +update_on: +- regex: TRESS_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TRESS diff --git a/prepare/r-tricycle/PKGBUILD b/prepare/r-tricycle/PKGBUILD new file mode 100644 index 0000000000..b301656525 --- /dev/null +++ b/prepare/r-tricycle/PKGBUILD @@ -0,0 +1,50 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tricycle +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='tricycle: Transferable Representation and Inference of cell cycle' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-circular + r-dplyr + r-genomicranges + r-ggplot2 + r-iranges + r-rcolorbrewer + r-s4vectors + r-scater + r-scattermore + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-circstats + r-cowplot + r-htmltools + r-knitr + r-org.hs.eg.db + r-org.mm.eg.db + r-rmarkdown + r-seurat + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tricycle/lilac.py b/prepare/r-tricycle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tricycle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tricycle/lilac.yaml b/prepare/r-tricycle/lilac.yaml new file mode 100644 index 0000000000..abffdad2ae --- /dev/null +++ b/prepare/r-tricycle/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-circular +- r-dplyr +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-rcolorbrewer +- r-s4vectors +- r-scater +- r-scattermore +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: tricycle_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tricycle diff --git a/prepare/r-triebeard/PKGBUILD b/prepare/r-triebeard/PKGBUILD new file mode 100644 index 0000000000..036cb82a9a --- /dev/null +++ b/prepare/r-triebeard/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=triebeard +_pkgver=0.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="'Radix' Trees in 'Rcpp'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-rcpp +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-triebeard/lilac.py b/prepare/r-triebeard/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-triebeard/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-triebeard/lilac.yaml b/prepare/r-triebeard/lilac.yaml new file mode 100644 index 0000000000..ab722fc1bf --- /dev/null +++ b/prepare/r-triebeard/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: triebeard_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=triebeard diff --git a/prepare/r-trigger/PKGBUILD b/prepare/r-trigger/PKGBUILD new file mode 100644 index 0000000000..5388cd6491 --- /dev/null +++ b/prepare/r-trigger/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=trigger +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Transcriptional Regulatory Inference from Genetics of Gene ExpRession' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-corpcor + r-qtl + r-qvalue + r-sva +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-trigger/lilac.py b/prepare/r-trigger/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-trigger/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-trigger/lilac.yaml b/prepare/r-trigger/lilac.yaml new file mode 100644 index 0000000000..2d756270d0 --- /dev/null +++ b/prepare/r-trigger/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-corpcor +- r-qtl +- r-qvalue +- r-sva +update_on: +- regex: trigger_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/trigger diff --git a/prepare/r-trio/PKGBUILD b/prepare/r-trio/PKGBUILD new file mode 100644 index 0000000000..ee6ffab580 --- /dev/null +++ b/prepare/r-trio/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=trio +_pkgver=3.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Testing of SNPs and SNP Interactions in Case-Parent Trio Studies' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-logicreg + r-siggenes +) +optdepends=( + r-haplo.stats + r-kernsmooth + r-logicfs + r-mcbiopi + r-splines + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-trio/lilac.py b/prepare/r-trio/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-trio/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-trio/lilac.yaml b/prepare/r-trio/lilac.yaml new file mode 100644 index 0000000000..d14088f8f0 --- /dev/null +++ b/prepare/r-trio/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-logicreg +- r-siggenes +update_on: +- regex: trio_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/trio diff --git a/prepare/r-triplex/PKGBUILD b/prepare/r-triplex/PKGBUILD new file mode 100644 index 0000000000..3d2a6ecda2 --- /dev/null +++ b/prepare/r-triplex/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=triplex +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Search and visualize intramolecular triplex-forming sequences in DNA' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r + r-biostrings + r-genomicranges + r-iranges + r-s4vectors + r-xvector +) +optdepends=( + r-bsgenome.celegans.ucsc.ce10 + r-rgl + r-rtracklayer +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-triplex/lilac.py b/prepare/r-triplex/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-triplex/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-triplex/lilac.yaml b/prepare/r-triplex/lilac.yaml new file mode 100644 index 0000000000..cd456d637e --- /dev/null +++ b/prepare/r-triplex/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-genomicranges +- r-iranges +- r-s4vectors +- r-xvector +update_on: +- regex: triplex_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/triplex diff --git a/prepare/r-tripr/PKGBUILD b/prepare/r-tripr/PKGBUILD new file mode 100644 index 0000000000..7c553c858e --- /dev/null +++ b/prepare/r-tripr/PKGBUILD @@ -0,0 +1,62 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tripr +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='T-cell Receptor/Immunoglobulin Profiler (TRIP)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-config + r-data.table + r-dplyr + r-dt + r-golem + r-gridextra + r-plot3d + r-plotly + r-plyr + r-pryr + r-rcolorbrewer + r-shiny + r-shinybs + r-shinyfiles + r-shinyjs + r-stringdist + r-stringr +) +optdepends=( + r-biocgenerics + r-biocmanager + r-biocstyle + r-biocthis + r-biostrings + r-fs + r-knitr + r-motifstack + r-parallel + r-refmanager + r-rlist + r-rmarkdown + r-shinycssloaders + r-testthat + r-tidyverse + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tripr/lilac.py b/prepare/r-tripr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tripr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tripr/lilac.yaml b/prepare/r-tripr/lilac.yaml new file mode 100644 index 0000000000..21088729f7 --- /dev/null +++ b/prepare/r-tripr/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-config +- r-data.table +- r-dplyr +- r-dt +- r-golem +- r-gridextra +- r-plot3d +- r-plotly +- r-plyr +- r-pryr +- r-rcolorbrewer +- r-shiny +- r-shinybs +- r-shinyfiles +- r-shinyjs +- r-stringdist +- r-stringr +update_on: +- regex: tripr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tripr diff --git a/prepare/r-trna/PKGBUILD b/prepare/r-trna/PKGBUILD new file mode 100644 index 0000000000..b4d69e6f43 --- /dev/null +++ b/prepare/r-trna/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tRNA +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analyzing tRNA sequences and structures' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-genomicranges + r-ggplot2 + r-iranges + r-modstrings + r-s4vectors + r-scales + r-stringr + r-structstrings + r-xvector +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat + r-trnascanimport +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-trna/lilac.py b/prepare/r-trna/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-trna/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-trna/lilac.yaml b/prepare/r-trna/lilac.yaml new file mode 100644 index 0000000000..c8e6644e07 --- /dev/null +++ b/prepare/r-trna/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-modstrings +- r-s4vectors +- r-scales +- r-stringr +- r-structstrings +- r-xvector +update_on: +- regex: tRNA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tRNA diff --git a/prepare/r-trnadbimport/PKGBUILD b/prepare/r-trnadbimport/PKGBUILD new file mode 100644 index 0000000000..a33ff1dd6b --- /dev/null +++ b/prepare/r-trnadbimport/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tRNAdbImport +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Importing from tRNAdb and mitotRNAdb as GRanges objects' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-genomicranges + r-httr + r-iranges + r-modstrings + r-s4vectors + r-stringr + r-structstrings + r-trna + r-xml2 +) +optdepends=( + r-biocstyle + r-httptest + r-knitr + r-rmarkdown + r-rtracklayer + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-trnadbimport/lilac.py b/prepare/r-trnadbimport/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-trnadbimport/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-trnadbimport/lilac.yaml b/prepare/r-trnadbimport/lilac.yaml new file mode 100644 index 0000000000..5eb3738261 --- /dev/null +++ b/prepare/r-trnadbimport/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-genomicranges +- r-httr +- r-iranges +- r-modstrings +- r-s4vectors +- r-stringr +- r-structstrings +- r-trna +- r-xml2 +update_on: +- regex: tRNAdbImport_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tRNAdbImport diff --git a/prepare/r-trnascanimport/PKGBUILD b/prepare/r-trnascanimport/PKGBUILD new file mode 100644 index 0000000000..8104796e8c --- /dev/null +++ b/prepare/r-trnascanimport/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tRNAscanImport +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Importing a tRNAscan-SE result file as GRanges object' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-iranges + r-rsamtools + r-rtracklayer + r-s4vectors + r-stringr + r-structstrings + r-trna + r-xvector +) +optdepends=( + r-biocstyle + r-bsgenome.scerevisiae.ucsc.saccer3 + r-ggplot2 + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-trnascanimport/lilac.py b/prepare/r-trnascanimport/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-trnascanimport/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-trnascanimport/lilac.yaml b/prepare/r-trnascanimport/lilac.yaml new file mode 100644 index 0000000000..31f820a518 --- /dev/null +++ b/prepare/r-trnascanimport/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-stringr +- r-structstrings +- r-trna +- r-xvector +update_on: +- regex: tRNAscanImport_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tRNAscanImport diff --git a/prepare/r-tronco/PKGBUILD b/prepare/r-tronco/PKGBUILD new file mode 100644 index 0000000000..1d28032878 --- /dev/null +++ b/prepare/r-tronco/PKGBUILD @@ -0,0 +1,48 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TRONCO +_pkgver=2.26.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='TRONCO, an R package for TRanslational ONCOlogy' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bnlearn + r-cgdsr + r-circlize + r-doparallel + r-foreach + r-gridextra + r-gtable + r-gtools + r-igraph + r-iterators + r-r.matlab + r-rcolorbrewer + r-rgraphviz + r-scales + r-xtable +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-rwikipathways + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tronco/lilac.py b/prepare/r-tronco/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tronco/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tronco/lilac.yaml b/prepare/r-tronco/lilac.yaml new file mode 100644 index 0000000000..730b545a68 --- /dev/null +++ b/prepare/r-tronco/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bnlearn +- r-cgdsr +- r-circlize +- r-doparallel +- r-foreach +- r-gridextra +- r-gtable +- r-gtools +- r-igraph +- r-iterators +- r-r.matlab +- r-rcolorbrewer +- r-rgraphviz +- r-scales +- r-xtable +update_on: +- regex: TRONCO_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TRONCO diff --git a/prepare/r-truncdist/PKGBUILD b/prepare/r-truncdist/PKGBUILD new file mode 100644 index 0000000000..d5ec85fb25 --- /dev/null +++ b/prepare/r-truncdist/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=truncdist +_pkgver=1.0-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Truncated Random Variables' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-evd +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-truncdist/lilac.py b/prepare/r-truncdist/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-truncdist/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-truncdist/lilac.yaml b/prepare/r-truncdist/lilac.yaml new file mode 100644 index 0000000000..a976dc85d3 --- /dev/null +++ b/prepare/r-truncdist/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-evd +update_on: +- regex: truncdist_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=truncdist diff --git a/prepare/r-truncnorm/PKGBUILD b/prepare/r-truncnorm/PKGBUILD new file mode 100644 index 0000000000..1e352bbed8 --- /dev/null +++ b/prepare/r-truncnorm/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=truncnorm +_pkgver=1.0-8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Truncated Normal Distribution' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-truncnorm/lilac.py b/prepare/r-truncnorm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-truncnorm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-truncnorm/lilac.yaml b/prepare/r-truncnorm/lilac.yaml new file mode 100644 index 0000000000..382313c667 --- /dev/null +++ b/prepare/r-truncnorm/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: truncnorm_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=truncnorm diff --git a/prepare/r-trust/PKGBUILD b/prepare/r-trust/PKGBUILD new file mode 100644 index 0000000000..ce66201ee2 --- /dev/null +++ b/prepare/r-trust/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=trust +_pkgver=0.1-8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Trust Region Optimization' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-trust/lilac.py b/prepare/r-trust/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-trust/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-trust/lilac.yaml b/prepare/r-trust/lilac.yaml new file mode 100644 index 0000000000..33ce831d63 --- /dev/null +++ b/prepare/r-trust/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: trust_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=trust diff --git a/prepare/r-tscan/PKGBUILD b/prepare/r-tscan/PKGBUILD new file mode 100644 index 0000000000..f6e725e73e --- /dev/null +++ b/prepare/r-tscan/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TSCAN +_pkgver=1.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Single-Cell Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-combinat + r-delayedarray + r-fastica + r-ggplot2 + r-gplots + r-igraph + r-mclust + r-plyr + r-s4vectors + r-shiny + r-singlecellexperiment + r-summarizedexperiment + r-trajectoryutils +) +optdepends=( + r-batchelor + r-biocneighbors + r-biocparallel + r-knitr + r-metapod + r-scran + r-scuttle + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tscan/lilac.py b/prepare/r-tscan/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tscan/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tscan/lilac.yaml b/prepare/r-tscan/lilac.yaml new file mode 100644 index 0000000000..781800a044 --- /dev/null +++ b/prepare/r-tscan/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-combinat +- r-delayedarray +- r-fastica +- r-ggplot2 +- r-gplots +- r-igraph +- r-mclust +- r-plyr +- r-s4vectors +- r-shiny +- r-singlecellexperiment +- r-summarizedexperiment +- r-trajectoryutils +update_on: +- regex: TSCAN_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TSCAN diff --git a/prepare/r-tscr/PKGBUILD b/prepare/r-tscr/PKGBUILD new file mode 100644 index 0000000000..8082389add --- /dev/null +++ b/prepare/r-tscr/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tscR +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A time series clustering package combining slope and Frechet distances' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-dtw + r-genomicranges + r-ggplot2 + r-gridextra + r-iranges + r-kmlshape + r-knitr + r-latex2exp + r-prettydoc + r-rcolorbrewer + r-rmarkdown + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tscr/lilac.py b/prepare/r-tscr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tscr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tscr/lilac.yaml b/prepare/r-tscr/lilac.yaml new file mode 100644 index 0000000000..08ea5736a4 --- /dev/null +++ b/prepare/r-tscr/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-dtw +- r-genomicranges +- r-ggplot2 +- r-gridextra +- r-iranges +- r-kmlshape +- r-knitr +- r-latex2exp +- r-prettydoc +- r-rcolorbrewer +- r-rmarkdown +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: tscR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tscR diff --git a/prepare/r-tseries/PKGBUILD b/prepare/r-tseries/PKGBUILD new file mode 100644 index 0000000000..cd86861af6 --- /dev/null +++ b/prepare/r-tseries/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tseries +_pkgver=0.10-49 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Time Series Analysis and Computational Finance' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-quadprog + r-quantmod + r-zoo +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tseries/lilac.py b/prepare/r-tseries/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tseries/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tseries/lilac.yaml b/prepare/r-tseries/lilac.yaml new file mode 100644 index 0000000000..94b1c854d0 --- /dev/null +++ b/prepare/r-tseries/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-quadprog +- r-quantmod +- r-zoo +update_on: +- regex: tseries_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tseries diff --git a/prepare/r-tsne/PKGBUILD b/prepare/r-tsne/PKGBUILD new file mode 100644 index 0000000000..777b6f2a6d --- /dev/null +++ b/prepare/r-tsne/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tsne +_pkgver=0.1-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='T-Distributed Stochastic Neighbor Embedding for R (t-SNE)' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tsne/lilac.py b/prepare/r-tsne/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tsne/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tsne/lilac.yaml b/prepare/r-tsne/lilac.yaml new file mode 100644 index 0000000000..5dbf8d674e --- /dev/null +++ b/prepare/r-tsne/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: tsne_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tsne diff --git a/prepare/r-tsp/PKGBUILD b/prepare/r-tsp/PKGBUILD new file mode 100644 index 0000000000..77bb37ad27 --- /dev/null +++ b/prepare/r-tsp/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TSP +_pkgver=1.1-11 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Traveling Salesperson Problem (TSP)' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-foreach +) +optdepends=( + r-maps + r-maptools + r-sp + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tsp/lilac.py b/prepare/r-tsp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tsp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tsp/lilac.yaml b/prepare/r-tsp/lilac.yaml new file mode 100644 index 0000000000..c8dfd4394a --- /dev/null +++ b/prepare/r-tsp/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-foreach +update_on: +- regex: TSP_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=TSP diff --git a/prepare/r-tspair/PKGBUILD b/prepare/r-tspair/PKGBUILD new file mode 100644 index 0000000000..25182f5342 --- /dev/null +++ b/prepare/r-tspair/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tspair +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Top Scoring Pairs for Microarray Classification' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tspair/lilac.py b/prepare/r-tspair/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tspair/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tspair/lilac.yaml b/prepare/r-tspair/lilac.yaml new file mode 100644 index 0000000000..c388331a20 --- /dev/null +++ b/prepare/r-tspair/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: tspair_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tspair diff --git a/prepare/r-tsrchitect/PKGBUILD b/prepare/r-tsrchitect/PKGBUILD new file mode 100644 index 0000000000..f1dc4f6f0f --- /dev/null +++ b/prepare/r-tsrchitect/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TSRchitect +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Promoter identification from large-scale TSS profiling data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationhub + r-biocgenerics + r-biocparallel + r-dplyr + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-gtools + r-iranges + r-readxl + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-encodexplorer + r-ggplot2 + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tsrchitect/lilac.py b/prepare/r-tsrchitect/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tsrchitect/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tsrchitect/lilac.yaml b/prepare/r-tsrchitect/lilac.yaml new file mode 100644 index 0000000000..2d60a9863b --- /dev/null +++ b/prepare/r-tsrchitect/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationhub +- r-biocgenerics +- r-biocparallel +- r-dplyr +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-gtools +- r-iranges +- r-readxl +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: TSRchitect_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TSRchitect diff --git a/prepare/r-ttgsea/PKGBUILD b/prepare/r-ttgsea/PKGBUILD new file mode 100644 index 0000000000..357c425ae7 --- /dev/null +++ b/prepare/r-ttgsea/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ttgsea +_pkgver=1.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tokenizing Text of Gene Set Enrichment Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-data.table + r-diagrammer + r-keras + r-purrr + r-stopwords + r-text2vec + r-textstem + r-tm + r-tokenizers +) +optdepends=( + r-fgsea + r-knitr + r-reticulate + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ttgsea/lilac.py b/prepare/r-ttgsea/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ttgsea/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ttgsea/lilac.yaml b/prepare/r-ttgsea/lilac.yaml new file mode 100644 index 0000000000..4482b049e5 --- /dev/null +++ b/prepare/r-ttgsea/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-diagrammer +- r-keras +- r-purrr +- r-stopwords +- r-text2vec +- r-textstem +- r-tm +- r-tokenizers +update_on: +- regex: ttgsea_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ttgsea diff --git a/prepare/r-ttmap/PKGBUILD b/prepare/r-ttmap/PKGBUILD new file mode 100644 index 0000000000..4a0fbdf400 --- /dev/null +++ b/prepare/r-ttmap/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TTMap +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Two-Tier Mapper: a clustering tool based on topological data analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-colorramps + r-rgl + r-summarizedexperiment +) +optdepends=( + r-airway + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ttmap/lilac.py b/prepare/r-ttmap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ttmap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ttmap/lilac.yaml b/prepare/r-ttmap/lilac.yaml new file mode 100644 index 0000000000..4aaf2e6b2f --- /dev/null +++ b/prepare/r-ttmap/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-colorramps +- r-rgl +- r-summarizedexperiment +update_on: +- regex: TTMap_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TTMap diff --git a/prepare/r-ttr/PKGBUILD b/prepare/r-ttr/PKGBUILD new file mode 100644 index 0000000000..e50ff54bcd --- /dev/null +++ b/prepare/r-ttr/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TTR +_pkgver=0.24.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Technical Trading Rules' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-curl + r-xts + r-zoo +) +optdepends=( + r-quantmod + r-runit +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ttr/lilac.py b/prepare/r-ttr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ttr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ttr/lilac.yaml b/prepare/r-ttr/lilac.yaml new file mode 100644 index 0000000000..feab23c908 --- /dev/null +++ b/prepare/r-ttr/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-xts +- r-zoo +update_on: +- regex: TTR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=TTR diff --git a/prepare/r-turbonorm/PKGBUILD b/prepare/r-turbonorm/PKGBUILD new file mode 100644 index 0000000000..b25f05ed8f --- /dev/null +++ b/prepare/r-turbonorm/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TurboNorm +_pkgver=1.42.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A fast scatterplot smoother suitable for microarray normalization' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-affy + r-convert + r-limma + r-marray +) +optdepends=( + r-affydata + r-biocstyle +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-turbonorm/lilac.py b/prepare/r-turbonorm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-turbonorm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-turbonorm/lilac.yaml b/prepare/r-turbonorm/lilac.yaml new file mode 100644 index 0000000000..f1d8d8ad03 --- /dev/null +++ b/prepare/r-turbonorm/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-convert +- r-limma +- r-marray +update_on: +- regex: TurboNorm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TurboNorm diff --git a/prepare/r-tvtb/PKGBUILD b/prepare/r-tvtb/PKGBUILD new file mode 100644 index 0000000000..7da4f89b80 --- /dev/null +++ b/prepare/r-tvtb/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TVTB +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='TVTB: The VCF Tool Box' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationfilter + r-biocgenerics + r-biocparallel + r-biostrings + r-ensembldb + r-ensemblvep + r-genomeinfodb + r-genomicranges + r-ggally + r-ggplot2 + r-gviz + r-iranges + r-limma + r-reshape2 + r-rsamtools + r-s4vectors + r-summarizedexperiment + r-variantannotation +) +optdepends=( + r-biocstyle + r-covr + r-dt + r-ensdb.hsapiens.v75 + r-knitr + r-pander + r-rmarkdown + r-rtracklayer + r-shiny + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tvtb/lilac.py b/prepare/r-tvtb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tvtb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tvtb/lilac.yaml b/prepare/r-tvtb/lilac.yaml new file mode 100644 index 0000000000..bb1e95afb4 --- /dev/null +++ b/prepare/r-tvtb/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationfilter +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-ensembldb +- r-ensemblvep +- r-genomeinfodb +- r-genomicranges +- r-ggally +- r-ggplot2 +- r-gviz +- r-iranges +- r-limma +- r-reshape2 +- r-rsamtools +- r-s4vectors +- r-summarizedexperiment +- r-variantannotation +update_on: +- regex: TVTB_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TVTB diff --git a/prepare/r-tweedeseq/PKGBUILD b/prepare/r-tweedeseq/PKGBUILD new file mode 100644 index 0000000000..c143ae4c7d --- /dev/null +++ b/prepare/r-tweedeseq/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tweeDEseq +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='RNA-seq data analysis using the Poisson-Tweedie family of distributions' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cqn + r-edger + r-limma +) +optdepends=( + r-tweedeseqcountdata + r-xtable +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tweedeseq/lilac.py b/prepare/r-tweedeseq/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tweedeseq/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tweedeseq/lilac.yaml b/prepare/r-tweedeseq/lilac.yaml new file mode 100644 index 0000000000..370f0e60ac --- /dev/null +++ b/prepare/r-tweedeseq/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cqn +- r-edger +- r-limma +update_on: +- regex: tweeDEseq_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tweeDEseq diff --git a/prepare/r-tweedie/PKGBUILD b/prepare/r-tweedie/PKGBUILD new file mode 100644 index 0000000000..452bb3d5e3 --- /dev/null +++ b/prepare/r-tweedie/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tweedie +_pkgver=2.3.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Evaluation of Tweedie Exponential Family Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-stabledist + r-statmod +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tweedie/lilac.py b/prepare/r-tweedie/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tweedie/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tweedie/lilac.yaml b/prepare/r-tweedie/lilac.yaml new file mode 100644 index 0000000000..4cd14cb1db --- /dev/null +++ b/prepare/r-tweedie/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: tweedie_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tweedie diff --git a/prepare/r-tweenr/PKGBUILD b/prepare/r-tweenr/PKGBUILD new file mode 100644 index 0000000000..bbfb543b1a --- /dev/null +++ b/prepare/r-tweenr/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tweenr +_pkgver=1.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interpolate Data for Smooth Animations' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-farver + r-magrittr + r-rcpp + r-rlang +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tweenr/lilac.py b/prepare/r-tweenr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tweenr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tweenr/lilac.yaml b/prepare/r-tweenr/lilac.yaml new file mode 100644 index 0000000000..1c79464c65 --- /dev/null +++ b/prepare/r-tweenr/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-farver +- r-magrittr +- r-rcpp +- r-rlang +update_on: +- regex: tweenr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tweenr diff --git a/prepare/r-twilight/PKGBUILD b/prepare/r-twilight/PKGBUILD new file mode 100644 index 0000000000..a9e1add2b1 --- /dev/null +++ b/prepare/r-twilight/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=twilight +_pkgver=1.70.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Estimation of local false discovery rate' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase +) +optdepends=( + r-golubesets + r-vsn +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-twilight/lilac.py b/prepare/r-twilight/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-twilight/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-twilight/lilac.yaml b/prepare/r-twilight/lilac.yaml new file mode 100644 index 0000000000..d680c66580 --- /dev/null +++ b/prepare/r-twilight/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: twilight_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/twilight diff --git a/prepare/r-twoddpcr/PKGBUILD b/prepare/r-twoddpcr/PKGBUILD new file mode 100644 index 0000000000..83056cf796 --- /dev/null +++ b/prepare/r-twoddpcr/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=twoddpcr +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggplot2 + r-hexbin + r-rcolorbrewer + r-s4vectors + r-scales + r-shiny +) +optdepends=( + r-biocstyle + r-devtools + r-knitr + r-reshape2 + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-twoddpcr/lilac.py b/prepare/r-twoddpcr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-twoddpcr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-twoddpcr/lilac.yaml b/prepare/r-twoddpcr/lilac.yaml new file mode 100644 index 0000000000..0666c22806 --- /dev/null +++ b/prepare/r-twoddpcr/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-hexbin +- r-rcolorbrewer +- r-s4vectors +- r-scales +- r-shiny +update_on: +- regex: twoddpcr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/twoddpcr diff --git a/prepare/r-txcutr/PKGBUILD b/prepare/r-txcutr/PKGBUILD new file mode 100644 index 0000000000..d6c033025a --- /dev/null +++ b/prepare/r-txcutr/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=txcutr +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Transcriptome CUTteR' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-biocgenerics + r-biocparallel + r-biostrings + r-genomicfeatures + r-genomicranges + r-iranges + r-rtracklayer + r-s4vectors +) +optdepends=( + r-biocstyle + r-bsgenome.scerevisiae.ucsc.saccer3 + r-knitr + r-refmanager + r-rmarkdown + r-sessioninfo + r-testthat + r-txdb.scerevisiae.ucsc.saccer3.sgdgene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-txcutr/lilac.py b/prepare/r-txcutr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-txcutr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-txcutr/lilac.yaml b/prepare/r-txcutr/lilac.yaml new file mode 100644 index 0000000000..982baa1046 --- /dev/null +++ b/prepare/r-txcutr/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-rtracklayer +- r-s4vectors +update_on: +- regex: txcutr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/txcutr diff --git a/prepare/r-txdb.celegans.ucsc.ce6.ensgene/PKGBUILD b/prepare/r-txdb.celegans.ucsc.ce6.ensgene/PKGBUILD new file mode 100644 index 0000000000..3f2ef1d382 --- /dev/null +++ b/prepare/r-txdb.celegans.ucsc.ce6.ensgene/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TxDb.Celegans.UCSC.ce6.ensGene +_pkgver=3.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation package for TxDb object(s)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-genomicfeatures +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-txdb.celegans.ucsc.ce6.ensgene/lilac.py b/prepare/r-txdb.celegans.ucsc.ce6.ensgene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-txdb.celegans.ucsc.ce6.ensgene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-txdb.celegans.ucsc.ce6.ensgene/lilac.yaml b/prepare/r-txdb.celegans.ucsc.ce6.ensgene/lilac.yaml new file mode 100644 index 0000000000..6910ba415a --- /dev/null +++ b/prepare/r-txdb.celegans.ucsc.ce6.ensgene/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-genomicfeatures +update_on: +- regex: TxDb.Celegans.UCSC.ce6.ensGene_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene diff --git a/prepare/r-txdb.dmelanogaster.ucsc.dm3.ensgene/PKGBUILD b/prepare/r-txdb.dmelanogaster.ucsc.dm3.ensgene/PKGBUILD new file mode 100644 index 0000000000..48e8a4e471 --- /dev/null +++ b/prepare/r-txdb.dmelanogaster.ucsc.dm3.ensgene/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TxDb.Dmelanogaster.UCSC.dm3.ensGene +_pkgver=3.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation package for TxDb object(s)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-genomicfeatures +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-txdb.dmelanogaster.ucsc.dm3.ensgene/lilac.py b/prepare/r-txdb.dmelanogaster.ucsc.dm3.ensgene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-txdb.dmelanogaster.ucsc.dm3.ensgene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-txdb.dmelanogaster.ucsc.dm3.ensgene/lilac.yaml b/prepare/r-txdb.dmelanogaster.ucsc.dm3.ensgene/lilac.yaml new file mode 100644 index 0000000000..cb8b95b6a7 --- /dev/null +++ b/prepare/r-txdb.dmelanogaster.ucsc.dm3.ensgene/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-genomicfeatures +update_on: +- regex: TxDb.Dmelanogaster.UCSC.dm3.ensGene_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm3.ensGene diff --git a/prepare/r-txdb.dmelanogaster.ucsc.dm6.ensgene/PKGBUILD b/prepare/r-txdb.dmelanogaster.ucsc.dm6.ensgene/PKGBUILD new file mode 100644 index 0000000000..13a4e54470 --- /dev/null +++ b/prepare/r-txdb.dmelanogaster.ucsc.dm6.ensgene/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TxDb.Dmelanogaster.UCSC.dm6.ensGene +_pkgver=3.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation package for TxDb object(s)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-genomicfeatures +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-txdb.dmelanogaster.ucsc.dm6.ensgene/lilac.py b/prepare/r-txdb.dmelanogaster.ucsc.dm6.ensgene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-txdb.dmelanogaster.ucsc.dm6.ensgene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-txdb.dmelanogaster.ucsc.dm6.ensgene/lilac.yaml b/prepare/r-txdb.dmelanogaster.ucsc.dm6.ensgene/lilac.yaml new file mode 100644 index 0000000000..3a8a3b7458 --- /dev/null +++ b/prepare/r-txdb.dmelanogaster.ucsc.dm6.ensgene/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-genomicfeatures +update_on: +- regex: TxDb.Dmelanogaster.UCSC.dm6.ensGene_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene diff --git a/prepare/r-txdb.hsapiens.ucsc.hg18.knowngene/PKGBUILD b/prepare/r-txdb.hsapiens.ucsc.hg18.knowngene/PKGBUILD new file mode 100644 index 0000000000..5c793efaf8 --- /dev/null +++ b/prepare/r-txdb.hsapiens.ucsc.hg18.knowngene/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TxDb.Hsapiens.UCSC.hg18.knownGene +_pkgver=3.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation package for TxDb object(s)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-genomicfeatures +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-txdb.hsapiens.ucsc.hg18.knowngene/lilac.py b/prepare/r-txdb.hsapiens.ucsc.hg18.knowngene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-txdb.hsapiens.ucsc.hg18.knowngene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-txdb.hsapiens.ucsc.hg18.knowngene/lilac.yaml b/prepare/r-txdb.hsapiens.ucsc.hg18.knowngene/lilac.yaml new file mode 100644 index 0000000000..72b1b2d200 --- /dev/null +++ b/prepare/r-txdb.hsapiens.ucsc.hg18.knowngene/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-genomicfeatures +update_on: +- regex: TxDb.Hsapiens.UCSC.hg18.knownGene_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg18.knownGene diff --git a/prepare/r-txdb.hsapiens.ucsc.hg19.knowngene/PKGBUILD b/prepare/r-txdb.hsapiens.ucsc.hg19.knowngene/PKGBUILD new file mode 100644 index 0000000000..5d278832b5 --- /dev/null +++ b/prepare/r-txdb.hsapiens.ucsc.hg19.knowngene/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TxDb.Hsapiens.UCSC.hg19.knownGene +_pkgver=3.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation package for TxDb object(s)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-genomicfeatures +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-txdb.hsapiens.ucsc.hg19.knowngene/lilac.py b/prepare/r-txdb.hsapiens.ucsc.hg19.knowngene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-txdb.hsapiens.ucsc.hg19.knowngene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-txdb.hsapiens.ucsc.hg19.knowngene/lilac.yaml b/prepare/r-txdb.hsapiens.ucsc.hg19.knowngene/lilac.yaml new file mode 100644 index 0000000000..0ab7f7bdbb --- /dev/null +++ b/prepare/r-txdb.hsapiens.ucsc.hg19.knowngene/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-genomicfeatures +update_on: +- regex: TxDb.Hsapiens.UCSC.hg19.knownGene_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene diff --git a/prepare/r-txdb.hsapiens.ucsc.hg38.knowngene/PKGBUILD b/prepare/r-txdb.hsapiens.ucsc.hg38.knowngene/PKGBUILD new file mode 100644 index 0000000000..3b3a82651d --- /dev/null +++ b/prepare/r-txdb.hsapiens.ucsc.hg38.knowngene/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TxDb.Hsapiens.UCSC.hg38.knownGene +_pkgver=3.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation package for TxDb object(s)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-genomicfeatures +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-txdb.hsapiens.ucsc.hg38.knowngene/lilac.py b/prepare/r-txdb.hsapiens.ucsc.hg38.knowngene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-txdb.hsapiens.ucsc.hg38.knowngene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-txdb.hsapiens.ucsc.hg38.knowngene/lilac.yaml b/prepare/r-txdb.hsapiens.ucsc.hg38.knowngene/lilac.yaml new file mode 100644 index 0000000000..21ae40d295 --- /dev/null +++ b/prepare/r-txdb.hsapiens.ucsc.hg38.knowngene/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-genomicfeatures +update_on: +- regex: TxDb.Hsapiens.UCSC.hg38.knownGene_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene diff --git a/prepare/r-txdb.mmusculus.ucsc.mm10.knowngene/PKGBUILD b/prepare/r-txdb.mmusculus.ucsc.mm10.knowngene/PKGBUILD new file mode 100644 index 0000000000..46c4535192 --- /dev/null +++ b/prepare/r-txdb.mmusculus.ucsc.mm10.knowngene/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TxDb.Mmusculus.UCSC.mm10.knownGene +_pkgver=3.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation package for TxDb object(s)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-genomicfeatures +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-txdb.mmusculus.ucsc.mm10.knowngene/lilac.py b/prepare/r-txdb.mmusculus.ucsc.mm10.knowngene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-txdb.mmusculus.ucsc.mm10.knowngene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-txdb.mmusculus.ucsc.mm10.knowngene/lilac.yaml b/prepare/r-txdb.mmusculus.ucsc.mm10.knowngene/lilac.yaml new file mode 100644 index 0000000000..905de12097 --- /dev/null +++ b/prepare/r-txdb.mmusculus.ucsc.mm10.knowngene/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-genomicfeatures +update_on: +- regex: TxDb.Mmusculus.UCSC.mm10.knownGene_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene diff --git a/prepare/r-txdb.mmusculus.ucsc.mm9.knowngene/PKGBUILD b/prepare/r-txdb.mmusculus.ucsc.mm9.knowngene/PKGBUILD new file mode 100644 index 0000000000..129ace238b --- /dev/null +++ b/prepare/r-txdb.mmusculus.ucsc.mm9.knowngene/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TxDb.Mmusculus.UCSC.mm9.knownGene +_pkgver=3.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation package for TxDb object(s)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-genomicfeatures +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-txdb.mmusculus.ucsc.mm9.knowngene/lilac.py b/prepare/r-txdb.mmusculus.ucsc.mm9.knowngene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-txdb.mmusculus.ucsc.mm9.knowngene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-txdb.mmusculus.ucsc.mm9.knowngene/lilac.yaml b/prepare/r-txdb.mmusculus.ucsc.mm9.knowngene/lilac.yaml new file mode 100644 index 0000000000..f2293fd38f --- /dev/null +++ b/prepare/r-txdb.mmusculus.ucsc.mm9.knowngene/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-genomicfeatures +update_on: +- regex: TxDb.Mmusculus.UCSC.mm9.knownGene_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene diff --git a/prepare/r-txdb.rnorvegicus.ucsc.rn4.ensgene/PKGBUILD b/prepare/r-txdb.rnorvegicus.ucsc.rn4.ensgene/PKGBUILD new file mode 100644 index 0000000000..f6c6bd7d6e --- /dev/null +++ b/prepare/r-txdb.rnorvegicus.ucsc.rn4.ensgene/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TxDb.Rnorvegicus.UCSC.rn4.ensGene +_pkgver=3.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation package for TxDb object(s)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-genomicfeatures +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-txdb.rnorvegicus.ucsc.rn4.ensgene/lilac.py b/prepare/r-txdb.rnorvegicus.ucsc.rn4.ensgene/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-txdb.rnorvegicus.ucsc.rn4.ensgene/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-txdb.rnorvegicus.ucsc.rn4.ensgene/lilac.yaml b/prepare/r-txdb.rnorvegicus.ucsc.rn4.ensgene/lilac.yaml new file mode 100644 index 0000000000..aee69cd9ab --- /dev/null +++ b/prepare/r-txdb.rnorvegicus.ucsc.rn4.ensgene/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-genomicfeatures +update_on: +- regex: TxDb.Rnorvegicus.UCSC.rn4.ensGene_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TxDb.Rnorvegicus.UCSC.rn4.ensGene diff --git a/prepare/r-tximeta/PKGBUILD b/prepare/r-tximeta/PKGBUILD new file mode 100644 index 0000000000..7862c35c43 --- /dev/null +++ b/prepare/r-tximeta/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tximeta +_pkgver=1.12.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Transcript Quantification Import with Automatic Metadata' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-annotationhub + r-biocfilecache + r-biostrings + r-ensembldb + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-jsonlite + r-s4vectors + r-summarizedexperiment + r-tibble + r-tximport +) +optdepends=( + r-deseq2 + r-devtools + r-edger + r-knitr + r-limma + r-org.dm.eg.db + r-rmarkdown + r-testthat + r-tximportdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tximeta/lilac.py b/prepare/r-tximeta/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tximeta/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tximeta/lilac.yaml b/prepare/r-tximeta/lilac.yaml new file mode 100644 index 0000000000..46c4f7570c --- /dev/null +++ b/prepare/r-tximeta/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-biocfilecache +- r-biostrings +- r-ensembldb +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-jsonlite +- r-s4vectors +- r-summarizedexperiment +- r-tibble +- r-tximport +update_on: +- regex: tximeta_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tximeta diff --git a/prepare/r-tximport/PKGBUILD b/prepare/r-tximport/PKGBUILD new file mode 100644 index 0000000000..4aeac19aae --- /dev/null +++ b/prepare/r-tximport/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=tximport +_pkgver=1.22.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Import and summarize transcript-level estimates for transcript- and gene-level analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-deseq2 + r-edger + r-fishpond + r-jsonlite + r-knitr + r-limma + r-matrix + r-matrixstats + r-readr + r-rhdf5 + r-rmarkdown + r-testthat + r-txdb.hsapiens.ucsc.hg19.knowngene + r-tximportdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tximport/lilac.py b/prepare/r-tximport/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tximport/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tximport/lilac.yaml b/prepare/r-tximport/lilac.yaml new file mode 100644 index 0000000000..45359876a4 --- /dev/null +++ b/prepare/r-tximport/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: tximport_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/tximport diff --git a/prepare/r-typeinfo/PKGBUILD b/prepare/r-typeinfo/PKGBUILD new file mode 100644 index 0000000000..8d911b865a --- /dev/null +++ b/prepare/r-typeinfo/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=TypeInfo +_pkgver=1.60.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Optional Type Specification Prototype' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('BSD') +depends=( + r +) +optdepends=( + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-typeinfo/lilac.py b/prepare/r-typeinfo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-typeinfo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-typeinfo/lilac.yaml b/prepare/r-typeinfo/lilac.yaml new file mode 100644 index 0000000000..b13c50249e --- /dev/null +++ b/prepare/r-typeinfo/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: TypeInfo_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/TypeInfo diff --git a/prepare/r-tzdb/PKGBUILD b/prepare/r-tzdb/PKGBUILD new file mode 100644 index 0000000000..0ebd9f1055 --- /dev/null +++ b/prepare/r-tzdb/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=tzdb +_pkgver=0.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Time Zone Database Information' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-cpp11 +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-tzdb/lilac.py b/prepare/r-tzdb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-tzdb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-tzdb/lilac.yaml b/prepare/r-tzdb/lilac.yaml new file mode 100644 index 0000000000..5651e9a767 --- /dev/null +++ b/prepare/r-tzdb/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cpp11 +update_on: +- regex: tzdb_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=tzdb diff --git a/prepare/r-uchardet/PKGBUILD b/prepare/r-uchardet/PKGBUILD new file mode 100644 index 0000000000..bebb928d2f --- /dev/null +++ b/prepare/r-uchardet/PKGBUILD @@ -0,0 +1,33 @@ +# system requirements: C++11, GNU make +# Maintainer: Guoyi Zhang + +_pkgname=uchardet +_pkgver=1.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The Universal Character Encoding Detector' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-curl + r-knitr + r-rmarkdown + r-tinytest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-uchardet/lilac.py b/prepare/r-uchardet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-uchardet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-uchardet/lilac.yaml b/prepare/r-uchardet/lilac.yaml new file mode 100644 index 0000000000..69dd4bc247 --- /dev/null +++ b/prepare/r-uchardet/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: uchardet_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=uchardet diff --git a/prepare/r-udapi/PKGBUILD b/prepare/r-udapi/PKGBUILD new file mode 100644 index 0000000000..bc92b4e176 --- /dev/null +++ b/prepare/r-udapi/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=udapi +_pkgver=0.1.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Urban Dictionary API Client' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-curl + r-httr +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-udapi/lilac.py b/prepare/r-udapi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-udapi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-udapi/lilac.yaml b/prepare/r-udapi/lilac.yaml new file mode 100644 index 0000000000..6e3213885a --- /dev/null +++ b/prepare/r-udapi/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-httr +update_on: +- regex: udapi_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=udapi diff --git a/prepare/r-ularcirc/PKGBUILD b/prepare/r-ularcirc/PKGBUILD new file mode 100644 index 0000000000..25523b211b --- /dev/null +++ b/prepare/r-ularcirc/PKGBUILD @@ -0,0 +1,61 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Ularcirc +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-annotationdbi + r-annotationhub + r-biocgenerics + r-biostrings + r-bsgenome + r-data.table + r-dt + r-genomeinfodb + r-genomeinfodbdata + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggrepel + r-gsubfn + r-mirbase.db + r-moments + r-organism.dplyr + r-s4vectors + r-shiny + r-shinydashboard + r-shinyfiles + r-shinyjs + r-sushi + r-yaml +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg38 + r-httpuv + r-knitr + r-org.hs.eg.db + r-rmarkdown + r-txdb.hsapiens.ucsc.hg38.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-ularcirc/lilac.py b/prepare/r-ularcirc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-ularcirc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-ularcirc/lilac.yaml b/prepare/r-ularcirc/lilac.yaml new file mode 100644 index 0000000000..b845c8cc29 --- /dev/null +++ b/prepare/r-ularcirc/lilac.yaml @@ -0,0 +1,34 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationhub +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-data.table +- r-dt +- r-genomeinfodb +- r-genomeinfodbdata +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-ggrepel +- r-gsubfn +- r-mirbase.db +- r-moments +- r-organism.dplyr +- r-s4vectors +- r-shiny +- r-shinydashboard +- r-shinyfiles +- r-shinyjs +- r-sushi +- r-yaml +update_on: +- regex: Ularcirc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Ularcirc diff --git a/prepare/r-umap/PKGBUILD b/prepare/r-umap/PKGBUILD new file mode 100644 index 0000000000..3e4566604d --- /dev/null +++ b/prepare/r-umap/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=umap +_pkgver=0.2.7.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Uniform Manifold Approximation and Projection' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-openssl + r-rcpp + r-reticulate + r-rspectra +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-umap/lilac.py b/prepare/r-umap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-umap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-umap/lilac.yaml b/prepare/r-umap/lilac.yaml new file mode 100644 index 0000000000..86fc91b5bd --- /dev/null +++ b/prepare/r-umap/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-openssl +- r-rcpp +- r-reticulate +- r-rspectra +update_on: +- regex: umap_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=umap diff --git a/prepare/r-umi4cats/PKGBUILD b/prepare/r-umi4cats/PKGBUILD new file mode 100644 index 0000000000..c9013e7f32 --- /dev/null +++ b/prepare/r-umi4cats/PKGBUILD @@ -0,0 +1,67 @@ +# Maintainer: Guoyi Zhang + +_pkgname=UMI4Cats +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotate + r-biocfilecache + r-biocgenerics + r-biostrings + r-bsgenome + r-cowplot + r-deseq2 + r-dplyr + r-fda + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-magick + r-magrittr + r-org.hs.eg.db + r-r.utils + r-rappdirs + r-rbowtie2 + r-rcolorbrewer + r-regioner + r-reshape2 + r-rlang + r-rsamtools + r-s4vectors + r-scales + r-shortread + r-stringr + r-summarizedexperiment + r-txdb.hsapiens.ucsc.hg19.knowngene + r-zoo +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-knitr + r-rmarkdown + r-testthat + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-umi4cats/lilac.py b/prepare/r-umi4cats/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-umi4cats/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-umi4cats/lilac.yaml b/prepare/r-umi4cats/lilac.yaml new file mode 100644 index 0000000000..da69f6777a --- /dev/null +++ b/prepare/r-umi4cats/lilac.yaml @@ -0,0 +1,42 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotate +- r-biocfilecache +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-cowplot +- r-deseq2 +- r-dplyr +- r-fda +- r-genomeinfodb +- r-genomicalignments +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-magick +- r-magrittr +- r-org.hs.eg.db +- r-r.utils +- r-rappdirs +- r-rbowtie2 +- r-rcolorbrewer +- r-regioner +- r-reshape2 +- r-rlang +- r-rsamtools +- r-s4vectors +- r-scales +- r-shortread +- r-stringr +- r-summarizedexperiment +- r-txdb.hsapiens.ucsc.hg19.knowngene +- r-zoo +update_on: +- regex: UMI4Cats_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/UMI4Cats diff --git a/prepare/r-uncoverapplib/PKGBUILD b/prepare/r-uncoverapplib/PKGBUILD new file mode 100644 index 0000000000..69769a7af6 --- /dev/null +++ b/prepare/r-uncoverapplib/PKGBUILD @@ -0,0 +1,59 @@ +# Maintainer: Guoyi Zhang + +_pkgname=uncoverappLib +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Interactive graphical application for clinical assessment of sequence coverage at the base-pair level' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-biocfilecache + r-bsgenome.hsapiens.ucsc.hg19 + r-condformat + r-dt + r-ensdb.hsapiens.v75 + r-ensdb.hsapiens.v86 + r-genomicranges + r-gviz + r-homo.sapiens + r-markdown + r-openxlsx + r-org.hs.eg.db + r-organismdbi + r-processx + r-rappdirs + r-rlist + r-rsamtools + r-shiny + r-shinybs + r-shinycssloaders + r-shinyjs + r-shinywidgets + r-stringr + r-txdb.hsapiens.ucsc.hg19.knowngene + r-txdb.hsapiens.ucsc.hg38.knowngene +) +optdepends=( + r-biocstyle + r-dplyr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-uncoverapplib/lilac.py b/prepare/r-uncoverapplib/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-uncoverapplib/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-uncoverapplib/lilac.yaml b/prepare/r-uncoverapplib/lilac.yaml new file mode 100644 index 0000000000..f65f363332 --- /dev/null +++ b/prepare/r-uncoverapplib/lilac.yaml @@ -0,0 +1,34 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocfilecache +- r-bsgenome.hsapiens.ucsc.hg19 +- r-condformat +- r-dt +- r-ensdb.hsapiens.v75 +- r-ensdb.hsapiens.v86 +- r-genomicranges +- r-gviz +- r-homo.sapiens +- r-markdown +- r-openxlsx +- r-org.hs.eg.db +- r-organismdbi +- r-processx +- r-rappdirs +- r-rlist +- r-rsamtools +- r-shiny +- r-shinybs +- r-shinycssloaders +- r-shinyjs +- r-shinywidgets +- r-stringr +- r-txdb.hsapiens.ucsc.hg19.knowngene +- r-txdb.hsapiens.ucsc.hg38.knowngene +update_on: +- regex: uncoverappLib_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/uncoverappLib diff --git a/prepare/r-undo/PKGBUILD b/prepare/r-undo/PKGBUILD new file mode 100644 index 0000000000..174d609d1c --- /dev/null +++ b/prepare/r-undo/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=UNDO +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-nnls +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-undo/lilac.py b/prepare/r-undo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-undo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-undo/lilac.yaml b/prepare/r-undo/lilac.yaml new file mode 100644 index 0000000000..9ea1ac04d4 --- /dev/null +++ b/prepare/r-undo/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-nnls +update_on: +- regex: UNDO_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/UNDO diff --git a/prepare/r-unifiedwmwqpcr/PKGBUILD b/prepare/r-unifiedwmwqpcr/PKGBUILD new file mode 100644 index 0000000000..04a5db907d --- /dev/null +++ b/prepare/r-unifiedwmwqpcr/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=unifiedWMWqPCR +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-htqpcr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-unifiedwmwqpcr/lilac.py b/prepare/r-unifiedwmwqpcr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-unifiedwmwqpcr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-unifiedwmwqpcr/lilac.yaml b/prepare/r-unifiedwmwqpcr/lilac.yaml new file mode 100644 index 0000000000..f41dc4079d --- /dev/null +++ b/prepare/r-unifiedwmwqpcr/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-htqpcr +update_on: +- regex: unifiedWMWqPCR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/unifiedWMWqPCR diff --git a/prepare/r-uniprot.ws/PKGBUILD b/prepare/r-uniprot.ws/PKGBUILD new file mode 100644 index 0000000000..b55779f8be --- /dev/null +++ b/prepare/r-uniprot.ws/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=UniProt.ws +_pkgver=2.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='R Interface to UniProt Web Services' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biocfilecache + r-biocgenerics + r-rappdirs + r-rcurl + r-rsqlite +) +optdepends=( + r-biocstyle + r-knitr + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-uniprot.ws/lilac.py b/prepare/r-uniprot.ws/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-uniprot.ws/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-uniprot.ws/lilac.yaml b/prepare/r-uniprot.ws/lilac.yaml new file mode 100644 index 0000000000..7c0a9acf26 --- /dev/null +++ b/prepare/r-uniprot.ws/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biocfilecache +- r-biocgenerics +- r-rappdirs +- r-rcurl +- r-rsqlite +update_on: +- regex: UniProt.ws_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/UniProt.ws diff --git a/prepare/r-uniqtag/PKGBUILD b/prepare/r-uniqtag/PKGBUILD new file mode 100644 index 0000000000..3346b13246 --- /dev/null +++ b/prepare/r-uniqtag/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=uniqtag +_pkgver=1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Abbreviate Strings to Short, Unique Identifiers' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-uniqtag/lilac.py b/prepare/r-uniqtag/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-uniqtag/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-uniqtag/lilac.yaml b/prepare/r-uniqtag/lilac.yaml new file mode 100644 index 0000000000..d7a9078294 --- /dev/null +++ b/prepare/r-uniqtag/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: uniqtag_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=uniqtag diff --git a/prepare/r-uniquorn/PKGBUILD b/prepare/r-uniquorn/PKGBUILD new file mode 100644 index 0000000000..f895128002 --- /dev/null +++ b/prepare/r-uniquorn/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Uniquorn +_pkgver=2.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Identification of cancer cell lines based on their weighted mutational/ variational fingerprint' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-doparallel + r-foreach + r-genomicranges + r-iranges + r-r.utils + r-stringr + r-variantannotation + r-writexls +) +optdepends=( + r-biocgenerics + r-knitr + r-rmarkdown + r-runit + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-uniquorn/lilac.py b/prepare/r-uniquorn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-uniquorn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-uniquorn/lilac.yaml b/prepare/r-uniquorn/lilac.yaml new file mode 100644 index 0000000000..71c968f5d1 --- /dev/null +++ b/prepare/r-uniquorn/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-foreach +- r-genomicranges +- r-iranges +- r-r.utils +- r-stringr +- r-variantannotation +- r-writexls +update_on: +- regex: Uniquorn_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Uniquorn diff --git a/prepare/r-units/PKGBUILD b/prepare/r-units/PKGBUILD new file mode 100644 index 0000000000..c99ec96ff4 --- /dev/null +++ b/prepare/r-units/PKGBUILD @@ -0,0 +1,42 @@ +# system requirements: udunits-2 +# Maintainer: Guoyi Zhang + +_pkgname=units +_pkgver=0.7-2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Measurement Units for R Vectors' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rcpp +) +optdepends=( + r-dplyr + r-ggforce + r-knitr + r-magrittr + r-measurements + r-nistunits + r-pillar + r-rmarkdown + r-testthat + r-udunits2 + r-vctrs + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-units/lilac.py b/prepare/r-units/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-units/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-units/lilac.yaml b/prepare/r-units/lilac.yaml new file mode 100644 index 0000000000..38c2c5491f --- /dev/null +++ b/prepare/r-units/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +update_on: +- regex: units_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=units diff --git a/prepare/r-universalmotif/PKGBUILD b/prepare/r-universalmotif/PKGBUILD new file mode 100644 index 0000000000..165a6bdf99 --- /dev/null +++ b/prepare/r-universalmotif/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=universalmotif +_pkgver=1.12.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Import, Modify, and Export Motifs with R' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-ggplot2 + r-iranges + r-rcpp + r-rcppthread + r-rlang + r-s4vectors + r-yaml +) +optdepends=( + r-ape + r-biocparallel + r-bookdown + r-cowplot + r-dplyr + r-genomicranges + r-ggbio + r-ggseqlogo + r-ggtree + r-knitr + r-motifdb + r-motifstack + r-processx + r-pwmenrich + r-rgadem + r-rmarkdown + r-seqlogo + r-spelling + r-testthat + r-tfbstools +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-universalmotif/lilac.py b/prepare/r-universalmotif/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-universalmotif/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-universalmotif/lilac.yaml b/prepare/r-universalmotif/lilac.yaml new file mode 100644 index 0000000000..4d8ea89f6f --- /dev/null +++ b/prepare/r-universalmotif/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-ggplot2 +- r-iranges +- r-rcpp +- r-rcppthread +- r-rlang +- r-s4vectors +- r-yaml +update_on: +- regex: universalmotif_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/universalmotif diff --git a/prepare/r-upsetr/PKGBUILD b/prepare/r-upsetr/PKGBUILD new file mode 100644 index 0000000000..418b897390 --- /dev/null +++ b/prepare/r-upsetr/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=UpSetR +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-ggplot2 + r-gridextra + r-plyr + r-scales +) +optdepends=( + r-knitr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-upsetr/lilac.py b/prepare/r-upsetr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-upsetr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-upsetr/lilac.yaml b/prepare/r-upsetr/lilac.yaml new file mode 100644 index 0000000000..a092502f9e --- /dev/null +++ b/prepare/r-upsetr/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gridextra +- r-plyr +- r-scales +update_on: +- regex: UpSetR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=UpSetR diff --git a/prepare/r-urca/PKGBUILD b/prepare/r-urca/PKGBUILD new file mode 100644 index 0000000000..025a135c7e --- /dev/null +++ b/prepare/r-urca/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=urca +_pkgver=1.3-0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Unit Root and Cointegration Tests for Time Series Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-urca/lilac.py b/prepare/r-urca/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-urca/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-urca/lilac.yaml b/prepare/r-urca/lilac.yaml new file mode 100644 index 0000000000..c9cf0b877f --- /dev/null +++ b/prepare/r-urca/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: urca_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=urca diff --git a/prepare/r-urltools/PKGBUILD b/prepare/r-urltools/PKGBUILD new file mode 100644 index 0000000000..6207c82f8a --- /dev/null +++ b/prepare/r-urltools/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=urltools +_pkgver=1.7.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Vectorised Tools for URL Handling and Parsing' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-rcpp + r-triebeard +) +optdepends=( + r-knitr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-urltools/lilac.py b/prepare/r-urltools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-urltools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-urltools/lilac.yaml b/prepare/r-urltools/lilac.yaml new file mode 100644 index 0000000000..390a21e5d9 --- /dev/null +++ b/prepare/r-urltools/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcpp +- r-triebeard +update_on: +- regex: urltools_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=urltools diff --git a/prepare/r-usethis/PKGBUILD b/prepare/r-usethis/PKGBUILD new file mode 100644 index 0000000000..7f578dcb92 --- /dev/null +++ b/prepare/r-usethis/PKGBUILD @@ -0,0 +1,58 @@ +# Maintainer: Guoyi Zhang + +_pkgname=usethis +_pkgver=2.1.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Automate Package and Project Setup' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-cli + r-clipr + r-crayon + r-curl + r-desc + r-fs + r-gert + r-gh + r-glue + r-jsonlite + r-lifecycle + r-purrr + r-rappdirs + r-rlang + r-rprojroot + r-rstudioapi + r-whisker + r-withr + r-yaml +) +optdepends=( + r-covr + r-knitr + r-magick + r-mockr + r-pkgload + r-rmarkdown + r-roxygen2 + r-spelling + r-styler + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-usethis/lilac.py b/prepare/r-usethis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-usethis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-usethis/lilac.yaml b/prepare/r-usethis/lilac.yaml new file mode 100644 index 0000000000..ba9c449e8d --- /dev/null +++ b/prepare/r-usethis/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cli +- r-clipr +- r-crayon +- r-curl +- r-desc +- r-fs +- r-gert +- r-gh +- r-glue +- r-jsonlite +- r-lifecycle +- r-purrr +- r-rappdirs +- r-rlang +- r-rprojroot +- r-rstudioapi +- r-whisker +- r-withr +- r-yaml +update_on: +- regex: usethis_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=usethis diff --git a/prepare/r-usort/PKGBUILD b/prepare/r-usort/PKGBUILD new file mode 100644 index 0000000000..1888fd123b --- /dev/null +++ b/prepare/r-usort/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=uSORT +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='uSORT: A self-refining ordering pipeline for gene selection' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-fpc + r-gplots + r-igraph + r-monocle + r-plyr + r-rann + r-rspectra + r-vgam +) +optdepends=( + r-ggplot2 + r-knitr + r-runit + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-usort/lilac.py b/prepare/r-usort/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-usort/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-usort/lilac.yaml b/prepare/r-usort/lilac.yaml new file mode 100644 index 0000000000..0a0c0ab0b7 --- /dev/null +++ b/prepare/r-usort/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-fpc +- r-gplots +- r-igraph +- r-monocle +- r-plyr +- r-rann +- r-rspectra +- r-vgam +update_on: +- regex: uSORT_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/uSORT diff --git a/prepare/r-uuid/PKGBUILD b/prepare/r-uuid/PKGBUILD new file mode 100644 index 0000000000..3cd4922963 --- /dev/null +++ b/prepare/r-uuid/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=uuid +_pkgver=1.0-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Generating and Handling of UUIDs' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-uuid/lilac.py b/prepare/r-uuid/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-uuid/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-uuid/lilac.yaml b/prepare/r-uuid/lilac.yaml new file mode 100644 index 0000000000..caae76710b --- /dev/null +++ b/prepare/r-uuid/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: uuid_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=uuid diff --git a/prepare/r-uwot/PKGBUILD b/prepare/r-uwot/PKGBUILD new file mode 100644 index 0000000000..15f18ecaf4 --- /dev/null +++ b/prepare/r-uwot/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=uwot +_pkgver=0.1.11 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-dqrng + r-fnn + r-irlba + r-rcpp + r-rcppannoy + r-rcppprogress + r-rspectra +) +optdepends=( + r-bigstatsr + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-uwot/lilac.py b/prepare/r-uwot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-uwot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-uwot/lilac.yaml b/prepare/r-uwot/lilac.yaml new file mode 100644 index 0000000000..3e088b8365 --- /dev/null +++ b/prepare/r-uwot/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dqrng +- r-fnn +- r-irlba +- r-rcpp +- r-rcppannoy +- r-rcppprogress +- r-rspectra +update_on: +- regex: uwot_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=uwot diff --git a/prepare/r-v8/PKGBUILD b/prepare/r-v8/PKGBUILD new file mode 100644 index 0000000000..c0dc88433f --- /dev/null +++ b/prepare/r-v8/PKGBUILD @@ -0,0 +1,36 @@ +# system requirements: V8 engine version 6+ is needed for ES6 and WASMsupport. On Linux you can also build against libv8-dev (Debian)or v8-devel (Fedora). We also provide static libv8 binaries formost platforms, see the README for details. +# Maintainer: Guoyi Zhang + +_pkgname=V8 +_pkgver=4.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Embedded JavaScript and WebAssembly Engine for R' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-curl + r-jsonlite + r-rcpp +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-v8/lilac.py b/prepare/r-v8/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-v8/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-v8/lilac.yaml b/prepare/r-v8/lilac.yaml new file mode 100644 index 0000000000..6cf4645211 --- /dev/null +++ b/prepare/r-v8/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-jsonlite +- r-rcpp +update_on: +- regex: V8_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=V8 diff --git a/prepare/r-vaexprs/PKGBUILD b/prepare/r-vaexprs/PKGBUILD new file mode 100644 index 0000000000..be56fe3dbd --- /dev/null +++ b/prepare/r-vaexprs/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=VAExprs +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generating Samples of Gene Expression Data with Variational Autoencoders' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-catencoders + r-deeppincs + r-diagrammer + r-graddescent + r-keras + r-mclust + r-purrr + r-scater + r-singlecellexperiment + r-summarizedexperiment + r-tensorflow +) +optdepends=( + r-knitr + r-reticulate + r-rmarkdown + r-sc3 + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vaexprs/lilac.py b/prepare/r-vaexprs/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vaexprs/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vaexprs/lilac.yaml b/prepare/r-vaexprs/lilac.yaml new file mode 100644 index 0000000000..c8a4d11b67 --- /dev/null +++ b/prepare/r-vaexprs/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-catencoders +- r-deeppincs +- r-diagrammer +- r-graddescent +- r-keras +- r-mclust +- r-purrr +- r-scater +- r-singlecellexperiment +- r-summarizedexperiment +- r-tensorflow +update_on: +- regex: VAExprs_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/VAExprs diff --git a/prepare/r-valr/PKGBUILD b/prepare/r-valr/PKGBUILD new file mode 100644 index 0000000000..a991fa7e2a --- /dev/null +++ b/prepare/r-valr/PKGBUILD @@ -0,0 +1,56 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=valr +_pkgver=0.6.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Genome Interval Arithmetic' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-broom + r-dplyr + r-ggplot2 + r-rcpp + r-readr + r-rlang + r-rtracklayer + r-stringr + r-tibble +) +optdepends=( + r-bench + r-covr + r-cowplot + r-curl + r-dbi + r-dbplyr + r-devtools + r-dt + r-genomicranges + r-iranges + r-knitr + r-purrr + r-rmariadb + r-rmarkdown + r-s4vectors + r-testthat + r-tidyr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-valr/lilac.py b/prepare/r-valr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-valr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-valr/lilac.yaml b/prepare/r-valr/lilac.yaml new file mode 100644 index 0000000000..c1a5ec78c1 --- /dev/null +++ b/prepare/r-valr/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-broom +- r-dplyr +- r-ggplot2 +- r-rcpp +- r-readr +- r-rlang +- r-rtracklayer +- r-stringr +- r-tibble +update_on: +- regex: valr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=valr diff --git a/prepare/r-vam/PKGBUILD b/prepare/r-vam/PKGBUILD new file mode 100644 index 0000000000..d87f78a6f2 --- /dev/null +++ b/prepare/r-vam/PKGBUILD @@ -0,0 +1,31 @@ +# Maintainer: Guoyi Zhang + +_pkgname=VAM +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Variance-Adjusted Mahalanobis' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-sctransform + r-seurat + r-seuratobject +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vam/lilac.py b/prepare/r-vam/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vam/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vam/lilac.yaml b/prepare/r-vam/lilac.yaml new file mode 100644 index 0000000000..4956ba14b5 --- /dev/null +++ b/prepare/r-vam/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: VAM_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=VAM diff --git a/prepare/r-vanillaice/PKGBUILD b/prepare/r-vanillaice/PKGBUILD new file mode 100644 index 0000000000..89c094c0c8 --- /dev/null +++ b/prepare/r-vanillaice/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=VanillaICE +_pkgver=1.56.3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Hidden Markov Model for high throughput genotyping arrays' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-biocgenerics + r-bsgenome.hsapiens.ucsc.hg18 + r-crlmm + r-data.table + r-foreach + r-genomeinfodb + r-genomicranges + r-iranges + r-matrixgenerics + r-matrixstats + r-oligoclasses + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-domc + r-dompi + r-doparallel + r-doredis + r-dosnow + r-human610quadv1bcrlmm + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vanillaice/lilac.py b/prepare/r-vanillaice/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vanillaice/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vanillaice/lilac.yaml b/prepare/r-vanillaice/lilac.yaml new file mode 100644 index 0000000000..7f2ac5f2e2 --- /dev/null +++ b/prepare/r-vanillaice/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-bsgenome.hsapiens.ucsc.hg18 +- r-crlmm +- r-data.table +- r-foreach +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-matrixgenerics +- r-matrixstats +- r-oligoclasses +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: VanillaICE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/VanillaICE diff --git a/prepare/r-varcon/PKGBUILD b/prepare/r-varcon/PKGBUILD new file mode 100644 index 0000000000..2e00c711d6 --- /dev/null +++ b/prepare/r-varcon/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=VarCon +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='VarCon: an R package for retrieving neighboring nucleotides of an SNV' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-bsgenome + r-genomicranges + r-ggplot2 + r-iranges + r-shiny + r-shinycssloaders + r-shinyfiles +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-varcon/lilac.py b/prepare/r-varcon/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-varcon/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-varcon/lilac.yaml b/prepare/r-varcon/lilac.yaml new file mode 100644 index 0000000000..04c5c3191e --- /dev/null +++ b/prepare/r-varcon/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-shiny +- r-shinycssloaders +- r-shinyfiles +update_on: +- regex: VarCon_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/VarCon diff --git a/prepare/r-varfrompdb/PKGBUILD b/prepare/r-varfrompdb/PKGBUILD new file mode 100644 index 0000000000..6c328c8351 --- /dev/null +++ b/prepare/r-varfrompdb/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=VarfromPDB +_pkgver=2.2.10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Disease-Gene-Variant Relations Mining from the Public Databases and Literature' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-curl + r-rismed + r-stringi + r-stringr + r-xml + r-xml2r +) +optdepends=( + r-knitr + r-rmarkdown + r-tools +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-varfrompdb/lilac.py b/prepare/r-varfrompdb/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-varfrompdb/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-varfrompdb/lilac.yaml b/prepare/r-varfrompdb/lilac.yaml new file mode 100644 index 0000000000..b74ffe265e --- /dev/null +++ b/prepare/r-varfrompdb/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-rismed +- r-stringi +- r-stringr +- r-xml +- r-xml2r +update_on: +- regex: VarfromPDB_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=VarfromPDB diff --git a/prepare/r-varhandle/PKGBUILD b/prepare/r-varhandle/PKGBUILD new file mode 100644 index 0000000000..8b658941aa --- /dev/null +++ b/prepare/r-varhandle/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=varhandle +_pkgver=2.0.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Functions for Robust Variable Handling' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-varhandle/lilac.py b/prepare/r-varhandle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-varhandle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-varhandle/lilac.yaml b/prepare/r-varhandle/lilac.yaml new file mode 100644 index 0000000000..ea41c0cd29 --- /dev/null +++ b/prepare/r-varhandle/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: varhandle_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=varhandle diff --git a/prepare/r-variancepartition/PKGBUILD b/prepare/r-variancepartition/PKGBUILD new file mode 100644 index 0000000000..0d824c0948 --- /dev/null +++ b/prepare/r-variancepartition/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Guoyi Zhang + +_pkgname=variancePartition +_pkgver=1.24.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quantify and interpret divers of variation in multilevel gene expression experiments' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocparallel + r-doparallel + r-foreach + r-ggplot2 + r-gplots + r-iterators + r-limma + r-lme4 + r-lmertest + r-pbkrtest + r-progress + r-reshape2 + r-rlang + r-scales +) +optdepends=( + r-ballgown + r-biocgenerics + r-biocstyle + r-dendextend + r-deseq2 + r-edger + r-knitr + r-pander + r-r2glmm + r-readr + r-rmarkdown + r-runit + r-tximport + r-tximportdata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-variancepartition/lilac.py b/prepare/r-variancepartition/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-variancepartition/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-variancepartition/lilac.yaml b/prepare/r-variancepartition/lilac.yaml new file mode 100644 index 0000000000..e1a14f6e81 --- /dev/null +++ b/prepare/r-variancepartition/lilac.yaml @@ -0,0 +1,24 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocparallel +- r-doparallel +- r-foreach +- r-ggplot2 +- r-gplots +- r-iterators +- r-limma +- r-lme4 +- r-lmertest +- r-pbkrtest +- r-progress +- r-reshape2 +- r-rlang +- r-scales +update_on: +- regex: variancePartition_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/variancePartition diff --git a/prepare/r-variantannotation/PKGBUILD b/prepare/r-variantannotation/PKGBUILD new file mode 100644 index 0000000000..31c9768ff6 --- /dev/null +++ b/prepare/r-variantannotation/PKGBUILD @@ -0,0 +1,58 @@ +# system requirements: GNU make +# Maintainer: Guoyi Zhang + +_pkgname=VariantAnnotation +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Annotation of Genetic Variants' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biobase + r-biocgenerics + r-biostrings + r-bsgenome + r-dbi + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-matrixgenerics + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-xvector + r-zlibbioc +) +optdepends=( + r-annotationhub + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-ggplot2 + r-polyphen.hsapiens.dbsnp131 + r-runit + r-sift.hsapiens.dbsnp132 + r-sift.hsapiens.dbsnp137 + r-snplocs.hsapiens.dbsnp.20101109 + r-snpstats + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-variantannotation/lilac.py b/prepare/r-variantannotation/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-variantannotation/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-variantannotation/lilac.yaml b/prepare/r-variantannotation/lilac.yaml new file mode 100644 index 0000000000..a424ad3a84 --- /dev/null +++ b/prepare/r-variantannotation/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-biostrings +- r-bsgenome +- r-dbi +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-matrixgenerics +- r-rhtslib +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-summarizedexperiment +- r-xvector +- r-zlibbioc +update_on: +- regex: VariantAnnotation_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/VariantAnnotation diff --git a/prepare/r-variantexperiment/PKGBUILD b/prepare/r-variantexperiment/PKGBUILD new file mode 100644 index 0000000000..e53d505c27 --- /dev/null +++ b/prepare/r-variantexperiment/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=VariantExperiment +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-delayedarray + r-delayeddataframe + r-gdsarray + r-gdsfmt + r-genomicranges + r-iranges + r-s4vectors + r-seqarray + r-seqvartools + r-snprelate + r-summarizedexperiment +) +optdepends=( + r-knitr + r-markdown + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-variantexperiment/lilac.py b/prepare/r-variantexperiment/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-variantexperiment/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-variantexperiment/lilac.yaml b/prepare/r-variantexperiment/lilac.yaml new file mode 100644 index 0000000000..ea1f88b982 --- /dev/null +++ b/prepare/r-variantexperiment/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-delayedarray +- r-delayeddataframe +- r-gdsarray +- r-gdsfmt +- r-genomicranges +- r-iranges +- r-s4vectors +- r-seqarray +- r-seqvartools +- r-snprelate +- r-summarizedexperiment +update_on: +- regex: VariantExperiment_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/VariantExperiment diff --git a/prepare/r-variantfiltering/PKGBUILD b/prepare/r-variantfiltering/PKGBUILD new file mode 100644 index 0000000000..fcb2ebf29a --- /dev/null +++ b/prepare/r-variantfiltering/PKGBUILD @@ -0,0 +1,62 @@ +# Maintainer: Guoyi Zhang + +_pkgname=VariantFiltering +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Filtering of coding and non-coding genetic variants' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-dt + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-genomicscores + r-graph + r-gviz + r-iranges + r-rbgl + r-rsamtools + r-s4vectors + r-shiny + r-shinyjs + r-shinythemes + r-shinytree + r-summarizedexperiment + r-variantannotation + r-xvector +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.1000genomes.hs37d5 + r-mafdb.1kgenomes.phase1.hs37d5 + r-org.hs.eg.db + r-phastcons100way.ucsc.hg19 + r-polyphen.hsapiens.dbsnp131 + r-runit + r-sift.hsapiens.dbsnp137 + r-snplocs.hsapiens.dbsnp144.grch37 + r-txdb.hsapiens.ucsc.hg19.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-variantfiltering/lilac.py b/prepare/r-variantfiltering/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-variantfiltering/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-variantfiltering/lilac.yaml b/prepare/r-variantfiltering/lilac.yaml new file mode 100644 index 0000000000..ea8f3c348c --- /dev/null +++ b/prepare/r-variantfiltering/lilac.yaml @@ -0,0 +1,33 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-dt +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-genomicscores +- r-graph +- r-gviz +- r-iranges +- r-rbgl +- r-rsamtools +- r-s4vectors +- r-shiny +- r-shinyjs +- r-shinythemes +- r-shinytree +- r-summarizedexperiment +- r-variantannotation +- r-xvector +update_on: +- regex: VariantFiltering_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/VariantFiltering diff --git a/prepare/r-varianttools/PKGBUILD b/prepare/r-varianttools/PKGBUILD new file mode 100644 index 0000000000..6e19287310 --- /dev/null +++ b/prepare/r-varianttools/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=VariantTools +_pkgver=1.36.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for Exploratory Analysis of Variant Calls' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-rsamtools + r-rtracklayer + r-s4vectors + r-variantannotation +) +optdepends=( + r-gmapr + r-graph + r-lungcancerlines + r-rbgl + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-varianttools/lilac.py b/prepare/r-varianttools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-varianttools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-varianttools/lilac.yaml b/prepare/r-varianttools/lilac.yaml new file mode 100644 index 0000000000..81b1f6c5e5 --- /dev/null +++ b/prepare/r-varianttools/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-biostrings +- r-bsgenome +- r-genomeinfodb +- r-genomicfeatures +- r-genomicranges +- r-iranges +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-variantannotation +update_on: +- regex: VariantTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/VariantTools diff --git a/prepare/r-varselrf/PKGBUILD b/prepare/r-varselrf/PKGBUILD new file mode 100644 index 0000000000..5ad2d46d44 --- /dev/null +++ b/prepare/r-varselrf/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=varSelRF +_pkgver=0.7-8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Variable Selection using Random Forests' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-randomforest +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-varselrf/lilac.py b/prepare/r-varselrf/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-varselrf/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-varselrf/lilac.yaml b/prepare/r-varselrf/lilac.yaml new file mode 100644 index 0000000000..ce2e28bbd3 --- /dev/null +++ b/prepare/r-varselrf/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-randomforest +update_on: +- regex: varSelRF_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=varSelRF diff --git a/prepare/r-vasp/PKGBUILD b/prepare/r-vasp/PKGBUILD new file mode 100644 index 0000000000..30427a0cdd --- /dev/null +++ b/prepare/r-vasp/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=VaSP +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Quantification and Visualization of Variations of Splicing in Population' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ballgown + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-matrixstats + r-rsamtools + r-s4vectors + r-sushi +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vasp/lilac.py b/prepare/r-vasp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vasp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vasp/lilac.yaml b/prepare/r-vasp/lilac.yaml new file mode 100644 index 0000000000..e8f0eadb72 --- /dev/null +++ b/prepare/r-vasp/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ballgown +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-iranges +- r-matrixstats +- r-rsamtools +- r-s4vectors +- r-sushi +update_on: +- regex: VaSP_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/VaSP diff --git a/prepare/r-vbmp/PKGBUILD b/prepare/r-vbmp/PKGBUILD new file mode 100644 index 0000000000..5ee77987dd --- /dev/null +++ b/prepare/r-vbmp/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=vbmp +_pkgver=1.62.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Variational Bayesian Multinomial Probit Regression' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-biobase + r-statmod +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vbmp/lilac.py b/prepare/r-vbmp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vbmp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vbmp/lilac.yaml b/prepare/r-vbmp/lilac.yaml new file mode 100644 index 0000000000..5db082ef00 --- /dev/null +++ b/prepare/r-vbmp/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: vbmp_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/vbmp diff --git a/prepare/r-vbsr/PKGBUILD b/prepare/r-vbsr/PKGBUILD new file mode 100644 index 0000000000..3ce26e033a --- /dev/null +++ b/prepare/r-vbsr/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=vbsr +_pkgver=0.0.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Variational Bayes Spike Regression Regularized Linear Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vbsr/lilac.py b/prepare/r-vbsr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vbsr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vbsr/lilac.yaml b/prepare/r-vbsr/lilac.yaml new file mode 100644 index 0000000000..26a996466b --- /dev/null +++ b/prepare/r-vbsr/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: vbsr_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=vbsr diff --git a/prepare/r-vcd/PKGBUILD b/prepare/r-vcd/PKGBUILD new file mode 100644 index 0000000000..c7f8ef2775 --- /dev/null +++ b/prepare/r-vcd/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=vcd +_pkgver=1.4-9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualizing Categorical Data' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-colorspace + r-lmtest +) +optdepends=( + r-coin + r-hsaur3 + r-kernlab + r-kernsmooth + r-mvtnorm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vcd/lilac.py b/prepare/r-vcd/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vcd/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vcd/lilac.yaml b/prepare/r-vcd/lilac.yaml new file mode 100644 index 0000000000..6de3cac6e7 --- /dev/null +++ b/prepare/r-vcd/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colorspace +- r-lmtest +update_on: +- regex: vcd_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=vcd diff --git a/prepare/r-vcfarray/PKGBUILD b/prepare/r-vcfarray/PKGBUILD new file mode 100644 index 0000000000..b3587f2dce --- /dev/null +++ b/prepare/r-vcfarray/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=VCFArray +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Representing on-disk / remote VCF files as array-like objects' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-delayedarray + r-genomicfiles + r-genomicranges + r-rsamtools + r-s4vectors + r-variantannotation +) +optdepends=( + r-biocmanager + r-biocstyle + r-knitr + r-rmarkdown + r-seqarray + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vcfarray/lilac.py b/prepare/r-vcfarray/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vcfarray/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vcfarray/lilac.yaml b/prepare/r-vcfarray/lilac.yaml new file mode 100644 index 0000000000..8e4d449138 --- /dev/null +++ b/prepare/r-vcfarray/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-delayedarray +- r-genomicfiles +- r-genomicranges +- r-rsamtools +- r-s4vectors +- r-variantannotation +update_on: +- regex: VCFArray_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/VCFArray diff --git a/prepare/r-vcfr/PKGBUILD b/prepare/r-vcfr/PKGBUILD new file mode 100644 index 0000000000..51fc98dd42 --- /dev/null +++ b/prepare/r-vcfr/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=vcfR +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Manipulate and Visualize VCF Data' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-ape + r-dplyr + r-magrittr + r-memuse + r-pinfsc50 + r-rcpp + r-stringr + r-tibble + r-vegan + r-viridislite +) +optdepends=( + r-adegenet + r-ggplot2 + r-knitr + r-poppr + r-reshape2 + r-rmarkdown + r-scales + r-testthat + r-tidyr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vcfr/lilac.py b/prepare/r-vcfr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vcfr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vcfr/lilac.yaml b/prepare/r-vcfr/lilac.yaml new file mode 100644 index 0000000000..4d03411a3d --- /dev/null +++ b/prepare/r-vcfr/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-dplyr +- r-magrittr +- r-memuse +- r-pinfsc50 +- r-rcpp +- r-stringr +- r-tibble +- r-vegan +- r-viridislite +update_on: +- regex: vcfR_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=vcfR diff --git a/prepare/r-vegamc/PKGBUILD b/prepare/r-vegamc/PKGBUILD new file mode 100644 index 0000000000..dcd02df04b --- /dev/null +++ b/prepare/r-vegamc/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=VegaMC +_pkgver=3.32.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biomart +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vegamc/lilac.py b/prepare/r-vegamc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vegamc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vegamc/lilac.yaml b/prepare/r-vegamc/lilac.yaml new file mode 100644 index 0000000000..f1b5874d66 --- /dev/null +++ b/prepare/r-vegamc/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biomart +update_on: +- regex: VegaMC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/VegaMC diff --git a/prepare/r-vegan/PKGBUILD b/prepare/r-vegan/PKGBUILD new file mode 100644 index 0000000000..ee545e47ab --- /dev/null +++ b/prepare/r-vegan/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=vegan +_pkgver=2.5-7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Community Ecology Package' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-permute +) +optdepends=( + r-knitr + r-markdown + r-parallel + r-tcltk +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vegan/lilac.py b/prepare/r-vegan/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vegan/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vegan/lilac.yaml b/prepare/r-vegan/lilac.yaml new file mode 100644 index 0000000000..2abec076b9 --- /dev/null +++ b/prepare/r-vegan/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-permute +update_on: +- regex: vegan_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=vegan diff --git a/prepare/r-velociraptor/PKGBUILD b/prepare/r-velociraptor/PKGBUILD new file mode 100644 index 0000000000..123856573f --- /dev/null +++ b/prepare/r-velociraptor/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Guoyi Zhang + +_pkgname=velociraptor +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Toolkit for Single-Cell Velocity' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-basilisk + r-biocgenerics + r-biocparallel + r-biocsingular + r-delayedarray + r-reticulate + r-s4vectors + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-zellkonverter +) +optdepends=( + r-biocstyle + r-cowplot + r-ggally + r-ggplot2 + r-graphics + r-grdevices + r-knitr + r-metr + r-patchwork + r-pkgdown + r-rmarkdown + r-rtsne + r-scater + r-scran + r-scrnaseq + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-velociraptor/lilac.py b/prepare/r-velociraptor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-velociraptor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-velociraptor/lilac.yaml b/prepare/r-velociraptor/lilac.yaml new file mode 100644 index 0000000000..38c79f2883 --- /dev/null +++ b/prepare/r-velociraptor/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-basilisk +- r-biocgenerics +- r-biocparallel +- r-biocsingular +- r-delayedarray +- r-reticulate +- r-s4vectors +- r-scuttle +- r-singlecellexperiment +- r-summarizedexperiment +- r-zellkonverter +update_on: +- regex: velociraptor_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/velociraptor diff --git a/prepare/r-veloviz/PKGBUILD b/prepare/r-veloviz/PKGBUILD new file mode 100644 index 0000000000..4daf9b42f0 --- /dev/null +++ b/prepare/r-veloviz/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=veloviz +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-igraph + r-rcpp + r-rspectra +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-veloviz/lilac.py b/prepare/r-veloviz/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-veloviz/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-veloviz/lilac.yaml b/prepare/r-veloviz/lilac.yaml new file mode 100644 index 0000000000..256fc1c257 --- /dev/null +++ b/prepare/r-veloviz/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-igraph +- r-rcpp +- r-rspectra +update_on: +- regex: veloviz_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/veloviz diff --git a/prepare/r-venn/PKGBUILD b/prepare/r-venn/PKGBUILD new file mode 100644 index 0000000000..93d4c02ef3 --- /dev/null +++ b/prepare/r-venn/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=venn +_pkgver=1.10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Draw Venn Diagrams' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-admisc +) +optdepends=( + r-ggplot2 + r-ggpolypath + r-qca +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-venn/lilac.py b/prepare/r-venn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-venn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-venn/lilac.yaml b/prepare/r-venn/lilac.yaml new file mode 100644 index 0000000000..005e4ff8ff --- /dev/null +++ b/prepare/r-venn/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-admisc +update_on: +- regex: venn_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=venn diff --git a/prepare/r-venndetail/PKGBUILD b/prepare/r-venndetail/PKGBUILD new file mode 100644 index 0000000000..52cd430256 --- /dev/null +++ b/prepare/r-venndetail/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=VennDetail +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A package for visualization and extract details' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-dplyr + r-futile.logger + r-ggplot2 + r-magrittr + r-purrr + r-tibble + r-upsetr + r-venndiagram +) +optdepends=( + r-knitr + r-markdown + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-venndetail/lilac.py b/prepare/r-venndetail/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-venndetail/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-venndetail/lilac.yaml b/prepare/r-venndetail/lilac.yaml new file mode 100644 index 0000000000..da0229ceef --- /dev/null +++ b/prepare/r-venndetail/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-futile.logger +- r-ggplot2 +- r-magrittr +- r-purrr +- r-tibble +- r-upsetr +- r-venndiagram +update_on: +- regex: VennDetail_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/VennDetail diff --git a/prepare/r-venndiagram/PKGBUILD b/prepare/r-venndiagram/PKGBUILD new file mode 100644 index 0000000000..081c1c3f93 --- /dev/null +++ b/prepare/r-venndiagram/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=VennDiagram +_pkgver=1.7.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Generate High-Resolution Venn and Euler Plots' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-futile.logger +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-venndiagram/lilac.py b/prepare/r-venndiagram/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-venndiagram/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-venndiagram/lilac.yaml b/prepare/r-venndiagram/lilac.yaml new file mode 100644 index 0000000000..ccc38da23a --- /dev/null +++ b/prepare/r-venndiagram/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-futile.logger +update_on: +- regex: VennDiagram_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=VennDiagram diff --git a/prepare/r-verification/PKGBUILD b/prepare/r-verification/PKGBUILD new file mode 100644 index 0000000000..ee9326b57a --- /dev/null +++ b/prepare/r-verification/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=verification +_pkgver=1.42 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Weather Forecast Verification Utilities' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-circstats + r-dtw + r-fields +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-verification/lilac.py b/prepare/r-verification/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-verification/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-verification/lilac.yaml b/prepare/r-verification/lilac.yaml new file mode 100644 index 0000000000..fe9d43864e --- /dev/null +++ b/prepare/r-verification/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-circstats +- r-dtw +- r-fields +update_on: +- regex: verification_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=verification diff --git a/prepare/r-verso/PKGBUILD b/prepare/r-verso/PKGBUILD new file mode 100644 index 0000000000..7df7bec835 --- /dev/null +++ b/prepare/r-verso/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=VERSO +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Viral Evolution ReconStructiOn (VERSO)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-ape + r-rfast +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-verso/lilac.py b/prepare/r-verso/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-verso/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-verso/lilac.yaml b/prepare/r-verso/lilac.yaml new file mode 100644 index 0000000000..8d57e9d7c6 --- /dev/null +++ b/prepare/r-verso/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ape +- r-rfast +update_on: +- regex: VERSO_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/VERSO diff --git a/prepare/r-vgam/PKGBUILD b/prepare/r-vgam/PKGBUILD new file mode 100644 index 0000000000..06d00f619a --- /dev/null +++ b/prepare/r-vgam/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=VGAM +_pkgver=1.1-5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Vector Generalized Linear and Additive Models' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-mass + r-mgcv + r-vgamdata + r-vgamextra +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vgam/lilac.py b/prepare/r-vgam/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vgam/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vgam/lilac.yaml b/prepare/r-vgam/lilac.yaml new file mode 100644 index 0000000000..164c68c3a1 --- /dev/null +++ b/prepare/r-vgam/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: VGAM_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=VGAM diff --git a/prepare/r-vidger/PKGBUILD b/prepare/r-vidger/PKGBUILD new file mode 100644 index 0000000000..46bdcbeddb --- /dev/null +++ b/prepare/r-vidger/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=vidger +_pkgver=1.14.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Create rapid visualizations of RNAseq data in R' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-deseq2 + r-edger + r-ggally + r-ggplot2 + r-ggrepel + r-knitr + r-rcolorbrewer + r-rmarkdown + r-scales + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-biocstyle + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vidger/lilac.py b/prepare/r-vidger/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vidger/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vidger/lilac.yaml b/prepare/r-vidger/lilac.yaml new file mode 100644 index 0000000000..91d30295b2 --- /dev/null +++ b/prepare/r-vidger/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-deseq2 +- r-edger +- r-ggally +- r-ggplot2 +- r-ggrepel +- r-knitr +- r-rcolorbrewer +- r-rmarkdown +- r-scales +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: vidger_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/vidger diff --git a/prepare/r-vim/PKGBUILD b/prepare/r-vim/PKGBUILD new file mode 100644 index 0000000000..957499b512 --- /dev/null +++ b/prepare/r-vim/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=VIM +_pkgver=6.1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualization and Imputation of Missing Values' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-car + r-colorspace + r-data.table + r-e1071 + r-laeken + r-magrittr + r-ranger + r-rcpp + r-robustbase + r-sp + r-vcd +) +optdepends=( + r-dplyr + r-knitr + r-reactable + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vim/lilac.py b/prepare/r-vim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vim/lilac.yaml b/prepare/r-vim/lilac.yaml new file mode 100644 index 0000000000..413d7f0753 --- /dev/null +++ b/prepare/r-vim/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-car +- r-colorspace +- r-data.table +- r-e1071 +- r-laeken +- r-magrittr +- r-ranger +- r-rcpp +- r-robustbase +- r-sp +- r-vcd +update_on: +- regex: VIM_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=VIM diff --git a/prepare/r-vioplot/PKGBUILD b/prepare/r-vioplot/PKGBUILD new file mode 100644 index 0000000000..e77c49ddda --- /dev/null +++ b/prepare/r-vioplot/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=vioplot +_pkgver=0.3.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Violin Plot' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r + r-sm + r-zoo +) +optdepends=( + r-base + r-ggplot2 + r-knitr + r-rcolorbrewer + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vioplot/lilac.py b/prepare/r-vioplot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vioplot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vioplot/lilac.yaml b/prepare/r-vioplot/lilac.yaml new file mode 100644 index 0000000000..6e4b9e9567 --- /dev/null +++ b/prepare/r-vioplot/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-sm +- r-zoo +update_on: +- regex: vioplot_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=vioplot diff --git a/prepare/r-viper/PKGBUILD b/prepare/r-viper/PKGBUILD new file mode 100644 index 0000000000..e840ae773e --- /dev/null +++ b/prepare/r-viper/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=viper +_pkgver=1.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Virtual Inference of Protein-activity by Enriched Regulon analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('custom') +depends=( + r + r-biobase + r-e1071 + r-mixtools +) +optdepends=( + r-bcellviper +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-viper/lilac.py b/prepare/r-viper/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-viper/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-viper/lilac.yaml b/prepare/r-viper/lilac.yaml new file mode 100644 index 0000000000..ba5b88ccc5 --- /dev/null +++ b/prepare/r-viper/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-e1071 +- r-mixtools +update_on: +- regex: viper_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/viper diff --git a/prepare/r-vipor/PKGBUILD b/prepare/r-vipor/PKGBUILD new file mode 100644 index 0000000000..13b772ca34 --- /dev/null +++ b/prepare/r-vipor/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=vipor +_pkgver=0.4.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Plot Categorical Data Using Quasirandom Noise and Density Estimates' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-beanplot + r-beeswarm + r-ggbeeswarm + r-ggplot2 + r-lattice + r-testthat + r-vioplot +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vipor/lilac.py b/prepare/r-vipor/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vipor/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vipor/lilac.yaml b/prepare/r-vipor/lilac.yaml new file mode 100644 index 0000000000..9af398487c --- /dev/null +++ b/prepare/r-vipor/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: vipor_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=vipor diff --git a/prepare/r-viridis/PKGBUILD b/prepare/r-viridis/PKGBUILD new file mode 100644 index 0000000000..1eaafd2742 --- /dev/null +++ b/prepare/r-viridis/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=viridis +_pkgver=0.6.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Colorblind-Friendly Color Maps for R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-ggplot2 + r-gridextra + r-viridislite +) +optdepends=( + r-colorspace + r-covr + r-dichromat + r-hexbin + r-httr + r-knitr + r-mapproj + r-maps + r-mass + r-raster + r-rastervis + r-rgdal + r-rmarkdown + r-scales + r-svglite + r-testthat + r-vdiffr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-viridis/lilac.py b/prepare/r-viridis/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-viridis/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-viridis/lilac.yaml b/prepare/r-viridis/lilac.yaml new file mode 100644 index 0000000000..547bd91a63 --- /dev/null +++ b/prepare/r-viridis/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggplot2 +- r-gridextra +- r-viridislite +update_on: +- regex: viridis_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=viridis diff --git a/prepare/r-viridislite/PKGBUILD b/prepare/r-viridislite/PKGBUILD new file mode 100644 index 0000000000..0505d02c0a --- /dev/null +++ b/prepare/r-viridislite/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=viridisLite +_pkgver=0.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Colorblind-Friendly Color Maps (Lite Version)' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-covr + r-ggplot2 + r-hexbin + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-viridislite/lilac.py b/prepare/r-viridislite/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-viridislite/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-viridislite/lilac.yaml b/prepare/r-viridislite/lilac.yaml new file mode 100644 index 0000000000..32bfb40626 --- /dev/null +++ b/prepare/r-viridislite/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: viridisLite_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=viridisLite diff --git a/prepare/r-viseago/PKGBUILD b/prepare/r-viseago/PKGBUILD new file mode 100644 index 0000000000..28cce9c493 --- /dev/null +++ b/prepare/r-viseago/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Guoyi Zhang + +_pkgname=ViSEAGO +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-annotationforge + r-biomart + r-data.table + r-dendextend + r-diagrammer + r-dt + r-dynamictreecut + r-fgsea + r-ggplot2 + r-go.db + r-gosemsim + r-heatmaply + r-htmlwidgets + r-igraph + r-plotly + r-processx + r-r.utils + r-rcolorbrewer + r-scales + r-topgo + r-upsetr +) +optdepends=( + r-biocmanager + r-biocstyle + r-corrplot + r-htmltools + r-knitr + r-limma + r-org.mm.eg.db + r-remotes + r-rgraphviz + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-viseago/lilac.py b/prepare/r-viseago/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-viseago/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-viseago/lilac.yaml b/prepare/r-viseago/lilac.yaml new file mode 100644 index 0000000000..145e1607c9 --- /dev/null +++ b/prepare/r-viseago/lilac.yaml @@ -0,0 +1,31 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-annotationforge +- r-biomart +- r-data.table +- r-dendextend +- r-diagrammer +- r-dt +- r-dynamictreecut +- r-fgsea +- r-ggplot2 +- r-go.db +- r-gosemsim +- r-heatmaply +- r-htmlwidgets +- r-igraph +- r-plotly +- r-processx +- r-r.utils +- r-rcolorbrewer +- r-scales +- r-topgo +- r-upsetr +update_on: +- regex: ViSEAGO_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/ViSEAGO diff --git a/prepare/r-visnetwork/PKGBUILD b/prepare/r-visnetwork/PKGBUILD new file mode 100644 index 0000000000..635a82fea4 --- /dev/null +++ b/prepare/r-visnetwork/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=visNetwork +_pkgver=2.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Network Visualization using 'vis.js' Library" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmltools + r-htmlwidgets + r-jsonlite + r-magrittr +) +optdepends=( + r-colourpicker + r-flashclust + r-ggraph + r-igraph + r-knitr + r-rmarkdown + r-rpart + r-shiny + r-shinywidgets + r-sparkline + r-tidygraph + r-webshot +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-visnetwork/lilac.py b/prepare/r-visnetwork/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-visnetwork/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-visnetwork/lilac.yaml b/prepare/r-visnetwork/lilac.yaml new file mode 100644 index 0000000000..154e40cc12 --- /dev/null +++ b/prepare/r-visnetwork/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-htmlwidgets +- r-jsonlite +- r-magrittr +update_on: +- regex: visNetwork_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=visNetwork diff --git a/prepare/r-visse/PKGBUILD b/prepare/r-visse/PKGBUILD new file mode 100644 index 0000000000..0dfcccb2a7 --- /dev/null +++ b/prepare/r-visse/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=vissE +_pkgver=1.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Visualising Set Enrichment Analysis Results' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-ggforce + r-ggplot2 + r-ggraph + r-ggrepel + r-ggwordcloud + r-gseabase + r-igraph + r-msigdb + r-plyr + r-rcolorbrewer + r-reshape2 + r-scales + r-scico + r-textstem + r-tidygraph + r-tm +) +optdepends=( + r-biocstyle + r-covr + r-knitr + r-org.hs.eg.db + r-org.mm.eg.db + r-patchwork + r-pkgdown + r-prettydoc + r-rmarkdown + r-singscore + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-visse/lilac.py b/prepare/r-visse/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-visse/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-visse/lilac.yaml b/prepare/r-visse/lilac.yaml new file mode 100644 index 0000000000..ff125802f6 --- /dev/null +++ b/prepare/r-visse/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-ggforce +- r-ggplot2 +- r-ggraph +- r-ggrepel +- r-ggwordcloud +- r-gseabase +- r-igraph +- r-msigdb +- r-plyr +- r-rcolorbrewer +- r-reshape2 +- r-scales +- r-scico +- r-textstem +- r-tidygraph +- r-tm +update_on: +- regex: vissE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/vissE diff --git a/prepare/r-vplotr/PKGBUILD b/prepare/r-vplotr/PKGBUILD new file mode 100644 index 0000000000..7d33f8c5e4 --- /dev/null +++ b/prepare/r-vplotr/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=VplotR +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Set of tools to make V-plots and compute footprint profiles' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-cowplot + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-magrittr + r-rcolorbrewer + r-reshape2 + r-rsamtools + r-s4vectors + r-zoo +) +optdepends=( + r-covr + r-genomicfeatures + r-knitr + r-pkgdown + r-rmarkdown + r-testthat + r-txdb.scerevisiae.ucsc.saccer3.sgdgene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vplotr/lilac.py b/prepare/r-vplotr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vplotr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vplotr/lilac.yaml b/prepare/r-vplotr/lilac.yaml new file mode 100644 index 0000000000..a98bc5241e --- /dev/null +++ b/prepare/r-vplotr/lilac.yaml @@ -0,0 +1,21 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cowplot +- r-genomeinfodb +- r-genomicalignments +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-magrittr +- r-rcolorbrewer +- r-reshape2 +- r-rsamtools +- r-s4vectors +- r-zoo +update_on: +- regex: VplotR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/VplotR diff --git a/prepare/r-vroom/PKGBUILD b/prepare/r-vroom/PKGBUILD new file mode 100644 index 0000000000..dc641e75f3 --- /dev/null +++ b/prepare/r-vroom/PKGBUILD @@ -0,0 +1,65 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=vroom +_pkgver=1.5.7 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Read and Write Rectangular Text Data Quickly' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-bit64 + r-cli + r-cpp11 + r-crayon + r-glue + r-hms + r-lifecycle + r-progress + r-rlang + r-tibble + r-tidyselect + r-tzdb + r-vctrs + r-withr +) +optdepends=( + r-archive + r-bench + r-covr + r-curl + r-dplyr + r-forcats + r-fs + r-ggplot2 + r-knitr + r-patchwork + r-prettyunits + r-purrr + r-rmarkdown + r-rstudioapi + r-scales + r-spelling + r-testthat + r-tidyr + r-utils + r-waldo + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vroom/lilac.py b/prepare/r-vroom/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vroom/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vroom/lilac.yaml b/prepare/r-vroom/lilac.yaml new file mode 100644 index 0000000000..808d15bbf4 --- /dev/null +++ b/prepare/r-vroom/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bit64 +- r-cli +- r-cpp11 +- r-crayon +- r-glue +- r-hms +- r-lifecycle +- r-progress +- r-rlang +- r-tibble +- r-tidyselect +- r-tzdb +- r-vctrs +- r-withr +update_on: +- regex: vroom_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=vroom diff --git a/prepare/r-vsn/PKGBUILD b/prepare/r-vsn/PKGBUILD new file mode 100644 index 0000000000..4451b7a970 --- /dev/null +++ b/prepare/r-vsn/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=vsn +_pkgver=3.62.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Variance stabilization and calibration for microarray data' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-affy + r-biobase + r-ggplot2 + r-limma +) +optdepends=( + r-affydata + r-biocstyle + r-dplyr + r-hgu95av2cdf + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vsn/lilac.py b/prepare/r-vsn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vsn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vsn/lilac.yaml b/prepare/r-vsn/lilac.yaml new file mode 100644 index 0000000000..14c73a255f --- /dev/null +++ b/prepare/r-vsn/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-biobase +- r-ggplot2 +- r-limma +update_on: +- regex: vsn_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/vsn diff --git a/prepare/r-vtpnet/PKGBUILD b/prepare/r-vtpnet/PKGBUILD new file mode 100644 index 0000000000..01303f0c02 --- /dev/null +++ b/prepare/r-vtpnet/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=vtpnet +_pkgver=0.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='variant-transcription factor-phenotype networks' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-doparallel + r-foreach + r-genomicranges + r-graph + r-gwascat +) +optdepends=( + r-motifdb + r-rgraphviz + r-variantannotation +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vtpnet/lilac.py b/prepare/r-vtpnet/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vtpnet/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vtpnet/lilac.yaml b/prepare/r-vtpnet/lilac.yaml new file mode 100644 index 0000000000..0d4c879acd --- /dev/null +++ b/prepare/r-vtpnet/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-doparallel +- r-foreach +- r-genomicranges +- r-graph +- r-gwascat +update_on: +- regex: vtpnet_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/vtpnet diff --git a/prepare/r-vulcan/PKGBUILD b/prepare/r-vulcan/PKGBUILD new file mode 100644 index 0000000000..4fba07fd00 --- /dev/null +++ b/prepare/r-vulcan/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=vulcan +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='VirtUaL ChIP-Seq data Analysis using Networks' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-catools + r-chippeakanno + r-csaw + r-deseq2 + r-diffbind + r-genomicranges + r-gplots + r-locfit + r-s4vectors + r-txdb.hsapiens.ucsc.hg19.knowngene + r-viper + r-wordcloud + r-zoo +) +optdepends=( + r-vulcandata +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-vulcan/lilac.py b/prepare/r-vulcan/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-vulcan/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-vulcan/lilac.yaml b/prepare/r-vulcan/lilac.yaml new file mode 100644 index 0000000000..1029214d1c --- /dev/null +++ b/prepare/r-vulcan/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-catools +- r-chippeakanno +- r-csaw +- r-deseq2 +- r-diffbind +- r-genomicranges +- r-gplots +- r-locfit +- r-s4vectors +- r-txdb.hsapiens.ucsc.hg19.knowngene +- r-viper +- r-wordcloud +- r-zoo +update_on: +- regex: vulcan_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/vulcan diff --git a/prepare/r-waddr/PKGBUILD b/prepare/r-waddr/PKGBUILD new file mode 100644 index 0000000000..540a41a4ff --- /dev/null +++ b/prepare/r-waddr/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=waddR +_pkgver=1.8.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Statistical tests for detecting differential distributions based on the 2-Wasserstein distance' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-arm + r-biocfilecache + r-biocparallel + r-eva + r-rcpp + r-rcpparmadillo + r-singlecellexperiment +) +optdepends=( + r-devtools + r-knitr + r-rmarkdown + r-roxygen2 + r-rprojroot + r-scater + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-waddr/lilac.py b/prepare/r-waddr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-waddr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-waddr/lilac.yaml b/prepare/r-waddr/lilac.yaml new file mode 100644 index 0000000000..de16afbc6a --- /dev/null +++ b/prepare/r-waddr/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-arm +- r-biocfilecache +- r-biocparallel +- r-eva +- r-rcpp +- r-rcpparmadillo +- r-singlecellexperiment +update_on: +- regex: waddR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/waddR diff --git a/prepare/r-waffle/PKGBUILD b/prepare/r-waffle/PKGBUILD new file mode 100644 index 0000000000..987b2497da --- /dev/null +++ b/prepare/r-waffle/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=waffle +_pkgver=0.7.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Create Waffle Chart Visualizations in R' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-extrafont + r-ggplot2 + r-gridextra + r-gtable + r-rcolorbrewer +) +optdepends=( + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-waffle/lilac.py b/prepare/r-waffle/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-waffle/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-waffle/lilac.yaml b/prepare/r-waffle/lilac.yaml new file mode 100644 index 0000000000..afe2756a9d --- /dev/null +++ b/prepare/r-waffle/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-extrafont +- r-ggplot2 +- r-gridextra +- r-gtable +- r-rcolorbrewer +update_on: +- regex: waffle_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=waffle diff --git a/prepare/r-waiter/PKGBUILD b/prepare/r-waiter/PKGBUILD new file mode 100644 index 0000000000..6664f92e70 --- /dev/null +++ b/prepare/r-waiter/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=waiter +_pkgver=0.2.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Loading Screen for 'Shiny'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-htmltools + r-r6 + r-shiny +) +optdepends=( + r-httr + r-knitr + r-packer + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-waiter/lilac.py b/prepare/r-waiter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-waiter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-waiter/lilac.yaml b/prepare/r-waiter/lilac.yaml new file mode 100644 index 0000000000..6859c947d4 --- /dev/null +++ b/prepare/r-waiter/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-htmltools +- r-r6 +- r-shiny +update_on: +- regex: waiter_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=waiter diff --git a/prepare/r-waldo/PKGBUILD b/prepare/r-waldo/PKGBUILD new file mode 100644 index 0000000000..c515659389 --- /dev/null +++ b/prepare/r-waldo/PKGBUILD @@ -0,0 +1,41 @@ +# Maintainer: Guoyi Zhang + +_pkgname=waldo +_pkgver=0.3.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Find Differences Between R Objects' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-cli + r-diffobj + r-fansi + r-glue + r-rematch2 + r-rlang + r-tibble +) +optdepends=( + r-covr + r-r6 + r-testthat + r-withr + r-xml2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-waldo/lilac.py b/prepare/r-waldo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-waldo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-waldo/lilac.yaml b/prepare/r-waldo/lilac.yaml new file mode 100644 index 0000000000..f9dd0b9f14 --- /dev/null +++ b/prepare/r-waldo/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-cli +- r-diffobj +- r-fansi +- r-glue +- r-rematch2 +- r-rlang +- r-tibble +update_on: +- regex: waldo_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=waldo diff --git a/prepare/r-warp/PKGBUILD b/prepare/r-warp/PKGBUILD new file mode 100644 index 0000000000..56668cd039 --- /dev/null +++ b/prepare/r-warp/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=warp +_pkgver=0.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Group Dates' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-warp/lilac.py b/prepare/r-warp/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-warp/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-warp/lilac.yaml b/prepare/r-warp/lilac.yaml new file mode 100644 index 0000000000..faac9861aa --- /dev/null +++ b/prepare/r-warp/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: warp_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=warp diff --git a/prepare/r-watermelon/PKGBUILD b/prepare/r-watermelon/PKGBUILD new file mode 100644 index 0000000000..9785a9aa75 --- /dev/null +++ b/prepare/r-watermelon/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=wateRmelon +_pkgver=2.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Illumina 450 and EPIC methylation array normalization and metrics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-illuminahumanmethylation450kanno.ilmn12.hg19 + r-illuminaio + r-limma + r-lumi + r-matrixstats + r-methylumi + r-roc +) +optdepends=( + r-biocstyle + r-flowsorted.blood.450k + r-flowsorted.blood.epic + r-illuminahumanmethylationepicanno.ilm10b2.hg19 + r-illuminahumanmethylationepicmanifest + r-irlba + r-knitr + r-minfi + r-preprocesscore + r-rmarkdown + r-rpmm +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-watermelon/lilac.py b/prepare/r-watermelon/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-watermelon/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-watermelon/lilac.yaml b/prepare/r-watermelon/lilac.yaml new file mode 100644 index 0000000000..e5b7d2cd67 --- /dev/null +++ b/prepare/r-watermelon/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-illuminahumanmethylation450kanno.ilmn12.hg19 +- r-illuminaio +- r-limma +- r-lumi +- r-matrixstats +- r-methylumi +- r-roc +update_on: +- regex: wateRmelon_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/wateRmelon diff --git a/prepare/r-wavcluster/PKGBUILD b/prepare/r-wavcluster/PKGBUILD new file mode 100644 index 0000000000..becf395221 --- /dev/null +++ b/prepare/r-wavcluster/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Guoyi Zhang + +_pkgname=wavClusteR +_pkgver=2.28.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biocgenerics + r-biostrings + r-foreach + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-hmisc + r-iranges + r-mclust + r-rsamtools + r-rtracklayer + r-s4vectors + r-seqinr + r-stringr +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg19 + r-domc + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-wavcluster/lilac.py b/prepare/r-wavcluster/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-wavcluster/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-wavcluster/lilac.yaml b/prepare/r-wavcluster/lilac.yaml new file mode 100644 index 0000000000..e3075d6732 --- /dev/null +++ b/prepare/r-wavcluster/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-biostrings +- r-foreach +- r-genomicfeatures +- r-genomicranges +- r-ggplot2 +- r-hmisc +- r-iranges +- r-mclust +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-seqinr +- r-stringr +update_on: +- regex: wavClusteR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/wavClusteR diff --git a/prepare/r-waveslim/PKGBUILD b/prepare/r-waveslim/PKGBUILD new file mode 100644 index 0000000000..ee6285fd62 --- /dev/null +++ b/prepare/r-waveslim/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=waveslim +_pkgver=1.8.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Basic Wavelet Routines for One-, Two-, and Three-Dimensional Signal Processing' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +optdepends=( + r-covr + r-fftw +) +makedepends=( + gcc-fortran +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-waveslim/lilac.py b/prepare/r-waveslim/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-waveslim/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-waveslim/lilac.yaml b/prepare/r-waveslim/lilac.yaml new file mode 100644 index 0000000000..34ea1fce2d --- /dev/null +++ b/prepare/r-waveslim/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: waveslim_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=waveslim diff --git a/prepare/r-wavethresh/PKGBUILD b/prepare/r-wavethresh/PKGBUILD new file mode 100644 index 0000000000..c5fb4fe2c0 --- /dev/null +++ b/prepare/r-wavethresh/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=wavethresh +_pkgver=4.6.8 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Wavelets Statistics and Transforms' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-wavethresh/lilac.py b/prepare/r-wavethresh/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-wavethresh/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-wavethresh/lilac.yaml b/prepare/r-wavethresh/lilac.yaml new file mode 100644 index 0000000000..06ab8b1a43 --- /dev/null +++ b/prepare/r-wavethresh/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: wavethresh_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=wavethresh diff --git a/prepare/r-weaver/PKGBUILD b/prepare/r-weaver/PKGBUILD new file mode 100644 index 0000000000..4c616ef421 --- /dev/null +++ b/prepare/r-weaver/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=weaver +_pkgver=1.60.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools and extensions for processing Sweave documents' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-digest +) +optdepends=( + r-codetools +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-weaver/lilac.py b/prepare/r-weaver/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-weaver/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-weaver/lilac.yaml b/prepare/r-weaver/lilac.yaml new file mode 100644 index 0000000000..f331a10e8e --- /dev/null +++ b/prepare/r-weaver/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-digest +update_on: +- regex: weaver_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/weaver diff --git a/prepare/r-webbioc/PKGBUILD b/prepare/r-webbioc/PKGBUILD new file mode 100644 index 0000000000..7e5b21fc07 --- /dev/null +++ b/prepare/r-webbioc/PKGBUILD @@ -0,0 +1,35 @@ +# system requirements: Unix, Perl (>= 5.6.0), Netpbm +# Maintainer: Guoyi Zhang + +_pkgname=webbioc +_pkgver=1.66.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Bioconductor Web Interface' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-affy + r-annaffy + r-biobase + r-biocmanager + r-gcrma + r-multtest + r-qvalue + r-vsn +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-webbioc/lilac.py b/prepare/r-webbioc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-webbioc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-webbioc/lilac.yaml b/prepare/r-webbioc/lilac.yaml new file mode 100644 index 0000000000..d3a583179e --- /dev/null +++ b/prepare/r-webbioc/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-affy +- r-annaffy +- r-biobase +- r-biocmanager +- r-gcrma +- r-multtest +- r-qvalue +- r-vsn +update_on: +- regex: webbioc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/webbioc diff --git a/prepare/r-webchem/PKGBUILD b/prepare/r-webchem/PKGBUILD new file mode 100644 index 0000000000..30ac848071 --- /dev/null +++ b/prepare/r-webchem/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=webchem +_pkgver=1.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Chemical Information from the Web' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-base64enc + r-data.tree + r-dplyr + r-httr + r-jsonlite + r-purrr + r-rlang + r-rvest + r-stringr + r-tibble + r-xml2 +) +optdepends=( + r-covr + r-knitr + r-plot.matrix + r-rcdk + r-rmarkdown + r-robotstxt + r-testthat + r-usethis + r-vcr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-webchem/lilac.py b/prepare/r-webchem/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-webchem/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-webchem/lilac.yaml b/prepare/r-webchem/lilac.yaml new file mode 100644 index 0000000000..7cd446569b --- /dev/null +++ b/prepare/r-webchem/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-data.tree +- r-dplyr +- r-httr +- r-jsonlite +- r-purrr +- r-rlang +- r-rvest +- r-stringr +- r-tibble +- r-xml2 +update_on: +- regex: webchem_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=webchem diff --git a/prepare/r-webshot/PKGBUILD b/prepare/r-webshot/PKGBUILD new file mode 100644 index 0000000000..87be409633 --- /dev/null +++ b/prepare/r-webshot/PKGBUILD @@ -0,0 +1,36 @@ +# system requirements: PhantomJS (http://phantomjs.org) for takingscreenshots, ImageMagick (http://www.imagemagick.org) orGraphicsMagick (http://www.graphicsmagick.org) and OptiPNG(http://optipng.sourceforge.net) for manipulating images. +# Maintainer: Guoyi Zhang + +_pkgname=webshot +_pkgver=0.5.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Take Screenshots of Web Pages' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-callr + r-jsonlite + r-magrittr +) +optdepends=( + r-httpuv + r-knitr + r-rmarkdown + r-shiny +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-webshot/lilac.py b/prepare/r-webshot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-webshot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-webshot/lilac.yaml b/prepare/r-webshot/lilac.yaml new file mode 100644 index 0000000000..006062a107 --- /dev/null +++ b/prepare/r-webshot/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-callr +- r-jsonlite +- r-magrittr +update_on: +- regex: webshot_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=webshot diff --git a/prepare/r-webutils/PKGBUILD b/prepare/r-webutils/PKGBUILD new file mode 100644 index 0000000000..062bdbb27e --- /dev/null +++ b/prepare/r-webutils/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=webutils +_pkgver=1.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Utility Functions for Developing Web Applications' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-curl + r-jsonlite +) +optdepends=( + r-httpuv + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-webutils/lilac.py b/prepare/r-webutils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-webutils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-webutils/lilac.yaml b/prepare/r-webutils/lilac.yaml new file mode 100644 index 0000000000..2175f617c9 --- /dev/null +++ b/prepare/r-webutils/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-curl +- r-jsonlite +update_on: +- regex: webutils_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=webutils diff --git a/prepare/r-weitrix/PKGBUILD b/prepare/r-weitrix/PKGBUILD new file mode 100644 index 0000000000..07fc144ccd --- /dev/null +++ b/prepare/r-weitrix/PKGBUILD @@ -0,0 +1,58 @@ +# Maintainer: Guoyi Zhang + +_pkgname=weitrix +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for matrices with precision weights, test and explore weighted or sparse data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-assertthat + r-biocgenerics + r-biocparallel + r-ckmeans.1d.dp + r-delayedarray + r-delayedmatrixstats + r-dplyr + r-ggplot2 + r-glm2 + r-limma + r-purrr + r-reshape2 + r-rhpcblasctl + r-rlang + r-s4vectors + r-scales + r-summarizedexperiment + r-topconfects +) +optdepends=( + r-airway + r-annotationdbi + r-biocstyle + r-complexheatmap + r-edger + r-ensdb.hsapiens.v86 + r-knitr + r-org.sc.sgd.db + r-patchwork + r-rmarkdown + r-testthat + r-tidyverse +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-weitrix/lilac.py b/prepare/r-weitrix/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-weitrix/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-weitrix/lilac.yaml b/prepare/r-weitrix/lilac.yaml new file mode 100644 index 0000000000..9d686cc426 --- /dev/null +++ b/prepare/r-weitrix/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-biocgenerics +- r-biocparallel +- r-ckmeans.1d.dp +- r-delayedarray +- r-delayedmatrixstats +- r-dplyr +- r-ggplot2 +- r-glm2 +- r-limma +- r-purrr +- r-reshape2 +- r-rhpcblasctl +- r-rlang +- r-s4vectors +- r-scales +- r-summarizedexperiment +- r-topconfects +update_on: +- regex: weitrix_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/weitrix diff --git a/prepare/r-wesanderson/PKGBUILD b/prepare/r-wesanderson/PKGBUILD new file mode 100644 index 0000000000..2f62832e60 --- /dev/null +++ b/prepare/r-wesanderson/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=wesanderson +_pkgver=0.3.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A Wes Anderson Palette Generator' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-ggplot2 +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-wesanderson/lilac.py b/prepare/r-wesanderson/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-wesanderson/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-wesanderson/lilac.yaml b/prepare/r-wesanderson/lilac.yaml new file mode 100644 index 0000000000..ce61d47bc8 --- /dev/null +++ b/prepare/r-wesanderson/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: wesanderson_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=wesanderson diff --git a/prepare/r-wgcna/PKGBUILD b/prepare/r-wgcna/PKGBUILD new file mode 100644 index 0000000000..27ad38f1bf --- /dev/null +++ b/prepare/r-wgcna/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi Zhang + +_pkgname=WGCNA +_pkgver=1.70-3 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Weighted Correlation Network Analysis' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-annotationdbi + r-doparallel + r-dynamictreecut + r-fastcluster + r-foreach + r-go.db + r-hmisc + r-impute + r-matrixstats + r-preprocesscore + r-rcpp +) +optdepends=( + r-entropy + r-infotheo + r-minet + r-org.hs.eg.db + r-org.mm.eg.db +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-wgcna/lilac.py b/prepare/r-wgcna/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-wgcna/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-wgcna/lilac.yaml b/prepare/r-wgcna/lilac.yaml new file mode 100644 index 0000000000..fd057f6dd1 --- /dev/null +++ b/prepare/r-wgcna/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-annotationdbi +- r-doparallel +- r-dynamictreecut +- r-fastcluster +- r-foreach +- r-go.db +- r-hmisc +- r-impute +- r-matrixstats +- r-preprocesscore +- r-rcpp +update_on: +- regex: WGCNA_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=WGCNA diff --git a/prepare/r-wheatmap/PKGBUILD b/prepare/r-wheatmap/PKGBUILD new file mode 100644 index 0000000000..de8543a8da --- /dev/null +++ b/prepare/r-wheatmap/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=wheatmap +_pkgver=0.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Incrementally Build Complex Plots using Natural Semantics' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-colorspace + r-rcolorbrewer +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-wheatmap/lilac.py b/prepare/r-wheatmap/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-wheatmap/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-wheatmap/lilac.yaml b/prepare/r-wheatmap/lilac.yaml new file mode 100644 index 0000000000..b4928b9ad7 --- /dev/null +++ b/prepare/r-wheatmap/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-colorspace +- r-rcolorbrewer +update_on: +- regex: wheatmap_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=wheatmap diff --git a/prepare/r-whisker/PKGBUILD b/prepare/r-whisker/PKGBUILD new file mode 100644 index 0000000000..07373317c2 --- /dev/null +++ b/prepare/r-whisker/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=whisker +_pkgver=0.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='{{mustache}} for R, Logicless Templating' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-markdown +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-whisker/lilac.py b/prepare/r-whisker/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-whisker/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-whisker/lilac.yaml b/prepare/r-whisker/lilac.yaml new file mode 100644 index 0000000000..51c7fd3aba --- /dev/null +++ b/prepare/r-whisker/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: whisker_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=whisker diff --git a/prepare/r-widgettools/PKGBUILD b/prepare/r-widgettools/PKGBUILD new file mode 100644 index 0000000000..2c2052d5b8 --- /dev/null +++ b/prepare/r-widgettools/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=widgetTools +_pkgver=1.72.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Creates an interactive tcltk widget' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +optdepends=( + r-biobase +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-widgettools/lilac.py b/prepare/r-widgettools/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-widgettools/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-widgettools/lilac.yaml b/prepare/r-widgettools/lilac.yaml new file mode 100644 index 0000000000..9846413311 --- /dev/null +++ b/prepare/r-widgettools/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: widgetTools_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/widgetTools diff --git a/prepare/r-wiggleplotr/PKGBUILD b/prepare/r-wiggleplotr/PKGBUILD new file mode 100644 index 0000000000..2eb1f627fa --- /dev/null +++ b/prepare/r-wiggleplotr/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=wiggleplotr +_pkgver=1.18.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Make read coverage plots from BigWig files' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Apache') +depends=( + r + r-assertthat + r-cowplot + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-purrr + r-rtracklayer + r-s4vectors +) +optdepends=( + r-annotationdbi + r-annotationfilter + r-biomart + r-ensdb.hsapiens.v86 + r-ensembldb + r-genomicfeatures + r-knitr + r-org.hs.eg.db + r-rmarkdown + r-testthat + r-txdb.hsapiens.ucsc.hg38.knowngene +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-wiggleplotr/lilac.py b/prepare/r-wiggleplotr/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-wiggleplotr/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-wiggleplotr/lilac.yaml b/prepare/r-wiggleplotr/lilac.yaml new file mode 100644 index 0000000000..d868967ffa --- /dev/null +++ b/prepare/r-wiggleplotr/lilac.yaml @@ -0,0 +1,19 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-assertthat +- r-cowplot +- r-dplyr +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-iranges +- r-purrr +- r-rtracklayer +- r-s4vectors +update_on: +- regex: wiggleplotr_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/wiggleplotr diff --git a/prepare/r-wk/PKGBUILD b/prepare/r-wk/PKGBUILD new file mode 100644 index 0000000000..923cf7a1fb --- /dev/null +++ b/prepare/r-wk/PKGBUILD @@ -0,0 +1,35 @@ +# system requirements: C++11 +# Maintainer: Guoyi Zhang + +_pkgname=wk +_pkgver=0.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Lightweight Well-Known Geometry Parsing' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-readr + r-sf + r-testthat + r-tibble + r-vctrs +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-wk/lilac.py b/prepare/r-wk/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-wk/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-wk/lilac.yaml b/prepare/r-wk/lilac.yaml new file mode 100644 index 0000000000..a274d27d18 --- /dev/null +++ b/prepare/r-wk/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: wk_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=wk diff --git a/prepare/r-wordcloud/PKGBUILD b/prepare/r-wordcloud/PKGBUILD new file mode 100644 index 0000000000..632bf261a9 --- /dev/null +++ b/prepare/r-wordcloud/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=wordcloud +_pkgver=2.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Word Clouds' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('LGPL') +depends=( + r + r-rcolorbrewer + r-rcpp +) +optdepends=( + r-slam + r-tm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-wordcloud/lilac.py b/prepare/r-wordcloud/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-wordcloud/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-wordcloud/lilac.yaml b/prepare/r-wordcloud/lilac.yaml new file mode 100644 index 0000000000..c6e1b9f5bc --- /dev/null +++ b/prepare/r-wordcloud/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rcolorbrewer +- r-rcpp +update_on: +- regex: wordcloud_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=wordcloud diff --git a/prepare/r-wordcloud2/PKGBUILD b/prepare/r-wordcloud2/PKGBUILD new file mode 100644 index 0000000000..c710810877 --- /dev/null +++ b/prepare/r-wordcloud2/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=wordcloud2 +_pkgver=0.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Create Word Cloud by 'htmlwidget'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-base64enc + r-htmlwidgets +) +optdepends=( + r-knitr + r-rmarkdown + r-shiny + r-webshot +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-wordcloud2/lilac.py b/prepare/r-wordcloud2/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-wordcloud2/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-wordcloud2/lilac.yaml b/prepare/r-wordcloud2/lilac.yaml new file mode 100644 index 0000000000..b0b982d426 --- /dev/null +++ b/prepare/r-wordcloud2/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-base64enc +- r-htmlwidgets +update_on: +- regex: wordcloud2_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=wordcloud2 diff --git a/prepare/r-wpm/PKGBUILD b/prepare/r-wpm/PKGBUILD new file mode 100644 index 0000000000..8d2a677a81 --- /dev/null +++ b/prepare/r-wpm/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Guoyi Zhang + +_pkgname=wpm +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Well Plate Maker' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-cli + r-config + r-dplyr + r-dt + r-ggplot2 + r-golem + r-logging + r-rcolorbrewer + r-rlang + r-shiny + r-shinycustomloader + r-shinydashboard + r-shinywidgets + r-stringr + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-knitr + r-msnbase + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-wpm/lilac.py b/prepare/r-wpm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-wpm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-wpm/lilac.yaml b/prepare/r-wpm/lilac.yaml new file mode 100644 index 0000000000..ee0d0c13af --- /dev/null +++ b/prepare/r-wpm/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-cli +- r-config +- r-dplyr +- r-dt +- r-ggplot2 +- r-golem +- r-logging +- r-rcolorbrewer +- r-rlang +- r-shiny +- r-shinycustomloader +- r-shinydashboard +- r-shinywidgets +- r-stringr +- r-summarizedexperiment +update_on: +- regex: wpm_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/wpm diff --git a/prepare/r-wppi/PKGBUILD b/prepare/r-wppi/PKGBUILD new file mode 100644 index 0000000000..92880b2441 --- /dev/null +++ b/prepare/r-wppi/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: Guoyi Zhang + +_pkgname=wppi +_pkgver=1.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Weighting protein-protein interactions' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-dplyr + r-igraph + r-logger + r-magrittr + r-omnipathr + r-progress + r-purrr + r-rcurl + r-rlang + r-tibble + r-tidyr +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-wppi/lilac.py b/prepare/r-wppi/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-wppi/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-wppi/lilac.yaml b/prepare/r-wppi/lilac.yaml new file mode 100644 index 0000000000..374877502d --- /dev/null +++ b/prepare/r-wppi/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-dplyr +- r-igraph +- r-logger +- r-magrittr +- r-omnipathr +- r-progress +- r-purrr +- r-rcurl +- r-rlang +- r-tibble +- r-tidyr +update_on: +- regex: wppi_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/wppi diff --git a/prepare/r-wrench/PKGBUILD b/prepare/r-wrench/PKGBUILD new file mode 100644 index 0000000000..f8348c6cd4 --- /dev/null +++ b/prepare/r-wrench/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Wrench +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Wrench normalization for sparse count data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-limma + r-locfit + r-matrixstats +) +optdepends=( + r-deseq2 + r-edger + r-knitr + r-metagenomeseq + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-wrench/lilac.py b/prepare/r-wrench/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-wrench/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-wrench/lilac.yaml b/prepare/r-wrench/lilac.yaml new file mode 100644 index 0000000000..7b9e3d8880 --- /dev/null +++ b/prepare/r-wrench/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-limma +- r-locfit +- r-matrixstats +update_on: +- regex: Wrench_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Wrench diff --git a/prepare/r-writexl/PKGBUILD b/prepare/r-writexl/PKGBUILD new file mode 100644 index 0000000000..57aed77640 --- /dev/null +++ b/prepare/r-writexl/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=writexl +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Export Data Frames to Excel 'xlsx' Format" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('BSD') +depends=( + r +) +optdepends=( + r-bit64 + r-nycflights13 + r-readxl + r-spelling + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-writexl/lilac.py b/prepare/r-writexl/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-writexl/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-writexl/lilac.yaml b/prepare/r-writexl/lilac.yaml new file mode 100644 index 0000000000..70fb633ca6 --- /dev/null +++ b/prepare/r-writexl/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: writexl_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=writexl diff --git a/prepare/r-writexls/PKGBUILD b/prepare/r-writexls/PKGBUILD new file mode 100644 index 0000000000..cb0e802131 --- /dev/null +++ b/prepare/r-writexls/PKGBUILD @@ -0,0 +1,27 @@ +# system requirements: Perl +# Maintainer: Guoyi Zhang + +_pkgname=WriteXLS +_pkgver=6.3.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Cross-Platform Perl Based R Function to Create Excel 2003 (XLS) and Excel 2007 (XLSX) Files' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-writexls/lilac.py b/prepare/r-writexls/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-writexls/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-writexls/lilac.yaml b/prepare/r-writexls/lilac.yaml new file mode 100644 index 0000000000..9a09bc282f --- /dev/null +++ b/prepare/r-writexls/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: WriteXLS_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=WriteXLS diff --git a/prepare/r-xcir/PKGBUILD b/prepare/r-xcir/PKGBUILD new file mode 100644 index 0000000000..28b7956d75 --- /dev/null +++ b/prepare/r-xcir/PKGBUILD @@ -0,0 +1,38 @@ +# Maintainer: Guoyi Zhang + +_pkgname=XCIR +_pkgver=1.7.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='XCI-inference' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biomart + r-data.table + r-ggplot2 + r-iranges + r-readxl + r-s4vectors + r-seqminer + r-variantannotation +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xcir/lilac.py b/prepare/r-xcir/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-xcir/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-xcir/lilac.yaml b/prepare/r-xcir/lilac.yaml new file mode 100644 index 0000000000..89457e6c22 --- /dev/null +++ b/prepare/r-xcir/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biomart +- r-data.table +- r-ggplot2 +- r-iranges +- r-readxl +- r-s4vectors +- r-seqminer +- r-variantannotation +update_on: +- regex: XCIR_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/XCIR diff --git a/prepare/r-xcms/PKGBUILD b/prepare/r-xcms/PKGBUILD new file mode 100644 index 0000000000..59035bc09a --- /dev/null +++ b/prepare/r-xcms/PKGBUILD @@ -0,0 +1,63 @@ +# Maintainer: Guoyi Zhang + +_pkgname=xcms +_pkgver=3.16.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='LC-MS and GC-MS Data Analysis' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biobase + r-biocgenerics + r-biocparallel + r-iranges + r-massspecwavelet + r-mscoreutils + r-msfeatures + r-msnbase + r-mzr + r-plyr + r-protgenerics + r-rann + r-rcolorbrewer + r-robustbase + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-catools + r-faahko + r-knitr + r-magrittr + r-maldiquant + r-msbackendmgf + r-msdata + r-multtest + r-ncdf4 + r-pander + r-pheatmap + r-progress + r-rgl + r-rgraphviz + r-rmarkdown + r-spectra + r-testthat + r-xml +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xcms/lilac.py b/prepare/r-xcms/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-xcms/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-xcms/lilac.yaml b/prepare/r-xcms/lilac.yaml new file mode 100644 index 0000000000..81521685d4 --- /dev/null +++ b/prepare/r-xcms/lilac.yaml @@ -0,0 +1,25 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-biocparallel +- r-iranges +- r-massspecwavelet +- r-mscoreutils +- r-msfeatures +- r-msnbase +- r-mzr +- r-plyr +- r-protgenerics +- r-rann +- r-rcolorbrewer +- r-robustbase +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: xcms_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/xcms diff --git a/prepare/r-xde/PKGBUILD b/prepare/r-xde/PKGBUILD new file mode 100644 index 0000000000..c690ead345 --- /dev/null +++ b/prepare/r-xde/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Guoyi Zhang + +_pkgname=XDE +_pkgver=2.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r + r-biobase + r-biocgenerics + r-genefilter + r-genemeta + r-gtools + r-mvtnorm + r-rcolorbrewer + r-siggenes +) +optdepends=( + r-coda + r-mass + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xde/lilac.py b/prepare/r-xde/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-xde/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-xde/lilac.yaml b/prepare/r-xde/lilac.yaml new file mode 100644 index 0000000000..6ee36d72e0 --- /dev/null +++ b/prepare/r-xde/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biocgenerics +- r-genefilter +- r-genemeta +- r-gtools +- r-mvtnorm +- r-rcolorbrewer +- r-siggenes +update_on: +- regex: XDE_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/XDE diff --git a/prepare/r-xeva/PKGBUILD b/prepare/r-xeva/PKGBUILD new file mode 100644 index 0000000000..e608d790f3 --- /dev/null +++ b/prepare/r-xeva/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=Xeva +_pkgver=1.10.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Analysis of patient-derived xenograft (PDX) data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-bbmisc + r-biobase + r-complexheatmap + r-doparallel + r-downloader + r-ggplot2 + r-pharmacogx + r-rmisc + r-scales +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xeva/lilac.py b/prepare/r-xeva/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-xeva/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-xeva/lilac.yaml b/prepare/r-xeva/lilac.yaml new file mode 100644 index 0000000000..fd4bd81802 --- /dev/null +++ b/prepare/r-xeva/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-bbmisc +- r-biobase +- r-complexheatmap +- r-doparallel +- r-downloader +- r-ggplot2 +- r-pharmacogx +- r-rmisc +- r-scales +update_on: +- regex: Xeva_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/Xeva diff --git a/prepare/r-xfun/PKGBUILD b/prepare/r-xfun/PKGBUILD new file mode 100644 index 0000000000..3c27e22ebc --- /dev/null +++ b/prepare/r-xfun/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=xfun +_pkgver=0.29 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Supporting Functions for Packages Maintained by 'Yihui Xie'" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-codetools + r-curl + r-htmltools + r-jsonlite + r-knitr + r-markdown + r-mime + r-pak + r-parallel + r-remotes + r-renv + r-rhub + r-rmarkdown + r-rstudioapi + r-testit + r-tinytex +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xfun/lilac.py b/prepare/r-xfun/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-xfun/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-xfun/lilac.yaml b/prepare/r-xfun/lilac.yaml new file mode 100644 index 0000000000..33b9f4d824 --- /dev/null +++ b/prepare/r-xfun/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: xfun_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=xfun diff --git a/prepare/r-xgboost/PKGBUILD b/prepare/r-xgboost/PKGBUILD new file mode 100644 index 0000000000..a9c9153c73 --- /dev/null +++ b/prepare/r-xgboost/PKGBUILD @@ -0,0 +1,43 @@ +# system requirements: GNU make, C++14 +# Maintainer: Guoyi Zhang + +_pkgname=xgboost +_pkgver=1.5.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Extreme Gradient Boosting' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Apache') +depends=( + r + r-data.table + r-jsonlite +) +optdepends=( + r-ckmeans.1d.dp + r-crayon + r-diagrammer + r-float + r-ggplot2 + r-igraph + r-knitr + r-lintr + r-rmarkdown + r-testthat + r-titanic + r-vcd +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xgboost/lilac.py b/prepare/r-xgboost/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-xgboost/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-xgboost/lilac.yaml b/prepare/r-xgboost/lilac.yaml new file mode 100644 index 0000000000..ce1bb9531b --- /dev/null +++ b/prepare/r-xgboost/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-data.table +- r-jsonlite +update_on: +- regex: xgboost_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=xgboost diff --git a/prepare/r-xina/PKGBUILD b/prepare/r-xina/PKGBUILD new file mode 100644 index 0000000000..d7a2b8237a --- /dev/null +++ b/prepare/r-xina/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=XINA +_pkgver=1.12.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-alluvial + r-ggplot2 + r-gridextra + r-igraph + r-mclust + r-plyr + r-stringdb +) +optdepends=( + r-knitr + r-rmarkdown +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xina/lilac.py b/prepare/r-xina/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-xina/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-xina/lilac.yaml b/prepare/r-xina/lilac.yaml new file mode 100644 index 0000000000..9fa0b1c5e7 --- /dev/null +++ b/prepare/r-xina/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-alluvial +- r-ggplot2 +- r-gridextra +- r-igraph +- r-mclust +- r-plyr +- r-stringdb +update_on: +- regex: XINA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/XINA diff --git a/prepare/r-xlsx/PKGBUILD b/prepare/r-xlsx/PKGBUILD new file mode 100644 index 0000000000..9d626bbf46 --- /dev/null +++ b/prepare/r-xlsx/PKGBUILD @@ -0,0 +1,37 @@ +# system requirements: java (>= 1.6) +# Maintainer: Guoyi Zhang + +_pkgname=xlsx +_pkgver=0.6.5 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Files' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rjava + r-xlsxjars +) +optdepends=( + r-covr + r-knitr + r-rmarkdown + r-rprojroot + r-testthat + r-tibble +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xlsx/lilac.py b/prepare/r-xlsx/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-xlsx/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-xlsx/lilac.yaml b/prepare/r-xlsx/lilac.yaml new file mode 100644 index 0000000000..0c7f12de27 --- /dev/null +++ b/prepare/r-xlsx/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rjava +- r-xlsxjars +update_on: +- regex: xlsx_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=xlsx diff --git a/prepare/r-xlsxjars/PKGBUILD b/prepare/r-xlsxjars/PKGBUILD new file mode 100644 index 0000000000..0d62a962cd --- /dev/null +++ b/prepare/r-xlsxjars/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=xlsxjars +_pkgver=0.6.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Package required POI jars for the xlsx package' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-rjava +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xlsxjars/lilac.py b/prepare/r-xlsxjars/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-xlsxjars/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-xlsxjars/lilac.yaml b/prepare/r-xlsxjars/lilac.yaml new file mode 100644 index 0000000000..3fca81b2d2 --- /dev/null +++ b/prepare/r-xlsxjars/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-rjava +update_on: +- regex: xlsxjars_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=xlsxjars diff --git a/prepare/r-xmapbridge/PKGBUILD b/prepare/r-xmapbridge/PKGBUILD new file mode 100644 index 0000000000..2155e31be3 --- /dev/null +++ b/prepare/r-xmapbridge/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=xmapbridge +_pkgver=1.52.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Export plotting files to the xmapBridge for visualisation in X:Map' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('LGPL') +depends=( + r +) +optdepends=( + r-rcolorbrewer + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xmapbridge/lilac.py b/prepare/r-xmapbridge/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-xmapbridge/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-xmapbridge/lilac.yaml b/prepare/r-xmapbridge/lilac.yaml new file mode 100644 index 0000000000..04cb15b9e8 --- /dev/null +++ b/prepare/r-xmapbridge/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: xmapbridge_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/xmapbridge diff --git a/prepare/r-xml2r/PKGBUILD b/prepare/r-xml2r/PKGBUILD new file mode 100644 index 0000000000..f5b07c03d4 --- /dev/null +++ b/prepare/r-xml2r/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=XML2R +_pkgver=0.0.6 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='EasieR XML data collection' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-plyr + r-rcurl + r-xml +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xml2r/lilac.py b/prepare/r-xml2r/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-xml2r/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-xml2r/lilac.yaml b/prepare/r-xml2r/lilac.yaml new file mode 100644 index 0000000000..64708298da --- /dev/null +++ b/prepare/r-xml2r/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-plyr +- r-rcurl +- r-xml +update_on: +- regex: XML2R_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=XML2R diff --git a/prepare/r-xnastring/PKGBUILD b/prepare/r-xnastring/PKGBUILD new file mode 100644 index 0000000000..05585795b8 --- /dev/null +++ b/prepare/r-xnastring/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=XNAString +_pkgver=1.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Efficient Manipulation of Modified Oligonucleotide Sequences' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-bsgenome + r-data.table + r-formattable + r-future.apply + r-genomicranges + r-iranges + r-rcpp + r-s4vectors + r-stringi + r-stringr +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg38 + r-knitr + r-markdown + r-pander + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xnastring/lilac.py b/prepare/r-xnastring/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-xnastring/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-xnastring/lilac.yaml b/prepare/r-xnastring/lilac.yaml new file mode 100644 index 0000000000..8491e48a30 --- /dev/null +++ b/prepare/r-xnastring/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome +- r-data.table +- r-formattable +- r-future.apply +- r-genomicranges +- r-iranges +- r-rcpp +- r-s4vectors +- r-stringi +- r-stringr +update_on: +- regex: XNAString_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/XNAString diff --git a/prepare/r-xopen/PKGBUILD b/prepare/r-xopen/PKGBUILD new file mode 100644 index 0000000000..68df747ff8 --- /dev/null +++ b/prepare/r-xopen/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=xopen +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Open System Files, 'URLs', Anything" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r + r-processx +) +optdepends=( + r-ps + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xopen/lilac.py b/prepare/r-xopen/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-xopen/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-xopen/lilac.yaml b/prepare/r-xopen/lilac.yaml new file mode 100644 index 0000000000..4ba9d7ba2a --- /dev/null +++ b/prepare/r-xopen/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-processx +update_on: +- regex: xopen_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=xopen diff --git a/prepare/r-xtable/PKGBUILD b/prepare/r-xtable/PKGBUILD new file mode 100644 index 0000000000..585776bd9d --- /dev/null +++ b/prepare/r-xtable/PKGBUILD @@ -0,0 +1,32 @@ +# Maintainer: Guoyi Zhang + +_pkgname=xtable +_pkgver=1.8-4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Export Tables to LaTeX or HTML' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-knitr + r-plm + r-survival + r-zoo +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xtable/lilac.py b/prepare/r-xtable/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-xtable/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-xtable/lilac.yaml b/prepare/r-xtable/lilac.yaml new file mode 100644 index 0000000000..284ca9a022 --- /dev/null +++ b/prepare/r-xtable/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: xtable_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=xtable diff --git a/prepare/r-xtrasnplocs.hsapiens.dbsnp144.grch37/PKGBUILD b/prepare/r-xtrasnplocs.hsapiens.dbsnp144.grch37/PKGBUILD new file mode 100644 index 0000000000..88e4abb411 --- /dev/null +++ b/prepare/r-xtrasnplocs.hsapiens.dbsnp144.grch37/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Guoyi Zhang + +_pkgname=XtraSNPlocs.Hsapiens.dbSNP144.GRCh37 +_pkgver=0.99.12 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Extra SNP locations for Homo sapiens (dbSNP Build 144)' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-bsgenome + r-genomeinfodb + r-genomicranges + r-iranges + r-s4vectors +) +optdepends=( + r-biostrings + r-bsgenome.hsapiens.ucsc.hg19 + r-snplocs.hsapiens.dbsnp144.grch37 +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xtrasnplocs.hsapiens.dbsnp144.grch37/lilac.py b/prepare/r-xtrasnplocs.hsapiens.dbsnp144.grch37/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-xtrasnplocs.hsapiens.dbsnp144.grch37/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-xtrasnplocs.hsapiens.dbsnp144.grch37/lilac.yaml b/prepare/r-xtrasnplocs.hsapiens.dbsnp144.grch37/lilac.yaml new file mode 100644 index 0000000000..0dd6d50db0 --- /dev/null +++ b/prepare/r-xtrasnplocs.hsapiens.dbsnp144.grch37/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-bsgenome +- r-genomeinfodb +- r-genomicranges +- r-iranges +- r-s4vectors +update_on: +- regex: XtraSNPlocs.Hsapiens.dbSNP144.GRCh37_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/XtraSNPlocs.Hsapiens.dbSNP144.GRCh37 diff --git a/prepare/r-xts/PKGBUILD b/prepare/r-xts/PKGBUILD new file mode 100644 index 0000000000..3dc9fed00c --- /dev/null +++ b/prepare/r-xts/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Guoyi Zhang + +_pkgname=xts +_pkgver=0.12.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='eXtensible Time Series' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-zoo +) +optdepends=( + r-chron + r-fts + r-runit + r-timedate + r-timeseries + r-tis + r-tseries +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xts/lilac.py b/prepare/r-xts/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-xts/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-xts/lilac.yaml b/prepare/r-xts/lilac.yaml new file mode 100644 index 0000000000..21e272d82a --- /dev/null +++ b/prepare/r-xts/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-zoo +update_on: +- regex: xts_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=xts diff --git a/prepare/r-xvector/PKGBUILD b/prepare/r-xvector/PKGBUILD new file mode 100644 index 0000000000..3dbe907197 --- /dev/null +++ b/prepare/r-xvector/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=XVector +_pkgver=0.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Foundation of external vector representation and manipulation in Bioconductor' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-iranges + r-s4vectors + r-zlibbioc +) +optdepends=( + r-biostrings + r-drosophila2probe + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-xvector/lilac.py b/prepare/r-xvector/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-xvector/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-xvector/lilac.yaml b/prepare/r-xvector/lilac.yaml new file mode 100644 index 0000000000..b4c747a2a0 --- /dev/null +++ b/prepare/r-xvector/lilac.yaml @@ -0,0 +1,13 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-iranges +- r-s4vectors +- r-zlibbioc +update_on: +- regex: XVector_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/XVector diff --git a/prepare/r-yaimpute/PKGBUILD b/prepare/r-yaimpute/PKGBUILD new file mode 100644 index 0000000000..7fc37d9943 --- /dev/null +++ b/prepare/r-yaimpute/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Guoyi Zhang + +_pkgname=yaImpute +_pkgver=1.0-32 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Nearest Neighbor Observation Imputation and Evaluation Tools' +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-ccapp + r-fastica + r-gam + r-gower + r-parallel + r-randomforest + r-vegan +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-yaimpute/lilac.py b/prepare/r-yaimpute/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-yaimpute/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-yaimpute/lilac.yaml b/prepare/r-yaimpute/lilac.yaml new file mode 100644 index 0000000000..207585515b --- /dev/null +++ b/prepare/r-yaimpute/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: yaImpute_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=yaImpute diff --git a/prepare/r-yamss/PKGBUILD b/prepare/r-yamss/PKGBUILD new file mode 100644 index 0000000000..8df15d4caa --- /dev/null +++ b/prepare/r-yamss/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=yamss +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Tools for high-throughput metabolomics' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocgenerics + r-data.table + r-ebimage + r-iranges + r-limma + r-mzr + r-s4vectors + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-digest + r-knitr + r-mtbls2 + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-yamss/lilac.py b/prepare/r-yamss/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-yamss/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-yamss/lilac.yaml b/prepare/r-yamss/lilac.yaml new file mode 100644 index 0000000000..ddfe13bdd5 --- /dev/null +++ b/prepare/r-yamss/lilac.yaml @@ -0,0 +1,17 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocgenerics +- r-data.table +- r-ebimage +- r-iranges +- r-limma +- r-mzr +- r-s4vectors +- r-summarizedexperiment +update_on: +- regex: yamss_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/yamss diff --git a/prepare/r-yapsa/PKGBUILD b/prepare/r-yapsa/PKGBUILD new file mode 100644 index 0000000000..2e1b502499 --- /dev/null +++ b/prepare/r-yapsa/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Guoyi Zhang + +_pkgname=YAPSA +_pkgver=1.20.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Yet Another Package for Signature Analysis' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-biostrings + r-bsgenome.hsapiens.ucsc.hg19 + r-circlize + r-complexheatmap + r-corrplot + r-dendextend + r-doparallel + r-dplyr + r-genomeinfodb + r-genomicranges + r-getoptlong + r-ggbeeswarm + r-ggplot2 + r-gridextra + r-gtrellis + r-keggrest + r-limsolve + r-magrittr + r-pmcmrplus + r-pracma + r-reshape2 + r-somaticsignatures + r-variantannotation +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-yapsa/lilac.py b/prepare/r-yapsa/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-yapsa/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-yapsa/lilac.yaml b/prepare/r-yapsa/lilac.yaml new file mode 100644 index 0000000000..be7a98408e --- /dev/null +++ b/prepare/r-yapsa/lilac.yaml @@ -0,0 +1,32 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biostrings +- r-bsgenome.hsapiens.ucsc.hg19 +- r-circlize +- r-complexheatmap +- r-corrplot +- r-dendextend +- r-doparallel +- r-dplyr +- r-genomeinfodb +- r-genomicranges +- r-getoptlong +- r-ggbeeswarm +- r-ggplot2 +- r-gridextra +- r-gtrellis +- r-keggrest +- r-limsolve +- r-magrittr +- r-pmcmrplus +- r-pracma +- r-reshape2 +- r-somaticsignatures +- r-variantannotation +update_on: +- regex: YAPSA_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/YAPSA diff --git a/prepare/r-yarn/PKGBUILD b/prepare/r-yarn/PKGBUILD new file mode 100644 index 0000000000..da0fd06e15 --- /dev/null +++ b/prepare/r-yarn/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=yarn +_pkgver=1.20.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase + r-biomart + r-downloader + r-edger + r-gplots + r-limma + r-matrixstats + r-preprocesscore + r-quantro + r-rcolorbrewer + r-readr +) +optdepends=( + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-yarn/lilac.py b/prepare/r-yarn/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-yarn/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-yarn/lilac.yaml b/prepare/r-yarn/lilac.yaml new file mode 100644 index 0000000000..8d009d6d06 --- /dev/null +++ b/prepare/r-yarn/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +- r-biomart +- r-downloader +- r-edger +- r-gplots +- r-limma +- r-matrixstats +- r-preprocesscore +- r-quantro +- r-rcolorbrewer +- r-readr +update_on: +- regex: yarn_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/yarn diff --git a/prepare/r-yeastcc/PKGBUILD b/prepare/r-yeastcc/PKGBUILD new file mode 100644 index 0000000000..4e887dfade --- /dev/null +++ b/prepare/r-yeastcc/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Guoyi Zhang + +_pkgname=yeastCC +_pkgver=1.34.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell cycle microarray data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biobase +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-yeastcc/lilac.py b/prepare/r-yeastcc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-yeastcc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-yeastcc/lilac.yaml b/prepare/r-yeastcc/lilac.yaml new file mode 100644 index 0000000000..eb637d14eb --- /dev/null +++ b/prepare/r-yeastcc/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biobase +update_on: +- regex: yeastCC_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/yeastCC diff --git a/prepare/r-yeastexpdata/PKGBUILD b/prepare/r-yeastexpdata/PKGBUILD new file mode 100644 index 0000000000..bef07ca229 --- /dev/null +++ b/prepare/r-yeastexpdata/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Guoyi Zhang + +_pkgname=yeastExpData +_pkgver=0.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Yeast Experimental Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-graph +) +optdepends=( + r-biobase + r-go.db + r-org.sc.sgd.db + r-rbgl +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-yeastexpdata/lilac.py b/prepare/r-yeastexpdata/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-yeastexpdata/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-yeastexpdata/lilac.yaml b/prepare/r-yeastexpdata/lilac.yaml new file mode 100644 index 0000000000..7c12a53507 --- /dev/null +++ b/prepare/r-yeastexpdata/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-graph +update_on: +- regex: yeastExpData_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/yeastExpData diff --git a/prepare/r-yesno/PKGBUILD b/prepare/r-yesno/PKGBUILD new file mode 100644 index 0000000000..3f1709ecaf --- /dev/null +++ b/prepare/r-yesno/PKGBUILD @@ -0,0 +1,30 @@ +# Maintainer: Guoyi Zhang + +_pkgname=yesno +_pkgver=0.1.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Ask Yes-No Questions' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-covr + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-yesno/lilac.py b/prepare/r-yesno/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-yesno/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-yesno/lilac.yaml b/prepare/r-yesno/lilac.yaml new file mode 100644 index 0000000000..e04d92ecd4 --- /dev/null +++ b/prepare/r-yesno/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: yesno_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=yesno diff --git a/prepare/r-yulab.utils/PKGBUILD b/prepare/r-yulab.utils/PKGBUILD new file mode 100644 index 0000000000..ce50e753f9 --- /dev/null +++ b/prepare/r-yulab.utils/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Guoyi Zhang + +_pkgname=yulab.utils +_pkgver=0.0.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Supporting Functions for Packages Maintained by 'YuLab-SMU'" +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +optdepends=( + r-pkgbuild +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-yulab.utils/lilac.py b/prepare/r-yulab.utils/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-yulab.utils/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-yulab.utils/lilac.yaml b/prepare/r-yulab.utils/lilac.yaml new file mode 100644 index 0000000000..19b85b3e38 --- /dev/null +++ b/prepare/r-yulab.utils/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: yulab.utils_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=yulab.utils diff --git a/prepare/r-zcompositions/PKGBUILD b/prepare/r-zcompositions/PKGBUILD new file mode 100644 index 0000000000..02a322cbee --- /dev/null +++ b/prepare/r-zcompositions/PKGBUILD @@ -0,0 +1,28 @@ +# Maintainer: Guoyi Zhang + +_pkgname=zCompositions +_pkgver=1.3.4 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Treatment of Zeros, Left-Censored and Missing Values in Compositional Data Sets' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r + r-nada + r-truncnorm +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-zcompositions/lilac.py b/prepare/r-zcompositions/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-zcompositions/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-zcompositions/lilac.yaml b/prepare/r-zcompositions/lilac.yaml new file mode 100644 index 0000000000..81f30ddbfc --- /dev/null +++ b/prepare/r-zcompositions/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-nada +- r-truncnorm +update_on: +- regex: zCompositions_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=zCompositions diff --git a/prepare/r-zeallot/PKGBUILD b/prepare/r-zeallot/PKGBUILD new file mode 100644 index 0000000000..3bc64dbcec --- /dev/null +++ b/prepare/r-zeallot/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=zeallot +_pkgver=0.1.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Multiple, Unpacking, and Destructuring Assignment' +arch=('any') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-knitr + r-magrittr + r-purrr + r-rmarkdown + r-testthat +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-zeallot/lilac.py b/prepare/r-zeallot/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-zeallot/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-zeallot/lilac.yaml b/prepare/r-zeallot/lilac.yaml new file mode 100644 index 0000000000..661124baa5 --- /dev/null +++ b/prepare/r-zeallot/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: zeallot_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=zeallot diff --git a/prepare/r-zellkonverter/PKGBUILD b/prepare/r-zellkonverter/PKGBUILD new file mode 100644 index 0000000000..fa812e989d --- /dev/null +++ b/prepare/r-zellkonverter/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Guoyi Zhang + +_pkgname=zellkonverter +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Conversion Between scRNA-seq Objects' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('MIT') +depends=( + r + r-basilisk + r-cli + r-delayedarray + r-reticulate + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment +) +optdepends=( + r-biocfilecache + r-biocstyle + r-covr + r-hdf5array + r-knitr + r-rhdf5 + r-rmarkdown + r-scrnaseq + r-spelling + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-zellkonverter/lilac.py b/prepare/r-zellkonverter/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-zellkonverter/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-zellkonverter/lilac.yaml b/prepare/r-zellkonverter/lilac.yaml new file mode 100644 index 0000000000..907f1b80e1 --- /dev/null +++ b/prepare/r-zellkonverter/lilac.yaml @@ -0,0 +1,16 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-basilisk +- r-cli +- r-delayedarray +- r-reticulate +- r-s4vectors +- r-singlecellexperiment +- r-summarizedexperiment +update_on: +- regex: zellkonverter_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/zellkonverter diff --git a/prepare/r-zfpkm/PKGBUILD b/prepare/r-zfpkm/PKGBUILD new file mode 100644 index 0000000000..1698ac7b21 --- /dev/null +++ b/prepare/r-zfpkm/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Guoyi Zhang + +_pkgname=zFPKM +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='A suite of functions to facilitate zFPKM transformations' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('GPL') +depends=( + r + r-checkmate + r-dplyr + r-ggplot2 + r-summarizedexperiment + r-tidyr +) +optdepends=( + r-edger + r-geoquery + r-knitr + r-limma + r-printr + r-rmarkdown + r-stringr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-zfpkm/lilac.py b/prepare/r-zfpkm/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-zfpkm/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-zfpkm/lilac.yaml b/prepare/r-zfpkm/lilac.yaml new file mode 100644 index 0000000000..dc5a03ec74 --- /dev/null +++ b/prepare/r-zfpkm/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-checkmate +- r-dplyr +- r-ggplot2 +- r-summarizedexperiment +- r-tidyr +update_on: +- regex: zFPKM_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/zFPKM diff --git a/prepare/r-zinbwave/PKGBUILD b/prepare/r-zinbwave/PKGBUILD new file mode 100644 index 0000000000..be4595eaec --- /dev/null +++ b/prepare/r-zinbwave/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Guoyi Zhang + +_pkgname=zinbwave +_pkgver=1.16.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='Zero-Inflated Negative Binomial Model for RNA-Seq Data' +arch=('any') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r + r-biocparallel + r-edger + r-genefilter + r-singlecellexperiment + r-softimpute + r-summarizedexperiment +) +optdepends=( + r-biocstyle + r-biomart + r-deseq2 + r-ggplot2 + r-knitr + r-magrittr + r-matrixstats + r-rmarkdown + r-rtsne + r-scrnaseq + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-zinbwave/lilac.py b/prepare/r-zinbwave/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-zinbwave/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-zinbwave/lilac.yaml b/prepare/r-zinbwave/lilac.yaml new file mode 100644 index 0000000000..6624f26124 --- /dev/null +++ b/prepare/r-zinbwave/lilac.yaml @@ -0,0 +1,15 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +repo_depends: +- r-biocparallel +- r-edger +- r-genefilter +- r-singlecellexperiment +- r-softimpute +- r-summarizedexperiment +update_on: +- regex: zinbwave_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/zinbwave diff --git a/prepare/r-zip/PKGBUILD b/prepare/r-zip/PKGBUILD new file mode 100644 index 0000000000..7146c45138 --- /dev/null +++ b/prepare/r-zip/PKGBUILD @@ -0,0 +1,34 @@ +# Maintainer: Guoyi Zhang + +_pkgname=zip +_pkgver=2.2.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="Cross-Platform 'zip' Compression" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('MIT') +depends=( + r +) +optdepends=( + r-covr + r-processx + r-r6 + r-testthat + r-withr +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-zip/lilac.py b/prepare/r-zip/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-zip/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-zip/lilac.yaml b/prepare/r-zip/lilac.yaml new file mode 100644 index 0000000000..d8679cc108 --- /dev/null +++ b/prepare/r-zip/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: zip_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=zip diff --git a/prepare/r-zlibbioc/PKGBUILD b/prepare/r-zlibbioc/PKGBUILD new file mode 100644 index 0000000000..08f4f50d73 --- /dev/null +++ b/prepare/r-zlibbioc/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Guoyi Zhang + +_pkgname=zlibbioc +_pkgver=1.40.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc='An R packaged zlib-1.2.5' +arch=('x86_64') +url="https://bioconductor.org/packages/${_pkgname}" +license=('Artistic2.0') +depends=( + r +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-zlibbioc/lilac.py b/prepare/r-zlibbioc/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-zlibbioc/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-zlibbioc/lilac.yaml b/prepare/r-zlibbioc/lilac.yaml new file mode 100644 index 0000000000..a74259d6d2 --- /dev/null +++ b/prepare/r-zlibbioc/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: zlibbioc_([\d._-]+).tar.gz + source: regex + url: https://bioconductor.org/packages/zlibbioc diff --git a/prepare/r-zoo/PKGBUILD b/prepare/r-zoo/PKGBUILD new file mode 100644 index 0000000000..abc0829862 --- /dev/null +++ b/prepare/r-zoo/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Guoyi Zhang + +_pkgname=zoo +_pkgver=1.8-9 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//[:-]/.} +pkgrel=1 +pkgdesc="S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)" +arch=('x86_64') +url="https://cran.r-project.org/package=${_pkgname}" +license=('GPL') +depends=( + r +) +optdepends=( + r-aer + r-chron + r-coda + r-fts + r-ggplot2 + r-mondate + r-scales + r-stinepack + r-strucchange + r-timedate + r-timeseries + r-tis + r-tseries + r-xts +) +source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +sha256sums=('a') + +build() { + R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" +} + +package() { + install -dm0755 "${pkgdir}/usr/lib/R/library" + cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" +} +# vim:set ts=2 sw=2 et: diff --git a/prepare/r-zoo/lilac.py b/prepare/r-zoo/lilac.py new file mode 100644 index 0000000000..620556bc87 --- /dev/null +++ b/prepare/r-zoo/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + for line in edit_file('PKGBUILD'): + if line.startswith('_pkgver='): + line = f'_pkgver={_G.newver}' + print(line) + update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + +def post_build(): + git_pkgbuild_commit() diff --git a/prepare/r-zoo/lilac.yaml b/prepare/r-zoo/lilac.yaml new file mode 100644 index 0000000000..524ad71197 --- /dev/null +++ b/prepare/r-zoo/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: starsareintherose + email: starsareintherose@outlook.com +update_on: +- regex: zoo_([\d._-]+).tar.gz + source: regex + url: https://cran.r-project.org/package=zoo